From ec4e94be955c86728cb4b463e0143de4f41b3530 Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Wed, 5 Oct 2016 18:37:19 +0200
Subject: [PATCH] renaming of model structures + javadoc update
---
.../annotation/services/ModelAnnotator.java | 12 +-
.../lcsb/mapviewer/run/ConsoleConverter.java | 12 +-
.../lcsb/mapviewer/run/ReactomeExport.java | 10 +-
.../java/lcsb/mapviewer/run/Statistics.java | 8 +-
.../run/UnknownReactionInReactome.java | 10 +-
.../lcsb/mapviewer/run/VibineSnippet.java | 4 +-
.../celldesigner/CellDesignerXmlParser.java | 12 +-
.../model/celldesigner/LayerXmlParser.java | 4 +-
.../alias/ComplexAliasXmlParser.java | 14 +-
.../alias/SpeciesAliasXmlParser.java | 14 +-
.../reaction/ReactionFromXml.java | 68 ++---
.../celldesigner/reaction/ReactionToXml.java | 80 +++---
.../species/SpeciesCollectionXmlParser.java | 2 +-
.../CellDesignerXmlParserTest.java | 2 +-
.../celldesigner/ComplexParserTests.java | 4 +-
.../celldesigner/LayerXmlParserTest.java | 2 +-
.../NestedComplexParsingTests.java | 30 +-
.../alias/CompartmentAliasXmlParserTest.java | 8 +-
.../alias/SpeciesAliasXmlParserTest.java | 18 +-
.../annotation/RestAnnotationParserTest.java | 2 +-
.../compartment/CompartmentParserTests.java | 8 +-
.../reaction/ReactionParserTests.java | 16 +-
.../reaction/ReactionToXmlTest.java | 4 +-
.../species/ComplexParserTest.java | 8 +-
.../model/sbgnml/SbgnmlXmlExporter.java | 24 +-
.../model/sbgnml/SbgnmlXmlParser.java | 52 ++--
.../graphics/AbstractImageGenerator.java | 8 +-
.../graphics/placefinder/PlaceFinder.java | 2 +-
.../graphics/species/ComplexConverter.java | 6 +-
.../graphics/species/ProteinConverter.java | 8 +-
.../SBGNNucleicAcidFeatureConverter.java | 8 +-
.../species/SimpleMoleculeConverter.java | 4 +-
.../graphics/species/SpeciesConverter.java | 2 +-
.../converter/graphics/ConverterTest.java | 8 +-
.../graphics/NormalImageGeneratorTest.java | 6 +-
.../graphics/PdfImageGeneratorTest.java | 6 +-
.../placefinder/AllPlaceFinderTest.java | 14 +-
.../converter/ComplexZipConverter.java | 16 +-
.../converter/ComplexZipConverterTest.java | 6 +-
.../gui/canvas/CanvasSelectMouseListener.java | 2 +-
.../gui/detailstab/ElementDetailsPanel.java | 4 +-
.../mapviewer/commands/ColorModelCommand.java | 10 +-
.../lcsb/mapviewer/commands/CopyCommand.java | 42 +--
.../commands/CreateHierarchyCommand.java | 70 ++---
.../lcsb/mapviewer/commands/MoveCommand.java | 2 +-
.../commands/MoveElementsCommand.java | 2 +-
.../mapviewer/commands/SubModelCommand.java | 14 +-
.../commands/CommandTestFunctions.java | 2 +-
.../mapviewer/commands/CopyCommandTest.java | 12 +-
.../commands/CreateHierarchyCommandTest.java | 22 +-
.../commands/SubModelCommandTest.java | 4 +-
...java => ElementInFewParentsException.java} | 48 ++--
.../compartment/BottomSquareCompartment.java | 42 +--
.../model/map/compartment/Compartment.java | 18 +-
.../compartment/CompartmentComparator.java | 37 +--
.../compartment/LeftSquareCompartment.java | 45 +--
.../map/compartment/OvalCompartment.java | 20 +-
.../map/compartment/PathwayCompartment.java | 10 +-
.../compartment/RightSquareCompartment.java | 68 +++--
.../map/compartment/SquareCompartment.java | 24 +-
.../map/compartment/TopSquareCompartment.java | 42 +--
.../model/map/layout/ElementGroup.java | 30 +-
.../map/model/AliasSubmodelConnection.java | 144 ----------
.../map/model/ElementSubmodelConnection.java | 144 ++++++++++
... ElementSubmodelConnectionComparator.java} | 51 ++--
.../lcsb/mapviewer/model/map/model/Model.java | 70 ++---
.../model/map/model/ModelComparator.java | 48 ++--
.../mapviewer/model/map/model/ModelData.java | 67 +++--
.../model/map/model/ModelFullIndexed.java | 187 +++++-------
.../model/SubmodelConnectionComparator.java | 12 +-
.../model/map/modifier/Catalysis.java | 10 +-
.../model/map/modifier/Inhibition.java | 10 +-
.../model/map/modifier/Modulation.java | 10 +-
.../map/modifier/PhysicalStimulation.java | 11 +-
.../mapviewer/model/map/modifier/Trigger.java | 10 +-
.../model/map/modifier/UnknownCatalysis.java | 11 +-
.../model/map/modifier/UnknownInhibition.java | 10 +-
.../model/map/reaction/Modifier.java | 8 +-
.../mapviewer/model/map/reaction/Product.java | 8 +-
.../model/map/reaction/Reactant.java | 8 +-
.../model/map/reaction/Reaction.java | 8 +-
.../model/map/reaction/ReactionNode.java | 39 ++-
.../map/reaction/ReactionNodeComparator.java | 8 +-
.../model/map/species/AntisenseRna.java | 8 +-
.../map/species/AntisenseRnaComparator.java | 10 +-
.../model/map/species/ChemicalComparator.java | 20 +-
.../mapviewer/model/map/species/Complex.java | 70 ++---
.../model/map/species/ComplexComparator.java | 42 +--
.../model/map/species/DegradedComparator.java | 8 +-
.../model/map/species/DrugComparator.java | 10 +-
.../mapviewer/model/map/species/Element.java | 144 +++++-----
.../model/map/species/ElementComparator.java | 10 +-
.../model/map/species/GeneComparator.java | 10 +-
.../map/species/GenericProteinComparator.java | 4 +-
.../species/IonChannelProteinComparator.java | 12 +-
.../model/map/species/IonComparator.java | 4 +-
.../map/species/PhenotypeComparator.java | 10 +-
.../model/map/species/ProteinComparator.java | 34 +--
.../species/ReceptorProteinComparator.java | 12 +-
.../model/map/species/RnaComparator.java | 10 +-
.../map/species/SimpleMoleculeComparator.java | 8 +-
.../mapviewer/model/map/species/Species.java | 110 ++++----
.../model/map/species/SpeciesComparator.java | 16 +-
.../species/TruncatedProteinComparator.java | 8 +-
.../model/map/species/UnknownComparator.java | 10 +-
.../lcsb/mapviewer/model/map/AllMapTests.java | 2 +-
... => ElementInFewParentsExceptionTest.java} | 4 +-
.../BottomSquareCompartmentTest.java | 12 +-
.../CompartmentComparatorTest.java | 148 +++++-----
.../map/compartment/CompartmentTest.java | 242 ++++++++--------
.../LeftSquareCompartmentTest.java | 12 +-
.../compartment/PathwayCompartmentTest.java | 12 +-
.../RightSquareCompartmentTest.java | 18 +-
.../compartment/TopSquareCompartmentTest.java | 12 +-
.../model/map/layout/ElementGroupTest.java | 12 +-
.../model/map/model/AllModelTests.java | 42 +--
...mentSubmodelConnectionComparatorTest.java} | 46 +--
...ava => ElementSubmodelConnectionTest.java} | 14 +-
.../model/map/model/ModelComparatorTest.java | 40 +--
.../model/map/model/ModelDataTest.java | 58 ++--
.../model/map/model/ModelFullIndexedTest.java | 266 +++++++++---------
...ModelSubmodelConnectionComparatorTest.java | 6 +-
.../mapviewer/model/map/model/ModelTest.java | 158 +++++------
.../SubmodelConnectionComparatorTest.java | 18 +-
.../reaction/NodeOperatorComparatorTest.java | 48 ++--
.../map/reaction/ReactionComparatorTest.java | 30 +-
.../reaction/ReactionNodeComparatorTest.java | 18 +-
.../model/map/reaction/ReactionTest.java | 16 +-
.../map/species/ComplexComparatorTest.java | 156 +++++-----
.../model/map/species/ComplexTest.java | 60 ++--
.../map/species/ElementComparatorTest.java | 34 +--
.../model/map/species/ElementTest.java | 223 +++++++--------
.../map/species/SpeciesComparatorTest.java | 86 +++---
.../model/map/species/SpeciesTest.java | 10 +-
.../wikipathway/XML/ModelContructor.java | 34 +--
.../wikipathway/XML/ModelToGPML.java | 40 +--
.../wikipathway/GPMLToModelTest.java | 2 +-
.../mapviewer/wikipathway/XML/BugTest.java | 2 +-
persist/src/db/10.0.3/fix_db_20161005.sql | 24 ++
.../mapviewer/persist/dao/ProjectDaoTest.java | 4 +-
.../persist/dao/map/CommentDaoTest.java | 4 +-
.../persist/dao/map/LayoutDaoTest.java | 4 +-
.../persist/dao/map/ModelDaoTest.java | 12 +-
.../dao/map/layout/alias/AliasDaoTest.java | 8 +-
.../map/layout/alias/AntisenseRnaTest.java | 4 +-
.../persist/dao/map/layout/alias/RnaTest.java | 4 +-
.../reactome/utils/ReactionComparator.java | 8 +-
.../reactome/utils/ReactomeQueryUtil.java | 2 +-
.../services/impl/CommentService.java | 2 +-
.../services/impl/DataMiningService.java | 8 +-
.../services/impl/ExporterService.java | 82 +++---
.../mapviewer/services/impl/ModelService.java | 6 +-
.../services/impl/ProjectService.java | 4 +-
.../services/impl/SearchService.java | 14 +-
.../services/interfaces/IExporterService.java | 8 +-
.../services/search/SearchResultFactory.java | 2 +-
.../search/data/FullReactionViewFactory.java | 2 +-
.../db/chemical/ChemicalViewFactory.java | 2 +-
.../search/db/drug/DrugViewFactory.java | 2 +-
.../search/db/mirna/MiRNAViewFactory.java | 2 +-
.../services/view/CommentViewFactory.java | 2 +-
.../services/impl/CommentServiceTest.java | 2 +-
.../services/impl/DataMiningServiceTest.java | 2 +-
.../services/impl/ExporterServiceTest.java | 6 +-
.../services/impl/LogServiceTest.java | 2 +-
.../services/impl/ModelServiceTest.java | 2 +-
.../services/impl/ProjectServiceTest.java | 2 +-
.../services/impl/SearchServiceTest.java | 2 +-
.../search/db/drug/DrugViewFactoryTest.java | 2 +-
.../utils/graph/MissingConnectionDaoTest.java | 2 +-
.../lcsb/mapviewer/bean/ChemicalBean.java | 2 +-
.../java/lcsb/mapviewer/bean/DrugBean.java | 4 +-
.../java/lcsb/mapviewer/bean/ExportBean.java | 8 +-
.../lcsb/mapviewer/bean/FeedbackBean.java | 6 +-
.../java/lcsb/mapviewer/bean/MiRNABean.java | 2 +-
175 files changed, 2347 insertions(+), 2324 deletions(-)
rename model/src/main/java/lcsb/mapviewer/model/map/{AliasInFewParentsException.java => ElementInFewParentsException.java} (59%)
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java
rename model/src/main/java/lcsb/mapviewer/model/map/model/{AliasSubmodelConnectionComparator.java => ElementSubmodelConnectionComparator.java} (52%)
rename model/src/test/java/lcsb/mapviewer/model/map/{AliasInFewParentsExceptionTest.java => ElementInFewParentsExceptionTest.java} (72%)
rename model/src/test/java/lcsb/mapviewer/model/map/model/{AliasSubmodelConnectionComparatorTest.java => ElementSubmodelConnectionComparatorTest.java} (63%)
rename model/src/test/java/lcsb/mapviewer/model/map/model/{AliasSubmodelConnectionTest.java => ElementSubmodelConnectionTest.java} (65%)
create mode 100644 persist/src/db/10.0.3/fix_db_20161005.sql
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 9ee6a4f7ab..2c5998efc2 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -240,7 +240,7 @@ public class ModelAnnotator {
*/
protected void copyAnnotationFromOtherSpecies(Model model, IProgressUpdater progressUpdater) {
double counter = 0;
- double amount = model.getAliases().size();
+ double amount = model.getElements().size();
for (Species element : model.getSpeciesList()) {
if (element.getMiriamData().size() == 0) {
List<Element> speciesList = model.getElementsByName(element.getName());
@@ -275,10 +275,10 @@ public class ModelAnnotator {
progressUpdater.setProgress(0);
double counter = 0;
- double amount = model.getAliases().size() + model.getReactions().size();
+ double amount = model.getElements().size() + model.getReactions().size();
// annotate all elements
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
List<ElementAnnotator> list = null;
if (annotators != null) {
list = annotators.get(element.getClass());
@@ -361,9 +361,9 @@ public class ModelAnnotator {
double modelCounter = 0;
for (Model model : models) {
double ratio = modelCounter / modelSize;
- double size = model.getAliases().size() + model.getReactions().size();
+ double size = model.getElements().size() + model.getReactions().size();
double counter = 0;
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
result.addAll(findImproperAnnotations(element, validAnnotations.get(element.getClass())));
counter++;
updater.setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (counter / size * IProgressUpdater.MAX_PROGRESS) / modelSize);
@@ -427,7 +427,7 @@ public class ModelAnnotator {
models.add(m);
models.addAll(m.getSubmodels());
for (Model model : models) {
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
result.addAll(findMissing(alias, requestedAnnotations.get(alias.getClass())));
}
for (Reaction reaction : model.getReactions()) {
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index badffff4c3..ef5e72cef0 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -124,7 +124,7 @@ public class ConsoleConverter {
double size = elements.size();
double x = 0;
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
alias.setWidth(inputOptions.getAliasWidth());
alias.setHeight(inputOptions.getAliasHeight());
double angle = x / size * 2 * Math.PI;
@@ -271,8 +271,8 @@ public class ConsoleConverter {
modifiers.add(modifier);
}
}
- Element alias1 = products.get(0).getAlias();
- Element alias2 = reactants.get(0).getAlias();
+ Element alias1 = products.get(0).getElement();
+ Element alias2 = reactants.get(0).getElement();
Point2D middle = new Point2D.Double((alias1.getCenterX() + alias2.getCenterX()) / 2, (alias1.getCenterY() + alias2.getCenterY()) / 2);
@@ -296,15 +296,15 @@ public class ConsoleConverter {
}
Reaction reaction = (Reaction) clazz.newInstance();
for (Product product : products) {
- product.setLine(new PolylineData(middle, product.getAlias().getCenter()));
+ product.setLine(new PolylineData(middle, product.getElement().getCenter()));
reaction.addProduct(product);
}
for (Reactant reactant : reactants) {
- reactant.setLine(new PolylineData(reactant.getAlias().getCenter(), middle));
+ reactant.setLine(new PolylineData(reactant.getElement().getCenter(), middle));
reaction.addReactant(reactant);
}
for (Modifier modifier : modifiers) {
- modifier.setLine(new PolylineData(middle, modifier.getAlias().getCenter()));
+ modifier.setLine(new PolylineData(middle, modifier.getElement().getCenter()));
reaction.addModifier(modifier);
}
reaction.addMiriamData(annotations);
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
index 6e14c62fea..79d565bd1e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
@@ -127,7 +127,7 @@ public class ReactomeExport {
result = id;
if (alias instanceof Complex) {
- for (Element a : ((Complex) alias).getAliases()) {
+ for (Element a : ((Complex) alias).getElements()) {
addElement(a);
}
} else if (alias instanceof Compartment) {
@@ -178,7 +178,7 @@ public class ReactomeExport {
private void printAliases(Model model) throws IOException {
print("<Nodes>\n");
List<Element> aliases = new ArrayList<Element>();
- aliases.addAll(model.getAliases());
+ aliases.addAll(model.getElements());
Collections.sort(aliases, Element.SIZE_COMPARATOR);
for (Element alias : aliases) {
if (!aliasFeasible(alias)) {
@@ -207,7 +207,7 @@ public class ReactomeExport {
}
parameters.put("displayName", alias.getName());
if (alias instanceof Complex) {
- for (Element a : ((Complex) alias).getAliases()) {
+ for (Element a : ((Complex) alias).getElements()) {
components.add(addElement(a));
}
}
@@ -298,7 +298,7 @@ public class ReactomeExport {
}
for (ReactionNode node : reaction.getReactionNodes()) {
- Integer id = tempIds.get(node.getAlias());
+ Integer id = tempIds.get(node.getElement());
if (node instanceof Reactant) {
inputs.put(id, getInputString((Reactant) node));
} else if (node instanceof Product) {
@@ -443,7 +443,7 @@ public class ReactomeExport {
*/
private boolean isReactionFeasible(Reaction reaction) {
for (ReactionNode node : reaction.getReactionNodes()) {
- if (!aliasFeasible(node.getAlias())) {
+ if (!aliasFeasible(node.getElement())) {
return false;
}
}
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index 52f1cf6540..bb399e4ae4 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -188,7 +188,7 @@ public class Statistics {
Map<String, Set<String>> typeNames = new HashMap<>();
for (Model model : models) {
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (element instanceof Species) {
names.add(element.getName());
Set<String> tmp = typeNames.get(element.getClass().getName());
@@ -223,7 +223,7 @@ public class Statistics {
Set<String> set = new HashSet<String>();
for (Model model : models) {
- for (Compartment comp : model.getCompartmentsAliases()) {
+ for (Compartment comp : model.getCompartments()) {
set.add(comp.getName());
}
}
@@ -255,7 +255,7 @@ public class Statistics {
}
print("-----------------------------");
print("Complex annotations:");
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (element instanceof Complex && element.getMiriamData().size() > 0) {
print(element.getClass().getSimpleName() + ";\t\tname=" + element.getName() + ";\t\tid=" + element.getElementId());
}
@@ -316,7 +316,7 @@ public class Statistics {
*/
protected String createPubmedExportString(Model model) throws Exception {
Map<String, List<String>> links = new HashMap<String, List<String>>();
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.PUBMED.equals(md.getDataType())) {
List<String> list = links.get(md.getResource());
diff --git a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
index f9153e1376..a528f95489 100644
--- a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
+++ b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
@@ -126,13 +126,13 @@ public class UnknownReactionInReactome {
MatchResult matchResult = new MatchResult();
matchResult.setLocalReaction(reaction);
for (ReactionNode node : reaction.getReactants()) {
- matchResult.addInvalidLocalInput(node.getAlias());
+ matchResult.addInvalidLocalInput(node.getElement());
}
for (ReactionNode node : reaction.getProducts()) {
- matchResult.addInvalidLocalOutput(node.getAlias());
+ matchResult.addInvalidLocalOutput(node.getElement());
}
for (ReactionNode node : reaction.getModifiers()) {
- matchResult.addInvalidLocalModifier(node.getAlias());
+ matchResult.addInvalidLocalModifier(node.getElement());
}
results.add(matchResult);
printResult(matchResult);
@@ -208,9 +208,9 @@ public class UnknownReactionInReactome {
Set<String> ontologies = new HashSet<String>();
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
for (ReactionNode node : result.getLocalReaction().getReactionNodes()) {
- if (alias.contains(node.getAlias())) {
+ if (alias.contains(node.getElement())) {
ontologies.add(alias.getName());
break;
}
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index 911a6e379b..04da1a646b 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -76,7 +76,7 @@ public class VibineSnippet {
logger.debug("File processed.");
logger.debug("-------------------------------");
- logger.debug("Number of elements: " + model.getAliases().size());
+ logger.debug("Number of elements: " + model.getElements().size());
logger.debug("Number of reactions: " + model.getReactions().size());
@@ -96,7 +96,7 @@ public class VibineSnippet {
logger.debug("Reaction with id: " + reactionId);
logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
for (ReactionNode node : reaction.getReactionNodes()) {
- logger.debug(node.getClass().getSimpleName() + "; points to " + node.getAlias().getClass().getSimpleName() + "[" + node.getAlias().getElementId() + "]");
+ logger.debug(node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
}
logger.debug("-------------------------------");
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 7badb62f75..4cfb43d3de 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -264,7 +264,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
double maxY = 0;
double minX = model.getWidth();
double minY = model.getHeight();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
maxX = Math.max(maxX, alias.getWidth() + alias.getX());
maxY = Math.max(maxY, alias.getHeight() + alias.getY());
@@ -503,7 +503,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
Complex complex = (Complex) model.getElementByElementId(complexId);
if (complex != null) {
- complex.addAlias(alias);
+ complex.addSpecies(alias);
alias.setParent(complex);
}
} else {
@@ -541,7 +541,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
Complex complex = (Complex) model.getElementByElementId(complexId);
if (complex != null) {
alias.setParent(complex);
- complex.addAlias((Species) alias);
+ complex.addSpecies((Species) alias);
}
}
} else {
@@ -586,7 +586,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
- result.append(compartmentCollectionXmlParser.toXml(model.getCompartmentsAliases()));
+ result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
@@ -615,7 +615,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
result.append(speciesCollectionXmlParser.speciesCollectionToXmlIncludedString(model.getSpeciesList()));
- result.append(aliasCollectionParser.compartmentAliasCollectionToXmlString(model.getCompartmentsAliases()));
+ result.append(aliasCollectionParser.compartmentAliasCollectionToXmlString(model.getCompartments()));
result.append(aliasCollectionParser.complexAliasCollectionToXmlString(model.getComplexList()));
result.append(aliasCollectionParser.speciesAliasCollectionToXmlString(model.getNotComplexSpeciesList()));
@@ -623,7 +623,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
List<Gene> genes = new ArrayList<>();
List<Rna> rnas = new ArrayList<>();
List<AntisenseRna> antisenseRnas = new ArrayList<>();
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (element instanceof Protein) {
proteins.add((Protein) element);
} else if (element instanceof Gene) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index 17895675ac..51b36f8732 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -144,7 +144,7 @@ public class LayerXmlParser extends XmlParser {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:group")) {
- model.addAliasGroup(getAliasGroup(node, model));
+ model.addElementGroup(getAliasGroup(node, model));
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfGroups: " + node.getNodeName());
}
@@ -176,7 +176,7 @@ public class LayerXmlParser extends XmlParser {
if (alias == null) {
throw new InvalidGroupException("Group \"" + id + "\" contains alias with id: \"" + string + "\", but such alias doesn't exist in the model.");
}
- result.addAlias(alias);
+ result.addElement(alias);
}
NodeList nodes = groupNode.getChildNodes();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
index 57f6280526..3cc2aeaeac 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
@@ -169,8 +169,8 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
if ("open".equalsIgnoreCase(state)) {
String prefix = getNodeAttr("prefix", node);
String label = getNodeAttr("label", node);
- alias.setAliasStatePrefix(prefix);
- alias.setAliasStateLabel(label);
+ alias.setStatePrefix(prefix);
+ alias.setStateLabel(label);
} else if ("empty".equalsIgnoreCase(state)) {
return;
} else if (state == null || state.isEmpty()) {
@@ -195,7 +195,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
throw new InvalidArgumentException("Parent complex alias does not exist: " + parentId + " for alias: " + alias.getElementId());
} else {
alias.setParent(ca);
- ca.addAlias(alias);
+ ca.addSpecies(alias);
}
}
}
@@ -207,12 +207,12 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
// exported to CellDesigner file
if (alias.getParent() instanceof Compartment && !(alias.getParent() instanceof PathwayCompartment)) {
ca = (Compartment) alias.getParent();
- } else if (alias.getCompartmentAlias() != null && !(alias.getCompartmentAlias() instanceof PathwayCompartment)) {
- ca = alias.getCompartmentAlias();
- } else if (alias.getComplexAlias() == null) {
+ } else if (alias.getCompartment() != null && !(alias.getCompartment() instanceof PathwayCompartment)) {
+ ca = alias.getCompartment();
+ } else if (alias.getComplex() == null) {
ModelData modelData = alias.getModelData();
if (modelData != null) {
- for (Compartment cAlias : modelData.getModel().getCompartmentsAliases()) {
+ for (Compartment cAlias : modelData.getModel().getCompartments()) {
if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
if (ca == null) {
ca = cAlias;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index 7b2e486120..9e37254363 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -126,7 +126,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
throw new InvalidXmlSchemaException("ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
} else {
result.setParent(alias);
- alias.addAlias(result);
+ alias.addSpecies(result);
}
}
return result;
@@ -145,8 +145,8 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
if ("open".equalsIgnoreCase(state)) {
String prefix = getNodeAttr("prefix", node);
String label = getNodeAttr("label", node);
- alias.setAliasStatePrefix(prefix);
- alias.setAliasStateLabel(label);
+ alias.setStatePrefix(prefix);
+ alias.setStateLabel(label);
} else if ("empty".equalsIgnoreCase(state)) {
return;
} else if (state == null || state.isEmpty()) {
@@ -163,10 +163,10 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
// artifitial compartment aliases should be excluded
if (alias.getParent() instanceof Compartment && !(alias.getParent() instanceof PathwayCompartment)) {
ca = (Compartment) alias.getParent();
- } else if (alias.getComplexAlias() == null) {
+ } else if (alias.getComplex() == null) {
ModelData model = alias.getModelData();
if (model != null) {
- for (Compartment cAlias : model.getModel().getCompartmentsAliases()) {
+ for (Compartment cAlias : model.getModel().getCompartments()) {
if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
if (ca == null) {
ca = cAlias;
@@ -231,8 +231,8 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
sb.append("<celldesigner:singleLine width=\"" + alias.getLineWidth() + "\"/>");
sb.append("<celldesigner:paint color=\"" + colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:briefView>\n");
- if (alias.getAliasStateLabel() != null || alias.getAliasStatePrefix() != null) {
- sb.append("<celldesigner:info state=\"open\" prefix=\"" + alias.getAliasStatePrefix() + "\" label=\"" + alias.getAliasStateLabel() + "\"/>\n");
+ if (alias.getStateLabel() != null || alias.getStatePrefix() != null) {
+ sb.append("<celldesigner:info state=\"open\" prefix=\"" + alias.getStatePrefix() + "\" label=\"" + alias.getStateLabel() + "\"/>\n");
}
sb.append("</celldesigner:speciesAlias>\n");
return sb.toString();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index dbad556ddb..afd11e0ff5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -365,7 +365,7 @@ public class ReactionFromXml extends XmlParser {
}
for (int i = 0; i < result.getModifiers().size(); i++) {
Modifier modifier = result.getModifiers().get(i);
- if (modifier.getAlias() == null) {
+ if (modifier.getElement() == null) {
List<Modifier> modifiers = new ArrayList<Modifier>();
modifiers.add(modifier);
for (Modifier modifier2 : result.getModifiers()) {
@@ -481,7 +481,7 @@ public class ReactionFromXml extends XmlParser {
* modifier to update
*/
private void createLineForModifier(Reaction reaction, Modifier modifier) {
- Element alias = modifier.getAlias();
+ Element alias = modifier.getElement();
CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias);
Point2D startPoint = converter.getPointCoordinates(alias, anchorsByNodes.get(modifier));
ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
@@ -820,16 +820,16 @@ public class ReactionFromXml extends XmlParser {
Product product2 = reaction.getProducts().get(1);
Reactant reactant = reaction.getReactants().get(0);
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getAlias());
- CellDesignerAliasConverter product1Converter = new CellDesignerAliasConverter(product1.getAlias());
- CellDesignerAliasConverter product2Converter = new CellDesignerAliasConverter(product2.getAlias());
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement());
+ CellDesignerAliasConverter product1Converter = new CellDesignerAliasConverter(product1.getElement());
+ CellDesignerAliasConverter product2Converter = new CellDesignerAliasConverter(product2.getElement());
- Point2D p1 = reactantConverter.getPointCoordinates(reactant.getAlias(), anchorsByNodes.get(reactant));
- Point2D p2 = product1Converter.getPointCoordinates(product1.getAlias(), anchorsByNodes.get(product1));
- Point2D p3 = product2Converter.getPointCoordinates(product2.getAlias(), anchorsByNodes.get(product2));
+ Point2D p1 = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
+ Point2D p2 = product1Converter.getPointCoordinates(product1.getElement(), anchorsByNodes.get(product1));
+ Point2D p3 = product2Converter.getPointCoordinates(product2.getElement(), anchorsByNodes.get(product2));
Point2D centerPoint = pointTransformation
- .getCoordinatesInNormalBase(product1.getAlias().getCenter(), product2.getAlias().getCenter(), reactant.getAlias().getCenter(), p);
+ .getCoordinatesInNormalBase(product1.getElement().getCenter(), product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
int startId0 = 0;
int num0 = points.getNum0();
@@ -847,13 +847,13 @@ public class ReactionFromXml extends XmlParser {
PolylineData reactantLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
- p1 = product2Converter.getAnchorPointCoordinates(product2.getAlias(), anchorsByNodes.get(product2), product2Line.reverse());
+ p1 = product2Converter.getAnchorPointCoordinates(product2.getElement(), anchorsByNodes.get(product2), product2Line.reverse());
product2Line.setEndPoint(p1);
- p1 = product1Converter.getAnchorPointCoordinates(product1.getAlias(), anchorsByNodes.get(product1), product1Line.reverse());
+ p1 = product1Converter.getAnchorPointCoordinates(product1.getElement(), anchorsByNodes.get(product1), product1Line.reverse());
product1Line.setEndPoint(p1);
- p1 = reactantConverter.getAnchorPointCoordinates(reactant.getAlias(), anchorsByNodes.get(reactant), reactantLine.reverse());
+ p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), reactantLine.reverse());
reactantLine.setEndPoint(p1);
product2Line.getEndAtd().setArrowType(ArrowType.FULL);
@@ -884,16 +884,16 @@ public class ReactionFromXml extends XmlParser {
Product product = reaction.getProducts().get(0);
Reactant reactant1 = reaction.getReactants().get(0);
Reactant reactant2 = reaction.getReactants().get(1);
- CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getAlias());
- CellDesignerAliasConverter reactantConverter1 = new CellDesignerAliasConverter(reactant1.getAlias());
- CellDesignerAliasConverter reactantConverter2 = new CellDesignerAliasConverter(reactant2.getAlias());
- Point2D p1 = reactantConverter1.getPointCoordinates(reactant1.getAlias(), anchorsByNodes.get(reactant1));
- Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getAlias(), anchorsByNodes.get(reactant2));
- Point2D p3 = productConverter.getPointCoordinates(product.getAlias(), anchorsByNodes.get(product));
+ CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement());
+ CellDesignerAliasConverter reactantConverter1 = new CellDesignerAliasConverter(reactant1.getElement());
+ CellDesignerAliasConverter reactantConverter2 = new CellDesignerAliasConverter(reactant2.getElement());
+ Point2D p1 = reactantConverter1.getPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1));
+ Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2));
+ Point2D p3 = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
- Element alias1 = reactant1.getAlias();
- Element alias2 = reactant2.getAlias();
- Element alias3 = product.getAlias();
+ Element alias1 = reactant1.getElement();
+ Element alias2 = reactant2.getElement();
+ Element alias3 = product.getElement();
Point2D pointA = alias2.getCenter();
Point2D pointC = alias1.getCenter();
@@ -932,15 +932,15 @@ public class ReactionFromXml extends XmlParser {
PolylineData productLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
- p1 = reactantConverter1.getAnchorPointCoordinates(reactant1.getAlias(), anchorsByNodes.get(reactant1), reactant1Line.reverse());
+ p1 = reactantConverter1.getAnchorPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1), reactant1Line.reverse());
reactant1Line.setEndPoint(p1);
reactant1Line = reactant1Line.reverse();
- p1 = reactantConverter2.getAnchorPointCoordinates(reactant2.getAlias(), anchorsByNodes.get(reactant2), reactant2Line.reverse());
+ p1 = reactantConverter2.getAnchorPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2), reactant2Line.reverse());
reactant2Line.setEndPoint(p1);
reactant2Line = reactant2Line.reverse();
- p1 = productConverter.getAnchorPointCoordinates(product.getAlias(), anchorsByNodes.get(product), productLine.reverse());
+ p1 = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product), productLine.reverse());
productLine.setEndPoint(p1);
if (hasGateMemebers) {
productLine.getEndAtd().setArrowType(ArrowType.OPEN);
@@ -967,11 +967,11 @@ public class ReactionFromXml extends XmlParser {
private void createLinesForSimpleReaction(Reaction reaction, EditPoints editPoints, ConnectScheme scheme) {
Product product = reaction.getProducts().get(0);
Reactant reactant = reaction.getReactants().get(0);
- CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getAlias());
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getAlias());
+ CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement());
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement());
- Point2D endPoint = productConverter.getPointCoordinates(product.getAlias(), anchorsByNodes.get(product));
- Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getAlias(), anchorsByNodes.get(reactant));
+ Point2D endPoint = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
+ Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
PolylineData ld = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint, editPoints.getPoints());
@@ -991,8 +991,8 @@ public class ReactionFromXml extends XmlParser {
if (index == null) {
index = 0;
}
- startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getAlias(), anchorsByNodes.get(reactant), ld);
- endPoint = productConverter.getAnchorPointCoordinates(product.getAlias(), anchorsByNodes.get(product), ld.reverse());
+ startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), ld);
+ endPoint = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product), ld.reverse());
ld.getPoints().set(0, startPoint);
ld.getPoints().set(ld.getPoints().size() - 1, endPoint);
@@ -1397,7 +1397,7 @@ public class ReactionFromXml extends XmlParser {
throw new UnknownModifierClassException(errorInfo, type, reaction.getIdReaction());
}
for (Modifier modifier : reaction.getModifiers()) {
- if (modifier.getAlias() == aliasList.get(0) && modifier.getClass() == mType.getClazz()) {
+ if (modifier.getElement() == aliasList.get(0) && modifier.getClass() == mType.getClazz()) {
result = modifier;
}
}
@@ -1461,12 +1461,12 @@ public class ReactionFromXml extends XmlParser {
for (int i = 1; i < modifiers.size(); i++) {
Modifier param = modifiers.get(i);
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(param.getAlias());
- startPoint = reactantConverter.getPointCoordinates(param.getAlias(), anchorsByNodes.get(param));
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(param.getElement());
+ startPoint = reactantConverter.getPointCoordinates(param.getElement(), anchorsByNodes.get(param));
PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint, pointsByModifier.get(param));
- startPoint = reactantConverter.getAnchorPointCoordinates(param.getAlias(), anchorsByNodes.get(param), polyline);
+ startPoint = reactantConverter.getAnchorPointCoordinates(param.getElement(), anchorsByNodes.get(param), polyline);
polyline.setStartPoint(startPoint);
param.setLine(polyline);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index 4c97f5884b..cb5690bad3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -179,7 +179,7 @@ public class ReactionToXml extends XmlParser {
* @return modifierSpeciesReference sbml node for given modifer
*/
private String getModifierReferenceXmlString(Modifier modifier) {
- Element alias = modifier.getAlias();
+ Element alias = modifier.getElement();
StringBuilder sb = new StringBuilder();
sb.append("<modifierSpeciesReference ");
sb.append("metaid=\"" + elements.getElementId(alias) + "\" ");
@@ -217,11 +217,11 @@ public class ReactionToXml extends XmlParser {
if (modifier instanceof Modifier) {
Modifier mod = (Modifier) modifier;
if (modifiers.equals("")) {
- modifiers = elements.getElementId(mod.getAlias());
- aliases = mod.getAlias().getElementId();
+ modifiers = elements.getElementId(mod.getElement());
+ aliases = mod.getElement().getElementId();
} else {
- modifiers += "," + elements.getElementId(mod.getAlias());
- aliases += "," + mod.getAlias().getElementId();
+ modifiers += "," + elements.getElementId(mod.getElement());
+ aliases += "," + mod.getElement().getElementId();
}
}
@@ -273,17 +273,17 @@ public class ReactionToXml extends XmlParser {
sb.append("<celldesigner:modification ");
String type = modifierTypeUtils.getStringTypeByModifier(modifier);
sb.append(" type=\"" + type + "\" ");
- sb.append(" modifiers=\"" + elements.getElementId(modifier.getAlias()) + "\" ");
- sb.append(" aliases=\"" + modifier.getAlias().getElementId() + "\" ");
+ sb.append(" modifiers=\"" + elements.getElementId(modifier.getElement()) + "\" ");
+ sb.append(" aliases=\"" + modifier.getElement().getElementId() + "\" ");
sb.append(" targetLineIndex=\"" + modifierTypeUtils.getTargetLineIndexByModifier(modifier) + "\" ");
PolylineData line = new PolylineData(modifier.getLine());
line.trimEnd(-modifierTypeUtils.getModifierTypeForClazz(modifier.getClass()).getTrimLength());
if (gate != null) {
line.setEndPoint(gate.getLine().getBeginPoint());
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(modifier.getAlias());
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(modifier.getAlias(), line.getBeginPoint());
- Point2D start = converter.getPointCoordinates(modifier.getAlias(), anchor);
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(modifier.getElement());
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(modifier.getElement(), line.getBeginPoint());
+ Point2D start = converter.getPointCoordinates(modifier.getElement(), anchor);
line.setStartPoint(start);
}
@@ -328,8 +328,8 @@ public class ReactionToXml extends XmlParser {
*/
private String getLinkTargetXmlString(Modifier modifier) {
StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:linkTarget species=\"" + elements.getElementId(modifier.getAlias()) + "\" alias=\"" + modifier.getAlias().getElementId() + "\">\n");
- sb.append(getAnchorXml(modifier.getAlias(), modifier.getLine().getBeginPoint()));
+ sb.append("<celldesigner:linkTarget species=\"" + elements.getElementId(modifier.getElement()) + "\" alias=\"" + modifier.getElement().getElementId() + "\">\n");
+ sb.append(getAnchorXml(modifier.getElement(), modifier.getLine().getBeginPoint()));
sb.append("</celldesigner:linkTarget>\n");
return sb.toString();
@@ -348,13 +348,13 @@ public class ReactionToXml extends XmlParser {
for (Product product : reaction.getProducts()) {
// metaid is missing, maybe it will work ;)
- Element alias = product.getAlias();
+ Element alias = product.getElement();
sb.append("<speciesReference species=\"" + elements.getElementId(alias) + "\">\n");
sb.append("<annotation>\n");
sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:alias>" + product.getAlias().getElementId() + "</celldesigner:alias>\n");
+ sb.append("<celldesigner:alias>" + product.getElement().getElementId() + "</celldesigner:alias>\n");
sb.append("</celldesigner:extension>\n");
sb.append("</annotation>\n");
sb.append("</speciesReference>\n");
@@ -375,20 +375,20 @@ public class ReactionToXml extends XmlParser {
sb.append("<listOfReactants>\n");
for (Reactant reactant : reaction.getReactants()) {
// metaid is missing, maybe it will work ;)
- Species species = (Species) reactant.getAlias();
+ Species species = (Species) reactant.getElement();
Set<Element> parents = new HashSet<>();
// we need top parent species
- while (species.getComplexAlias() != null) {
- species = species.getComplexAlias();
+ while (species.getComplex() != null) {
+ species = species.getComplex();
if (parents.contains(species)) {
throw new InvalidArgumentException(eu.getElementTag(species) + " Complex information is cyclic");
}
parents.add(species);
}
// and top parent alias (for sbml compliant view of celldesigner file)
- Element alias = reactant.getAlias();
+ Element alias = reactant.getElement();
while (alias.getParent() instanceof Complex) {
alias = alias.getParent();
}
@@ -466,8 +466,8 @@ public class ReactionToXml extends XmlParser {
result.append("<celldesigner:listOfGateMember>\n");
ReactionLineData lineData = ReactionLineData
.getByLineType(reaction.getProducts().get(0).getLine().getType(), reaction.getProducts().get(0).getLine().getEndAtd().getArrowType());
- Element alias1 = reactant1.getAlias();
- Element alias2 = reactant2.getAlias();
+ Element alias1 = reactant1.getElement();
+ Element alias2 = reactant2.getElement();
// product line
result.append("<celldesigner:GateMember type=\"" + type.getStringName() + "\"");
@@ -596,7 +596,7 @@ public class ReactionToXml extends XmlParser {
* @return xml node describing reactantLink
*/
private String getReactantLinkXmlString(Reactant reactant) {
- Element alias = reactant.getAlias();
+ Element alias = reactant.getElement();
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:reactantLink ");
sb.append("reactant=\"" + elements.getElementId(alias) + "\" ");
@@ -633,7 +633,7 @@ public class ReactionToXml extends XmlParser {
* @return xml node describing productLink
*/
private String getProductLinkXmlString(Product product) {
- Element alias = product.getAlias();
+ Element alias = product.getElement();
PolylineData[] lines = new PolylineData[] { product.getLine() };
StringBuilder sb = new StringBuilder();
@@ -818,19 +818,19 @@ public class ReactionToXml extends XmlParser {
}
Point2D endPoint = points.get(points.size() - 1);
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(product.getAlias());
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(product.getAlias(), endPoint);
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(product.getElement());
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(product.getElement(), endPoint);
if (anchor == null) { // when we have no anchor, then end point is set
// to
// the center of alias
- points.set(points.size() - 1, product.getAlias().getCenter());
+ points.set(points.size() - 1, product.getElement().getCenter());
}
PolylineData line3 = new PolylineData(points);
- Point2D pointC = reactant1.getAlias().getCenter();
- Point2D pointA = reactant2.getAlias().getCenter();
- Point2D pointB = product.getAlias().getCenter();
+ Point2D pointC = reactant1.getElement().getCenter();
+ Point2D pointA = reactant2.getElement().getCenter();
+ Point2D pointB = product.getElement().getCenter();
Point2D pointO = line3.getBeginPoint();
@@ -850,12 +850,12 @@ public class ReactionToXml extends XmlParser {
}
Point2D startPoint = points.get(0);
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(reactant.getAlias());
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(reactant.getAlias(), startPoint);
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(reactant.getElement());
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(reactant.getElement(), startPoint);
if (anchor == null) { // when we have no anchor, then end point is set
// to
// the center of alias
- points.set(points.size() - 1, reactant.getAlias().getCenter());
+ points.set(points.size() - 1, reactant.getElement().getCenter());
}
int index = points.size();
for (NodeOperator operator : reaction.getOperators()) {
@@ -880,9 +880,9 @@ public class ReactionToXml extends XmlParser {
PolylineData line2 = product1.getLine();
PolylineData line3 = product2.getLine();
- Point2D pointA = product1.getAlias().getCenter();
- Point2D pointB = product2.getAlias().getCenter();
- Point2D pointC = reactant.getAlias().getCenter();
+ Point2D pointA = product1.getElement().getCenter();
+ Point2D pointB = product2.getElement().getCenter();
+ Point2D pointC = reactant.getElement().getCenter();
Point2D pointO = line2.getBeginPoint();
@@ -972,10 +972,10 @@ public class ReactionToXml extends XmlParser {
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:baseProducts>\n");
for (Product product : products) {
- Element alias = product.getAlias();
+ Element alias = product.getElement();
sb.append("<celldesigner:baseProduct ");
- sb.append("species=\"" + elements.getElementId(product.getAlias()) + "\" ");
- sb.append("alias=\"" + product.getAlias().getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(product.getElement()) + "\" ");
+ sb.append("alias=\"" + product.getElement().getElementId() + "\" ");
sb.append(">\n");
sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
@@ -1002,10 +1002,10 @@ public class ReactionToXml extends XmlParser {
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:baseReactants>\n");
for (Reactant reactant : reactants) {
- Element alias = reactant.getAlias();
+ Element alias = reactant.getElement();
sb.append("<celldesigner:baseReactant ");
- sb.append("species=\"" + elements.getElementId(reactant.getAlias()) + "\" ");
- sb.append("alias=\"" + reactant.getAlias().getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(reactant.getElement()) + "\" ");
+ sb.append("alias=\"" + reactant.getElement().getElementId() + "\" ");
sb.append(">\n");
sb.append(getAnchorXml(alias, reactant.getLine().getBeginPoint()));
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
index 131b7beea9..f30064dec9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
@@ -429,7 +429,7 @@ public class SpeciesCollectionXmlParser extends XmlParser {
for (Element species : collection) {
if (species instanceof Complex) {
Complex cs = (Complex) species;
- for (Element element : cs.getAliases()) {
+ for (Element element : cs.getElements()) {
Species child = (Species) element;
sb.append(
"<celldesigner:species id=\"" + elements.getElementId(child) + "\" name=\"" + StringEscapeUtils.escapeXml(helpParser.encodeName(child.getName()))
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 7c2638d7d4..b01fa2e4f9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -577,7 +577,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
FileInputStream fis = new FileInputStream("testFiles/homodimer.xml");
Model model = parser.createModel(new ConverterParams().inputStream(fis));
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (element instanceof Species) {
assertTrue("Homodimer value for class" + element.getClass() + " not upadted", ((Species) element).getHomodimer() > 1);
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index dc31440d59..e4eb9356de 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -54,7 +54,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
- assertEquals(0, model.getCompartmentsAliases().size());
+ assertEquals(0, model.getCompartments().size());
} catch (Exception e) {
e.printStackTrace();
@@ -126,7 +126,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
Set<ModificationState> residues = new HashSet<ModificationState>();
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (element instanceof Species) {
Protein p = (Protein) element;
for (ModificationResidue mr : p.getModificationResidues()) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
index c653991cf3..512cb8fe4f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
@@ -425,7 +425,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
ElementGroup group = parser.getAliasGroup(node, model);
assertNotNull(group);
- assertEquals(4, group.getAliases().size());
+ assertEquals(4, group.getElements().size());
assertEquals("g74", group.getIdGroup());
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
index 78dbdab8bb..f849c74923 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
@@ -53,25 +53,25 @@ public class NestedComplexParsingTests extends CellDesignerTestFunctions {
Complex cs4 = (Complex) s4;
Complex cs5 = (Complex) s5;
Complex cs6 = (Complex) s6;
- assertEquals(2,cs1.getAliases().size());
- assertEquals(2,cs2.getAliases().size());
- assertEquals(0,cs3.getAliases().size());
- assertEquals(0,cs4.getAliases().size());
- assertEquals(2,cs5.getAliases().size());
- assertEquals(3,cs6.getAliases().size());
+ assertEquals(2,cs1.getElements().size());
+ assertEquals(2,cs2.getElements().size());
+ assertEquals(0,cs3.getElements().size());
+ assertEquals(0,cs4.getElements().size());
+ assertEquals(2,cs5.getElements().size());
+ assertEquals(3,cs6.getElements().size());
- assertTrue(cs1.getAliases().contains(s9));
- assertTrue(cs1.getAliases().contains(s3));
+ assertTrue(cs1.getElements().contains(s9));
+ assertTrue(cs1.getElements().contains(s3));
- assertTrue(cs2.getAliases().contains(s7));
- assertTrue(cs2.getAliases().contains(s8));
+ assertTrue(cs2.getElements().contains(s7));
+ assertTrue(cs2.getElements().contains(s8));
- assertTrue(cs5.getAliases().contains(s10));
- assertTrue(cs5.getAliases().contains(s11));
+ assertTrue(cs5.getElements().contains(s10));
+ assertTrue(cs5.getElements().contains(s11));
- assertTrue(cs6.getAliases().contains(s4));
- assertTrue(cs6.getAliases().contains(s5));
- assertTrue(cs6.getAliases().contains(s12));
+ assertTrue(cs6.getElements().contains(s4));
+ assertTrue(cs6.getElements().contains(s5));
+ assertTrue(cs6.getElements().contains(s12));
assertEquals(1,cs1.getAllSimpleChildren().size());
assertEquals(2,cs2.getAllSimpleChildren().size());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
index 04cb68566b..48582239cb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
@@ -189,7 +189,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testLeftToXml() throws Exception {
try {
- Compartment alias = new LeftSquareCompartment();
+ Compartment alias = new LeftSquareCompartment("id");
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -202,7 +202,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testRightToXml() throws Exception {
try {
- Compartment alias = new RightSquareCompartment();
+ Compartment alias = new RightSquareCompartment("id");
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -215,7 +215,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testTopToXml() throws Exception {
try {
- Compartment alias = new TopSquareCompartment();
+ Compartment alias = new TopSquareCompartment("id");
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -228,7 +228,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testBotttomToXml() throws Exception {
try {
- Compartment alias = new BottomSquareCompartment();
+ Compartment alias = new BottomSquareCompartment("id");
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
index d60228eb0a..95aa619a19 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
@@ -121,8 +121,8 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
assertEquals(alias.getX(), alias2.getX(), 1e-6);
assertEquals(alias.getY(), alias2.getY(), 1e-6);
assertEquals(alias.getParent().getElementId(), alias2.getParent().getElementId());
- assertEquals("Alias state label different", alias.getAliasStateLabel(), alias2.getAliasStateLabel());
- assertEquals("Alias state prefix different", alias.getAliasStatePrefix(), alias2.getAliasStatePrefix());
+ assertEquals("Alias state label different", alias.getStateLabel(), alias2.getStateLabel());
+ assertEquals("Alias state prefix different", alias.getStatePrefix(), alias2.getStatePrefix());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -142,8 +142,8 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
Species alias2 = parser.parseXmlAlias(xmlString2);
assertEquals(0, getWarnings().size());
- assertEquals("Alias state label different", alias.getAliasStateLabel(), alias2.getAliasStateLabel());
- assertEquals("Alias state prefix different", alias.getAliasStatePrefix(), alias2.getAliasStatePrefix());
+ assertEquals("Alias state label different", alias.getStateLabel(), alias2.getStateLabel());
+ assertEquals("Alias state prefix different", alias.getStatePrefix(), alias2.getStatePrefix());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -157,8 +157,8 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertNotNull(alias);
- assertEquals("test", alias.getAliasStateLabel());
- assertEquals("free input", alias.getAliasStatePrefix());
+ assertEquals("test", alias.getStateLabel());
+ assertEquals("free input", alias.getStatePrefix());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -172,8 +172,8 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertNotNull(alias);
- assertNull(alias.getAliasStateLabel());
- assertNull(alias.getAliasStatePrefix());
+ assertNull(alias.getStateLabel());
+ assertNull(alias.getStatePrefix());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -296,7 +296,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
list.add(ca2);
// ensure that we return list (firts bigger compartment, then smaller)
- when(model.getCompartmentsAliases()).thenReturn(list);
+ when(model.getCompartments()).thenReturn(list);
when(model.getModelData()).thenReturn(md);
Species alias = new Complex(testAliasId);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index 473a5ba731..fb7c3da3fe 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -207,7 +207,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
try {
Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
- Set<Element> elements = model.getAliases();
+ Set<Element> elements = model.getElements();
for (Element element : elements) {
if (element.getName().equals("blabla")) {
assertEquals(2, element.getMiriamData().size());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java
index 7d341cd183..87cac89e30 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java
@@ -28,7 +28,7 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/compartment/bottom_compartment.xml");
- assertEquals(1, model.getAliases().size());
+ assertEquals(1, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -42,7 +42,7 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/compartment/top_compartment.xml");
- assertEquals(1, model.getAliases().size());
+ assertEquals(1, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -56,7 +56,7 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/compartment/right_compartment.xml");
- assertEquals(1, model.getAliases().size());
+ assertEquals(1, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -70,7 +70,7 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/compartment/left_compartment.xml");
- assertEquals(1, model.getAliases().size());
+ assertEquals(1, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
index 82e37d7d14..b9b22b09e3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
@@ -739,8 +739,8 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
reaction2 = reaction;
}
Reactant reactant = reaction1.getReactants().get(0);
- Element alias1 = reaction1.getReactants().get(0).getAlias();
- Element alias2 = reaction1.getProducts().get(0).getAlias();
+ Element alias1 = reaction1.getReactants().get(0).getElement();
+ Element alias2 = reaction1.getProducts().get(0).getElement();
Product product = reaction1.getProducts().get(0);
Point2D point = new Point2D.Double(alias1.getX() + alias1.getWidth() / 2, alias1.getY() + alias1.getHeight());
Point2D point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
@@ -748,8 +748,8 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
reactant = reaction2.getReactants().get(0);
- alias1 = reaction2.getReactants().get(0).getAlias();
- alias2 = reaction2.getProducts().get(0).getAlias();
+ alias1 = reaction2.getReactants().get(0).getElement();
+ alias2 = reaction2.getProducts().get(0).getElement();
product = reaction2.getProducts().get(0);
point = new Point2D.Double(alias1.getX() + alias1.getWidth(), alias1.getY() + alias1.getHeight() / 2);
point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
@@ -830,7 +830,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
Reaction reaction = model.getReactions().iterator().next();
Reactant r = null;
for (Reactant reactant : reaction.getReactants()) {
- if (reactant.getAlias().getName().equals("s3")) {
+ if (reactant.getElement().getName().equals("s3")) {
r = reactant;
}
}
@@ -855,10 +855,10 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
Modifier sa3 = null;
Modifier sa4 = null;
for (Modifier modifier : modifiers) {
- if (modifier.getAlias().getElementId().equals("sa3")) {
+ if (modifier.getElement().getElementId().equals("sa3")) {
sa3 = modifier;
}
- if (modifier.getAlias().getElementId().equals("sa4")) {
+ if (modifier.getElement().getElementId().equals("sa4")) {
sa4 = modifier;
}
}
@@ -1785,7 +1785,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
public void testProteinsInsideComplex() throws Exception {
try {
Model model = getModelForFile("testFiles/problematic/proteins_inside_complex.xml");
- for (Element el : model.getAliases()) {
+ for (Element el : model.getElements()) {
assertFalse(el.getClass().equals(Protein.class));
}
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
index 6599085012..db03abd568 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
@@ -118,10 +118,10 @@ public class ReactionToXmlTest {
model.addElement(alias);
Complex complex = new Complex("4");
- complex.addAlias(alias);
+ complex.addSpecies(alias);
alias.setParent(complex);
- alias.setComplexAlias(complex);
+ alias.setComplex(complex);
model.addElement(complex);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
index 80dc4c55f2..25cc5a87f9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
@@ -193,7 +193,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
Complex alias = new Complex(testAliasId);
- alias.setCompartmentAlias(ca);
+ alias.setCompartment(ca);
model.addElement(alias);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
@@ -233,7 +233,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
list.add(ca2);
// ensure that we return list (firts bigger compartment, then smaller)
- when(model.getCompartmentsAliases()).thenReturn(list);
+ when(model.getCompartments()).thenReturn(list);
when(model.getModelData()).thenReturn(md);
Complex alias = new Complex(testAliasId);
@@ -340,8 +340,8 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml"));
assertNotNull(child);
- assertNull(child.getAliasStateLabel());
- assertNull(child.getAliasStatePrefix());
+ assertNull(child.getStateLabel());
+ assertNull(child.getStatePrefix());
} catch (Exception e) {
e.printStackTrace();
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 58f19ce531..f466407397 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -159,7 +159,7 @@ public class SbgnmlXmlExporter {
List<Species> aliases = model.getSpeciesList();
for (Species a : aliases) {
- if (a.getComplexAlias() == null) {
+ if (a.getComplex() == null) {
Glyph newGlyph = aliasToGlyph(a);
map.getGlyph().add(newGlyph);
}
@@ -234,7 +234,7 @@ public class SbgnmlXmlExporter {
if (alias instanceof Complex) {
Complex complexAlias = (Complex) alias;
- for (Species a : complexAlias.getAliases()) {
+ for (Species a : complexAlias.getElements()) {
Glyph childGlyph = aliasToGlyph(a);
newGlyph.getGlyph().add(childGlyph);
}
@@ -505,14 +505,14 @@ public class SbgnmlXmlExporter {
if (alias instanceof Species) {
Species speciesAlias = (Species) alias;
- if ((speciesAlias.getAliasStateLabel() != null) && (speciesAlias.getAliasStatePrefix() != null)) {
+ if ((speciesAlias.getStateLabel() != null) && (speciesAlias.getStatePrefix() != null)) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
- if (!speciesAlias.getAliasStatePrefix().equals("free input")) {
- uoiText = uoiText.concat(speciesAlias.getAliasStatePrefix()).concat(":");
+ if (!speciesAlias.getStatePrefix().equals("free input")) {
+ uoiText = uoiText.concat(speciesAlias.getStatePrefix()).concat(":");
}
- uoiText = uoiText.concat(speciesAlias.getAliasStateLabel());
+ uoiText = uoiText.concat(speciesAlias.getStateLabel());
}
}
@@ -716,12 +716,12 @@ public class SbgnmlXmlExporter {
throw new InvalidArgumentException();
}
- if (reaction.getProducts().get(0).getAlias() instanceof Phenotype) {
+ if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
logger.warn("Found Phenotype being a reactant in process. That is discouraged");
}
- arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getAlias().getElementId()));
- arc.setTarget(sourceTargetMap.get(reaction.getProducts().get(0).getAlias().getElementId()));
+ arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getElement().getElementId()));
+ arc.setTarget(sourceTargetMap.get(reaction.getProducts().get(0).getElement().getElementId()));
List<Point2D> pointList = reaction.getReactants().get(0).getLine().getPoints();
pointList.addAll(reaction.getProducts().get(0).getLine().getPoints());
@@ -870,13 +870,13 @@ public class SbgnmlXmlExporter {
}
if (node instanceof Reactant) {
- arc.setSource(sourceTargetMap.get(((Reactant) node).getAlias().getElementId()));
+ arc.setSource(sourceTargetMap.get(((Reactant) node).getElement().getElementId()));
arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction().concat(".1")));
} else if (node instanceof Product) {
arc.setSource(sourceTargetMap.get(node.getReaction().getIdReaction().concat(".2")));
- arc.setTarget(sourceTargetMap.get(((Product) node).getAlias().getElementId()));
+ arc.setTarget(sourceTargetMap.get(((Product) node).getElement().getElementId()));
} else if (node instanceof Modifier) {
- arc.setSource(sourceTargetMap.get(((Modifier) node).getAlias().getElementId()));
+ arc.setSource(sourceTargetMap.get(((Modifier) node).getElement().getElementId()));
if (!node.getLine().getEndAtd().getArrowType().equals(ArrowType.NONE)) {
arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction()));
} else {
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 0383f44f69..2f373637c0 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -543,7 +543,7 @@ public class SbgnmlXmlParser {
Reactant reactant = new Reactant();
reactant.setReaction(reaction);
Glyph source = (Glyph) a.getSource();
- reactant.setAlias(model.getElementByElementId(source.getId()));
+ reactant.setElement(model.getElementByElementId(source.getId()));
List<Point2D> reactantPointList = new ArrayList<>();
reactantPointList.add(new Point2D.Double(a.getStart().getX(), a.getStart().getY()));
reactantPointList.add(new Point2D.Double(a.getStart().getX(), a.getStart().getY()));
@@ -558,7 +558,7 @@ public class SbgnmlXmlParser {
Product product = new Product();
product.setReaction(reaction);
Glyph target = (Glyph) a.getTarget();
- product.setAlias(model.getElementByElementId(target.getId()));
+ product.setElement(model.getElementByElementId(target.getId()));
List<Point2D> productPointList = getLinePoints(a);
PolylineData productLine = parseLine(a, productPointList);
product.setLine(productLine);
@@ -589,8 +589,8 @@ public class SbgnmlXmlParser {
newSpecies.setName(g.getId());
}
// Add species to parent complex if there is one
- if (newSpecies.getComplexAlias() != null) {
- newSpecies.getComplexAlias().addAlias(newSpecies);
+ if (newSpecies.getComplex() != null) {
+ newSpecies.getComplex().addSpecies(newSpecies);
}
// If the species is a multimer, set it's cardinality.
if (!isHomodimer) {
@@ -647,17 +647,17 @@ public class SbgnmlXmlParser {
Glyph compartmentGlyph = (Glyph) g.getCompartmentRef();
Compartment compartmentAlias = model.getElementByElementId(compartmentGlyph.getId());
newAlias.setParent(compartmentAlias);
- newAlias.setCompartmentAlias(compartmentAlias);
+ newAlias.setCompartment(compartmentAlias);
compartmentAlias.addElement(newAlias);
- } else if (newAlias.getComplexAlias() == null) {
+ } else if (newAlias.getComplex() == null) {
// If the alias is in any compartment, assign it to that compartment
- for (Compartment compartmentAlias : model.getCompartmentsAliases()) {
+ for (Compartment compartmentAlias : model.getCompartments()) {
boolean dx1 = compartmentAlias.getX() + compartmentAlias.getWidth() - newAlias.getX() >= 0;
boolean dx2 = compartmentAlias.getX() - (newAlias.getX() + newAlias.getWidth()) <= 0;
boolean dy1 = compartmentAlias.getY() + compartmentAlias.getHeight() - newAlias.getY() >= 0;
boolean dy2 = compartmentAlias.getY() - (newAlias.getY() + newAlias.getHeight()) <= 0;
if (dx1 && dx2 && dy1 && dy2) {
- newAlias.setCompartmentAlias(compartmentAlias);
+ newAlias.setCompartment(compartmentAlias);
newAlias.setParent(compartmentAlias);
compartmentAlias.addElement(newAlias);
}
@@ -809,11 +809,11 @@ public class SbgnmlXmlParser {
if (unitOfInformationText.contains(":") && !unitOfInformationText.startsWith("N:")) {
String unitOfInformationPrefix = unitOfInformationText.substring(0, unitOfInformationText.indexOf(':'));
String unitOfInformationSuffix = unitOfInformationText.substring(unitOfInformationText.indexOf(':') + 1);
- alias.setAliasStatePrefix(unitOfInformationPrefix);
- alias.setAliasStateLabel(unitOfInformationSuffix);
+ alias.setStatePrefix(unitOfInformationPrefix);
+ alias.setStateLabel(unitOfInformationSuffix);
} else if (!unitOfInformationText.startsWith("N:")) {
- alias.setAliasStateLabel(unitOfInformationText);
- alias.setAliasStatePrefix("free input");
+ alias.setStateLabel(unitOfInformationText);
+ alias.setStatePrefix("free input");
}
}
@@ -832,7 +832,7 @@ public class SbgnmlXmlParser {
private void parseComplex(Glyph complexGlyph, Complex parentComplexSpecies, boolean isHomodimer, Model model) {
Complex complexSpecies = new Complex(complexGlyph.getId());
if (parentComplexSpecies != null) {
- complexSpecies.setComplexAlias(parentComplexSpecies);
+ complexSpecies.setComplex(parentComplexSpecies);
}
parseSpecies(complexGlyph, complexSpecies, isHomodimer, model);
@@ -842,37 +842,37 @@ public class SbgnmlXmlParser {
switch (GlyphClazz.fromClazz(child.getClazz())) {
case UNSPECIFIED_ENTITY:
newSpecies = new Unknown(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case SIMPLE_CHEMICAL:
newSpecies = new SimpleMolecule(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case MACROMOLECULE:
newSpecies = new GenericProtein(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case NUCLEIC_ACID_FEATURE:
newSpecies = new Gene(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case SIMPLE_CHEMICAL_MULTIMER:
newSpecies = new SimpleMolecule(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, false, model);
break;
case MACROMOLECULE_MULTIMER:
newSpecies = new GenericProtein(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, false, model);
break;
case NUCLEIC_ACID_FEATURE_MULTIMER:
newSpecies = new Gene(child.getId());
- newSpecies.setComplexAlias(complexSpecies);
+ newSpecies.setComplex(complexSpecies);
parseSpecies(child, newSpecies, false, model);
break;
case COMPLEX:
@@ -887,7 +887,7 @@ public class SbgnmlXmlParser {
Element newAlias = model.getElementByElementId(child.getId());
if (newAlias != null) {
newAlias.setParent(complexAlias);
- complexAlias.addAlias((Species) newAlias);
+ complexAlias.addSpecies((Species) newAlias);
}
}
}
@@ -1199,7 +1199,7 @@ public class SbgnmlXmlParser {
Reactant reactant = new Reactant();
reactant.setReaction(reaction);
Glyph source = (Glyph) a.getSource();
- reactant.setAlias(model.getElementByElementId(source.getId()));
+ reactant.setElement(model.getElementByElementId(source.getId()));
List<Point2D> pointList = getLinePoints(a);
if (p.getReagentArcs().size() == 1) {
pointList.add(getCenterPointFromProcess(p));
@@ -1220,7 +1220,7 @@ public class SbgnmlXmlParser {
Product product = new Product();
product.setReaction(reaction);
Glyph target = (Glyph) a.getTarget();
- product.setAlias(model.getElementByElementId(target.getId()));
+ product.setElement(model.getElementByElementId(target.getId()));
List<Point2D> pointList = getLinePoints(a);
if (p.getRevProductArcs().size() >= 1) {
pointList.add(0, getCenterPointFromProcess(p));
@@ -1238,7 +1238,7 @@ public class SbgnmlXmlParser {
Reactant reactant = new Reactant();
reactant.setReaction(reaction);
Glyph source = (Glyph) a.getTarget();
- reactant.setAlias(model.getElementByElementId(source.getId()));
+ reactant.setElement(model.getElementByElementId(source.getId()));
List<Point2D> pointList = getLinePoints(a);
if (p.getRevReagentArcs().size() <= 1) {
pointList.add(0, getCenterPointFromProcess(p));
@@ -1266,7 +1266,7 @@ public class SbgnmlXmlParser {
if (a.getSource() instanceof Glyph) {
Glyph sourceGlyph = (Glyph) a.getSource();
Species modifierAlias = (Species) model.getElementByElementId(sourceGlyph.getId());
- modifier.setAlias(modifierAlias);
+ modifier.setElement(modifierAlias);
List<Point2D> pointList = getLinePoints(a);
pointList.remove(pointList.size() - 1);
pointList.add(getModifierEndPoint(a, reaction));
@@ -1460,7 +1460,7 @@ public class SbgnmlXmlParser {
Glyph sourceGlyph = (Glyph) logicArc.getSource();
Species modifierAlias = (Species) model.getElementByElementId(sourceGlyph.getId());
- modifier.setAlias(modifierAlias);
+ modifier.setElement(modifierAlias);
List<Point2D> pointList = getLinePoints(logicArc);
pointList.add(operatorCenterPoint);
PolylineData newLine = parseLine(logicArc, pointList);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index 21cbca904f..d897681ce5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -575,7 +575,7 @@ public abstract class AbstractImageGenerator {
drawReaction(reaction, params.getVisibleLayoutsForElement(reaction));
}
// draw all compartments
- for (Compartment ca : params.getModel().getSortedCompartmentsAliases()) {
+ for (Compartment ca : params.getModel().getSortedCompartments()) {
// draw only aliases that don't have parents (aren't included in any
// compartment/complexes)
if (ca.getParent() == null) {
@@ -723,9 +723,9 @@ public abstract class AbstractImageGenerator {
boolean rescale = false;
if (alias instanceof Complex) {
- if (((Complex) alias).getAliases().size() == 0) {
+ if (((Complex) alias).getElements().size() == 0) {
rescale = true;
- } else if (((Complex) alias).getAliases().get(0).getVisibilityLevel() > level) {
+ } else if (((Complex) alias).getElements().get(0).getVisibilityLevel() > level) {
rescale = true;
}
}
@@ -751,7 +751,7 @@ public abstract class AbstractImageGenerator {
if (!complex.getState().equalsIgnoreCase("brief")) {
// depending on current zoom level, children are drawn or not
if (complex.getTransparencyLevel() <= level) {
- for (Species a : complex.getAliases()) {
+ for (Species a : complex.getElements()) {
drawAlias(a, visibleLayouts);
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
index 06b52123ff..36d9e96928 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
@@ -346,7 +346,7 @@ public class PlaceFinder {
List<Compartment> list = otherAliases.get(alias);
if (list == null) {
list = new ArrayList<Compartment>();
- for (Compartment compAlias : model.getCompartmentsAliases()) {
+ for (Compartment compAlias : model.getCompartments()) {
if (compAlias.getVisibilityLevel() <= alias.getVisibilityLevel() && compAlias.getTransparencyLevel() > alias.getVisibilityLevel()) {
if (compAlias.cross(alias) && compAlias.getSize() <= alias.getSize()) {
list.add(compAlias);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
index c9ac29e527..ac517c50d6 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
@@ -105,8 +105,8 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
// cardinality
if (params.isSbgnFormat()) {
String unitOfInformationText = null;
- if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
- unitOfInformationText = alias.getAliasStatePrefix() + ":" + alias.getAliasStateLabel();
+ if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
+ unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
}
if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
if (unitOfInformationText != null) {
@@ -129,7 +129,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
@Override
public void drawText(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
- if (((Complex) alias).getAliases().size() > 0) {
+ if (((Complex) alias).getElements().size() > 0) {
if (alias.getTransparencyLevel() <= params.getLevel()) {
super.drawText(alias, graphics, params);
return;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
index b3e3343d98..60d8260795 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
@@ -79,11 +79,11 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
// Unit of information text (multimer cardinality and/or ion channel's
// state)
String unitOfInformationText = "";
- if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
- if (alias.getAliasStatePrefix().equals("free input")) {
- unitOfInformationText = alias.getAliasStateLabel();
+ if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
+ if (alias.getStatePrefix().equals("free input")) {
+ unitOfInformationText = alias.getStateLabel();
} else {
- unitOfInformationText = alias.getAliasStatePrefix() + ":" + alias.getAliasStateLabel();
+ unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
index 599c7023d1..00048fa556 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
@@ -54,11 +54,11 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
public void drawAlias(Species alias, Graphics2D graphics, ConverterParams params) {
// Unit of information text - multimer cardinality
String unitOfInformationText = null;
- if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
- if (alias.getAliasStatePrefix().equals("free input")) {
- unitOfInformationText = alias.getAliasStateLabel();
+ if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
+ if (alias.getStatePrefix().equals("free input")) {
+ unitOfInformationText = alias.getStateLabel();
} else {
- unitOfInformationText = alias.getAliasStatePrefix() + ":" + alias.getAliasStateLabel();
+ unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
index fd4c02aa19..4825edbcbf 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
@@ -71,8 +71,8 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
// containing cardinality
if (params.isSbgnFormat() && (i == homodir - 1)) {
String unitOfInformationText = null;
- if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
- unitOfInformationText = alias.getAliasStatePrefix() + ":" + alias.getAliasStateLabel();
+ if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
+ unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
}
if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
if (unitOfInformationText != null) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
index 6413599429..66bb702701 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
@@ -289,7 +289,7 @@ public abstract class SpeciesConverter<T extends Species> implements IAliasConve
Point2D point = alias.getCenter();
if (alias instanceof Complex) {
- if (((Complex) alias).getAliases().size() > 0) {
+ if (((Complex) alias).getElements().size() > 0) {
if (alias.getTransparencyLevel() <= params.getLevel()) {
point.setLocation(point.getX(), alias.getY() + alias.getHeight() - graphics.getFontMetrics().getAscent());
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index 02e0979c11..cf5bba155b 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -24,10 +24,10 @@ public class ConverterTest {
@Test
public void test() {
try {
- new AliasConverter(new BottomSquareCompartment());
- new AliasConverter(new TopSquareCompartment());
- new AliasConverter(new LeftSquareCompartment());
- new AliasConverter(new RightSquareCompartment());
+ new AliasConverter(new BottomSquareCompartment("id1"));
+ new AliasConverter(new TopSquareCompartment("id2"));
+ new AliasConverter(new LeftSquareCompartment("id3"));
+ new AliasConverter(new RightSquareCompartment("id4"));
}catch (Exception e) {
e.printStackTrace();
fail("Unknown exception");
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index d2f9ef6899..3ba9e0c966 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -207,9 +207,9 @@ public class NormalImageGeneratorTest {
layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartmentsAliases().get(1).setTransparencyLevel(2);
- model.getCompartmentsAliases().get(0).setTransparencyLevel(2);
- model.getCompartmentsAliases().get(3).setTransparencyLevel(2);
+ model.getCompartments().get(1).setTransparencyLevel(2);
+ model.getCompartments().get(0).setTransparencyLevel(2);
+ model.getCompartments().get(3).setTransparencyLevel(2);
new PngImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
} catch (Exception e) {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
index 86428c73d4..3d191ad894 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
@@ -51,9 +51,9 @@ public class PdfImageGeneratorTest {
layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartmentsAliases().get(1).setTransparencyLevel(2);
- model.getCompartmentsAliases().get(0).setTransparencyLevel(2);
- model.getCompartmentsAliases().get(3).setTransparencyLevel(2);
+ model.getCompartments().get(1).setTransparencyLevel(2);
+ model.getCompartments().get(0).setTransparencyLevel(2);
+ model.getCompartments().get(3).setTransparencyLevel(2);
PdfImageGenerator pig = new PdfImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
index 15dd6e4f68..2ddcd62d38 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
@@ -29,12 +29,12 @@ public class AllPlaceFinderTest {
Model model = new ModelFullIndexed(null);
model.addElement(createCompartmentAlias(94.0, 70.0, 355.0, 173.0));
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
actual = pf.getRetangle(alias).toString();
}
String expected = "";
- Rectangle2D result = model.getCompartmentsAliases().get(0).getBorder();
+ Rectangle2D result = model.getCompartments().get(0).getBorder();
expected = result.toString();
assertEquals(expected, actual);
}
@@ -47,7 +47,7 @@ public class AllPlaceFinderTest {
model.addElement(createCompartmentAlias(332.0, 66.0, 188.0, 255.0));
String expected = "";
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
actual = pf.getRetangle(alias).toString();
Rectangle2D result = alias.getBorder();
@@ -77,7 +77,7 @@ public class AllPlaceFinderTest {
model.addElement(createCompartmentAlias(45.0, 38.0, 174.0, 169.0));
model.addElement(createCompartmentAlias(118.0, 85.0, 60.0, 68.0));
double actual = 0.0;
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias);
actual = rect.getWidth() * rect.getHeight();
@@ -93,12 +93,12 @@ public class AllPlaceFinderTest {
model.addElement(createCompartmentAlias(88.0, 70.0, 138.0, 112.0));
double actual = 0.0;
Rectangle2D result = null;
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias);
actual += rect.getWidth() * rect.getHeight();
}
- result = model.getCompartmentsAliases().get(0).getBorder();
+ result = model.getCompartments().get(0).getBorder();
assertEquals(result.getWidth() * result.getHeight(), actual, 0.01);
}
@@ -136,7 +136,7 @@ public class AllPlaceFinderTest {
model.addElement(createCompartmentAlias(4521.0, 0.0, 10000.0, 6000.0));
model.addElement(createCompartmentAlias(4828.0, 0.0, 5172.0, 6000.0));
double actual = 0.0;
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias);
actual = rect.getWidth() * rect.getHeight();
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index b330bbf2b8..95d5bd72fe 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -31,7 +31,7 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
@@ -211,8 +211,8 @@ public class ComplexZipConverter<T extends IConverter> {
topModel
.addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
} else {
- Element fromAlias = reaction.getReactants().get(0).getAlias();
- Element toAlias = reaction.getProducts().get(0).getAlias();
+ Element fromAlias = reaction.getReactants().get(0).getElement();
+ Element toAlias = reaction.getProducts().get(0).getElement();
if (!(fromAlias instanceof Species)) {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
@@ -220,8 +220,8 @@ public class ComplexZipConverter<T extends IConverter> {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
} else {
- Complex complexFrom = ((Species) fromAlias).getComplexAlias();
- Complex complexTo = ((Species) toAlias).getComplexAlias();
+ Complex complexFrom = ((Species) fromAlias).getComplex();
+ Complex complexTo = ((Species) toAlias).getComplex();
if (complexFrom == null) {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
@@ -255,9 +255,9 @@ public class ComplexZipConverter<T extends IConverter> {
} else if (fromAlias instanceof Phenotype) {
type = SubmodelType.PATHWAY;
}
- AliasSubmodelConnection connection = new AliasSubmodelConnection(toModel, type);
- connection.setFromAlias(source);
- connection.setToAlias(dest);
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(toModel, type);
+ connection.setFromElement(source);
+ connection.setToElement(dest);
connection.setName(toModel.getName());
source.setSubmodel(connection);
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index cc87a72141..8060021ba7 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -77,11 +77,11 @@ public class ComplexZipConverterTest {
Species sa5 = new GenericProtein("sa5");
sa5.setName("sa1");
result.addElement(sa5);
- ca1.addAlias(sa5);
+ ca1.addSpecies(sa5);
Species sa6 = new Phenotype("sa6");
sa6.setName("sa4");
result.addElement(sa6);
- ca1.addAlias(sa6);
+ ca1.addSpecies(sa6);
Complex ca2 = new Complex("ca2");
ca2.setName("s1");
@@ -89,7 +89,7 @@ public class ComplexZipConverterTest {
Species sa7 = new GenericProtein("sa7");
sa7.setName("sa1");
result.addElement(sa7);
- ca2.addAlias(sa7);
+ ca2.addSpecies(sa7);
Complex ca3 = new Complex("cs3");
ca3.setName("s2");
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java
index 6df8bb3626..b17ca82654 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java
@@ -56,7 +56,7 @@ public class CanvasSelectMouseListener implements MouseListener {
List<Object> result = new ArrayList<Object>();
- Set<Element> aliases = canvas.getModel().getAliases();
+ Set<Element> aliases = canvas.getModel().getElements();
for (Element alias : aliases) {
if (alias instanceof Species) {
if (alias.contains(point)) {
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java
index 06f4b6fbf9..988d9043da 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java
@@ -602,8 +602,8 @@ public class ElementDetailsPanel extends JPanel {
add(compartmentLabel, createLayoutConstraints(0, row));
add(compartmentText, createLayoutConstraints(1, row));
- if (alias.getCompartmentAlias() instanceof Compartment) {
- compartmentText.setText(alias.getCompartmentAlias().getElementId());
+ if (alias.getCompartment() instanceof Compartment) {
+ compartmentText.setText(alias.getCompartment().getElementId());
} else {
compartmentText.setText("N/A");
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index 527c666146..87d848c59c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -193,7 +193,7 @@ public class ColorModelCommand extends ModelCommand {
if (schema.getCompartments().size() > 0) {
boolean found = false;
- for (Compartment cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
+ for (Compartment cAlias : alias.getModelData().getModel().getCompartments()) {
for (String compartmentName : schema.getCompartments()) {
if (cAlias.getName().equalsIgnoreCase(compartmentName)) {
if (cAlias.cross(alias)) {
@@ -226,7 +226,7 @@ public class ColorModelCommand extends ModelCommand {
List<ColorSchema> result = new ArrayList<ColorSchema>();
for (ColorSchema schema : schemas) {
boolean found = false;
- for (Element alias : getModel().getAliases()) {
+ for (Element alias : getModel().getElements()) {
if (match(alias, schema)) {
found = true;
}
@@ -261,7 +261,7 @@ public class ColorModelCommand extends ModelCommand {
models.addAll(getModel().getSubmodels());
for (Model model2 : models) {
for (ColorSchema schema : schemas) {
- for (Element alias : model2.getAliases()) {
+ for (Element alias : model2.getElements()) {
if (match(alias, schema)) {
if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
throw new InvalidColorSchemaException("Alias " + alias.getElementId() + " is colored by more than one rule.");
@@ -306,7 +306,7 @@ public class ColorModelCommand extends ModelCommand {
*/
private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
- for (Element alias : result.getAliases()) {
+ for (Element alias : result.getElements()) {
alias.setColor(Color.WHITE);
}
for (Reaction reaction : result.getReactions()) {
@@ -316,7 +316,7 @@ public class ColorModelCommand extends ModelCommand {
}
for (ColorSchema schema : schemas) {
- for (Element alias : result.getAliases()) {
+ for (Element alias : result.getElements()) {
if (match(alias, schema)) {
schema.setMatches(schema.getMatches() + 1);
applyColor(alias, schema);
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index fbab64735f..1bad9ae54e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -137,10 +137,10 @@ public class CopyCommand extends NewModelCommand {
}
}
}
- for (Element alias : modelCopy.getAliases()) {
+ for (Element alias : modelCopy.getElements()) {
// if alias has connection to submodel
if (alias.getSubmodel() != null) {
- AliasSubmodelConnection connection = alias.getSubmodel();
+ ElementSubmodelConnection connection = alias.getSubmodel();
// copy information about submodel
Model original = connection.getSubmodel().getModel();
Model copy = copies.get(original);
@@ -150,12 +150,12 @@ public class CopyCommand extends NewModelCommand {
connection.setSubmodel(copy);
// copy information about original alias
- if (connection.getFromAlias() != null) {
- connection.setFromAlias(modelCopy.getElementByElementId(connection.getFromAlias().getElementId()));
+ if (connection.getFromElement() != null) {
+ connection.setFromElement(modelCopy.getElementByElementId(connection.getFromElement().getElementId()));
}
// copy information about reference alias
- if (connection.getToAlias() != null) {
- connection.setToAlias(modelCopy.getElementByElementId(connection.getToAlias().getElementId()));
+ if (connection.getToElement() != null) {
+ connection.setToElement(modelCopy.getElementByElementId(connection.getToElement().getElementId()));
}
}
}
@@ -174,7 +174,7 @@ public class CopyCommand extends NewModelCommand {
result.setSbgnFormat(model.isSbgnFormat());
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Compartment) {
Compartment copy = ((Compartment) alias).copy();
copy.getElements().clear();
@@ -183,12 +183,12 @@ public class CopyCommand extends NewModelCommand {
}
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Species) {
Species copy = ((Species) alias).copy();
- Compartment ca = copy.getCompartmentAlias();
+ Compartment ca = copy.getCompartment();
Element parent = copy.getParent();
- copy.setCompartmentAlias(null);
+ copy.setCompartment(null);
copy.setParent(null);
// the trick is that in addAlias also some connections are added, so
@@ -198,7 +198,7 @@ public class CopyCommand extends NewModelCommand {
if (ca != null) {
ca = result.getElementByElementId(ca.getElementId());
- copy.setCompartmentAlias(ca);
+ copy.setCompartment(ca);
}
if (parent instanceof Compartment) {
ca = (Compartment) parent;
@@ -227,7 +227,7 @@ public class CopyCommand extends NewModelCommand {
}
result.setProject(model.getProject());
- for (Element alias : result.getAliases()) {
+ for (Element alias : result.getElements()) {
updateAliasReferences(alias, result, model);
}
for (Reaction reaction : result.getReactions()) {
@@ -348,7 +348,7 @@ public class CopyCommand extends NewModelCommand {
private void updateReactionReferences(Reaction reaction, Model model) {
reaction.setModel(model);
for (ReactionNode rNode : reaction.getReactionNodes()) {
- rNode.setAlias(model.getElementByElementId(rNode.getAlias().getElementId()));
+ rNode.setElement(model.getElementByElementId(rNode.getElement().getElementId()));
}
}
@@ -375,17 +375,17 @@ public class CopyCommand extends NewModelCommand {
if (alias instanceof Complex) {
Complex ca = (Complex) alias;
- for (int i = 0; i < ca.getAliases().size(); i++) {
- Species newAlias = (Species) model.getElementByElementId(ca.getAliases().get(i).getElementId());
- ca.getAliases().set(i, newAlias);
+ for (int i = 0; i < ca.getElements().size(); i++) {
+ Species newAlias = (Species) model.getElementByElementId(ca.getElements().get(i).getElementId());
+ ca.getElements().set(i, newAlias);
}
}
if (alias instanceof Species) {
Species originalAlias = (Species) originalModel.getElementByElementId(alias.getElementId());
Species sa = (Species) alias;
- if (sa.getComplexAlias() != null) {
- sa.setComplexAlias((Complex) model.getElementByElementId(sa.getComplexAlias().getElementId()));
+ if (sa.getComplex() != null) {
+ sa.setComplex((Complex) model.getElementByElementId(sa.getComplex().getElementId()));
}
if (originalAlias.getParent() != null) {
@@ -401,8 +401,8 @@ public class CopyCommand extends NewModelCommand {
alias.setModel(model);
- if (alias.getCompartmentAlias() != null) {
- alias.setCompartmentAlias(model.getElementByElementId(alias.getCompartmentAlias().getElementId()));
+ if (alias.getCompartment() != null) {
+ alias.setCompartment(model.getElementByElementId(alias.getCompartment().getElementId()));
}
}
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 14ec54cc19..df7d815578 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -86,25 +86,25 @@ public class CreateHierarchyCommand extends ModelCommand {
}
Model model = getModel();
List<Species> compacts = new ArrayList<>();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Complex) {
if (((Complex) alias).getState().contains("brief")) {
compacts.add((Species) alias);
- compacts.addAll(((Complex) alias).getAliases());
+ compacts.addAll(((Complex) alias).getElements());
}
}
}
- model.getAliases().removeAll(compacts);
+ model.getElements().removeAll(compacts);
clean();
createArtificials();
assignAliases();
orderConcludingComplex();
orderConcludingCompartments();
- List<Element> sortedAliases = model.getAliasesSortedBySize();
+ List<Element> sortedAliases = model.getElementsSortedBySize();
setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
- model.getAliases().addAll(compacts);
- sortedAliases = model.getAliasesSortedBySize();
+ model.getElements().addAll(compacts);
+ sortedAliases = model.getElementsSortedBySize();
preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
settingOfTransparencyLevel(sortedAliases);
@@ -120,14 +120,14 @@ public class CreateHierarchyCommand extends ModelCommand {
* Cleans hierarchical information from the model.
*/
protected void clean() {
- for (Element alias : getModel().getAliases()) {
+ for (Element alias : getModel().getElements()) {
alias.setParent(null);
if (alias instanceof Complex) {
- ((Complex) alias).getAliases().clear();
+ ((Complex) alias).getElements().clear();
}
}
Set<PathwayCompartment> toRemove = new HashSet<>();
- for (Compartment alias : getModel().getCompartmentsAliases()) {
+ for (Compartment alias : getModel().getCompartments()) {
alias.setParent(null);
alias.getElements().clear();
if (alias instanceof PathwayCompartment) {
@@ -135,7 +135,7 @@ public class CreateHierarchyCommand extends ModelCommand {
}
}
for (PathwayCompartment alias : toRemove) {
- getModel().removeAlias(alias);
+ getModel().removeElement(alias);
}
}
@@ -191,9 +191,9 @@ public class CreateHierarchyCommand extends ModelCommand {
orderingComplexesInCompartments();
orderingComplexesInComplexes();
List<Element> list = new ArrayList<Element>();
- for (Element alias : getModel().getAliases()) {
+ for (Element alias : getModel().getElements()) {
if (alias instanceof Complex) {
- for (Species specAlias : ((Complex) alias).getAliases()) {
+ for (Species specAlias : ((Complex) alias).getElements()) {
if (list.contains(specAlias)) {
throw new InvalidStateException("Some aliases are in few Complexes");
}
@@ -207,7 +207,7 @@ public class CreateHierarchyCommand extends ModelCommand {
}
}
}
- for (Element alias : getModel().getAliases()) {
+ for (Element alias : getModel().getElements()) {
if (alias.getParent() != null) {
throw new InvalidStateException("WTF");
}
@@ -219,8 +219,8 @@ public class CreateHierarchyCommand extends ModelCommand {
* Checks if hierarchical structure of compartments is valid.
*/
private void orderConcludingCompartments() {
- for (Compartment compartment1 : getModel().getCompartmentsAliases()) {
- for (Compartment compartment2 : getModel().getCompartmentsAliases()) {
+ for (Compartment compartment1 : getModel().getCompartments()) {
+ for (Compartment compartment2 : getModel().getCompartments()) {
if (!compartment1.equals(compartment2)) {
if (compartment1.contains(compartment2)) {
Set<Element> duplicates = compartment2.getElements();
@@ -292,7 +292,7 @@ public class CreateHierarchyCommand extends ModelCommand {
int maxVisibilityLevel = Integer.MAX_VALUE;
double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Element child : complex.getAliases()) {
+ for (Element child : complex.getElements()) {
maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
}
if (maxVisibilityLevel >= zoomLevels) {
@@ -302,7 +302,7 @@ public class CreateHierarchyCommand extends ModelCommand {
maxVisibilityLevel = 1;
}
complex.setTransparencyLevel(maxVisibilityLevel);
- for (Element child : complex.getAliases()) {
+ for (Element child : complex.getElements()) {
child.setVisibilityLevel(complex.getTransparencyLevel());
}
}
@@ -352,11 +352,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* list of aliases
*/
private void setParentingOfNonComplexChildrens(List<Element> sortedAliases) {
- for (Element alias : getModel().getAliases()) {
+ for (Element alias : getModel().getElements()) {
if (alias.getParent() == null) {
for (Element complex : sortedAliases) {
if (complex instanceof Complex) {
- if (((Complex) complex).getAliases().contains(alias)) {
+ if (((Complex) complex).getElements().contains(alias)) {
alias.setParent(complex);
}
}
@@ -389,13 +389,13 @@ public class CreateHierarchyCommand extends ModelCommand {
* Assign aliases to compartments.
*/
private void assignToCompartments() {
- for (Compartment alias : getModel().getCompartmentsAliases()) {
- for (Compartment alias2 : getModel().getCompartmentsAliases()) {
+ for (Compartment alias : getModel().getCompartments()) {
+ for (Compartment alias2 : getModel().getCompartments()) {
if (alias.contains(alias2)) {
alias.addElement(alias2);
}
}
- for (Element alias2 : getModel().getAliases()) {
+ for (Element alias2 : getModel().getElements()) {
if (!(alias2 instanceof Compartment)) {
if (alias.contains(alias2)) {
alias.addElement(alias2);
@@ -409,11 +409,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* Assign aliases to complexes.
*/
private void assignToComplexes() {
- for (Element alias : getModel().getAliases()) {
+ for (Element alias : getModel().getElements()) {
if (alias instanceof Complex) {
- for (Element alias2 : getModel().getAliases()) {
+ for (Element alias2 : getModel().getElements()) {
if (alias.contains(alias2) && !alias.equals(alias2)) {
- ((Complex) alias).getAliases().add((Species) alias2);
+ ((Complex) alias).getElements().add((Species) alias2);
}
}
}
@@ -424,14 +424,14 @@ public class CreateHierarchyCommand extends ModelCommand {
* Remove subchildren from complexes.
*/
private void orderingComplexesInComplexes() {
- for (Element complex1 : getModel().getAliases()) {
+ for (Element complex1 : getModel().getElements()) {
if (complex1 instanceof Complex) {
- for (Element complex2 : getModel().getAliases()) {
+ for (Element complex2 : getModel().getElements()) {
if (complex2 instanceof Complex) {
if (!complex1.equals(complex2)) {
if (complex1.contains(complex2)) {
- List<Species> duplicates = ((Complex) complex2).getAliases();
- ((Complex) complex1).getAliases().removeAll(duplicates);
+ List<Species> duplicates = ((Complex) complex2).getElements();
+ ((Complex) complex1).getElements().removeAll(duplicates);
}
}
}
@@ -444,10 +444,10 @@ public class CreateHierarchyCommand extends ModelCommand {
* Remove subchildren from compartments by complexes.
*/
private void orderingComplexesInCompartments() {
- for (Compartment compartment : getModel().getCompartmentsAliases()) {
- for (Element complex : getModel().getAliases()) {
+ for (Compartment compartment : getModel().getCompartments()) {
+ for (Element complex : getModel().getElements()) {
if (complex instanceof Complex) {
- List<Species> duplicates = ((Complex) complex).getAliases();
+ List<Species> duplicates = ((Complex) complex).getElements();
compartment.getElements().removeAll(duplicates);
}
}
@@ -458,11 +458,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* Sets proper parents after creating hierarchical structure.
*/
private void parentingInComplexes() {
- for (Element complex : getModel().getAliases()) {
+ for (Element complex : getModel().getElements()) {
if (complex instanceof Complex) {
- for (Element child : ((Complex) complex).getAliases()) {
+ for (Element child : ((Complex) complex).getElements()) {
if (child instanceof Complex) {
- if (((Complex) child).getAliases().contains(complex)) {
+ if (((Complex) child).getElements().contains(complex)) {
if (complex.getParent() != null) {
throw new InvalidStateException(
child.getName() + " has parent " + child.getParent().getName() + " and now again try to add new parent " + complex.getName());
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
index 41c480ae8d..9451c64f4e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
@@ -57,7 +57,7 @@ public class MoveCommand extends ModelCommand {
Model model = getModel();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
alias.setX(alias.getX() + dx);
alias.setY(alias.getY() + dy);
if (alias instanceof Compartment) {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
index aade207264..9910d2e812 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
@@ -152,7 +152,7 @@ public class MoveElementsCommand extends ModelCommand {
// TODO this must be improved, we cannot do full search on every move
for (Reaction reaction : getModel().getReactions()) {
for (ReactionNode node : reaction.getReactionNodes()) {
- if (aliases.contains(node.getAlias())) {
+ if (aliases.contains(node.getElement())) {
if (node instanceof Reactant) {
Point2D point = node.getLine().getBeginPoint();
point.setLocation(point.getX() + dx, point.getY() + dy);
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
index 64302e7f96..3fbe876dbe 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -51,7 +51,7 @@ public class SubModelCommand extends NewModelCommand {
Set<Element> aliasNotToRemove = new HashSet<Element>();
- for (Element alias : result.getAliases()) {
+ for (Element alias : result.getElements()) {
if (polygon.intersects(alias.getBorder())) {
aliasNotToRemove.add(alias);
}
@@ -67,7 +67,7 @@ public class SubModelCommand extends NewModelCommand {
}
}
if (alias instanceof Species) {
- parent = ((Species) alias).getComplexAlias();
+ parent = ((Species) alias).getComplex();
if (parent != null) {
if (!aliasNotToRemove.contains(parent)) {
iterativeAliasNotToRemove.add(parent);
@@ -81,11 +81,11 @@ public class SubModelCommand extends NewModelCommand {
} while (added);
List<Element> aliasToRemove = new ArrayList<Element>();
- for (Element alias : result.getAliases()) {
+ for (Element alias : result.getElements()) {
if (!(polygon.intersects(alias.getBorder()))) {
boolean remove = true;
if (alias instanceof Species) {
- remove = ((Species) alias).getComplexAlias() == null;
+ remove = ((Species) alias).getComplex() == null;
}
if (aliasNotToRemove.contains(alias)) {
remove = false;
@@ -93,7 +93,7 @@ public class SubModelCommand extends NewModelCommand {
if (remove) {
aliasToRemove.add(alias);
if (alias instanceof Complex) {
- List<Species> aliases = ((Complex) alias).getAllChildrenAliases();
+ List<Species> aliases = ((Complex) alias).getAllChildren();
aliasToRemove.addAll(aliases);
}
}
@@ -101,7 +101,7 @@ public class SubModelCommand extends NewModelCommand {
}
for (Element alias : aliasToRemove) {
- result.removeAlias(alias);
+ result.removeElement(alias);
}
List<Reaction> reactionsToRemove = new ArrayList<Reaction>();
@@ -109,7 +109,7 @@ public class SubModelCommand extends NewModelCommand {
boolean remove = false;
for (AbstractNode node : reaction.getNodes()) {
if (node instanceof ReactionNode) {
- if (!result.getAliases().contains(((ReactionNode) node).getAlias())) {
+ if (!result.getElements().contains(((ReactionNode) node).getElement())) {
remove = true;
break;
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index 0ca7374b24..145d6e000e 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -55,7 +55,7 @@ public abstract class CommandTestFunctions {
Complex complexAlias = new Complex("complex_alias_id");
model.addElement(complexAlias);
- complexAlias.addAlias(alias);
+ complexAlias.addSpecies(alias);
model.addElement(alias);
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index cf881e785b..9625a3dab0 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -17,7 +17,7 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -82,14 +82,14 @@ public class CopyCommandTest extends CommandTestFunctions {
Complex complexAlias = new Complex("id2");
GenericProtein protein = new GenericProtein("A");
protein.setNotes(null);
- complexAlias.addAlias(protein);
+ complexAlias.addSpecies(protein);
model.addElement(protein);
model.addElement(complexAlias);
GenericProtein alias = new GenericProtein("B");
alias.setNotes(null);
- complexAlias.addAlias(alias);
+ complexAlias.addSpecies(alias);
model.addElement(alias);
Model copy = new CopyCommand(model).execute();
@@ -207,7 +207,7 @@ public class CopyCommandTest extends CommandTestFunctions {
model3.setNotes("ASDSA");
model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
Element alias = model2.getElementByElementId("a_id");
- alias.setSubmodel(new AliasSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
+ alias.setSubmodel(new ElementSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
Model copy = new CopyCommand(model2).execute();
ModelComparator comparator = new ModelComparator();
@@ -227,7 +227,7 @@ public class CopyCommandTest extends CommandTestFunctions {
model2.setNotes("ASDSA2");
model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- model.getElementByElementId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ model.getElementByElementId("a_id").setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
Model copy = new CopyCommand(model).execute();
ModelComparator comparator = new ModelComparator();
@@ -263,7 +263,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model model2 = getModel();
model2.setNotes("ASDSA2");
- model.getElementByElementId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ model.getElementByElementId("a_id").setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
try {
new CopyCommand(model).execute();
fail("Exception expected");
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index def0925b15..f6e249f3f0 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -54,7 +54,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
}
Set<Integer> levels = new HashSet<Integer>();
- for (Element a : model.getAliases()) {
+ for (Element a : model.getElements()) {
levels.add(a.getVisibilityLevel());
}
assertTrue(levels.size() > 2);
@@ -88,7 +88,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, 2, 2).execute();
boolean artifitial = false;
- for (Compartment a : model.getCompartmentsAliases()) {
+ for (Compartment a : model.getCompartments()) {
if (a instanceof PathwayCompartment) {
artifitial = true;
}
@@ -106,16 +106,16 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
try {
Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
- int aliasSize0 = model.getCompartmentsAliases().size();
+ int aliasSize0 = model.getCompartments().size();
new CreateHierarchyCommand(model, 2, 2).execute();
- int aliasSize = model.getCompartmentsAliases().size();
+ int aliasSize = model.getCompartments().size();
assertTrue(aliasSize0 != aliasSize);
new CreateHierarchyCommand(model, 2, 2).execute();
- int aliasSize2 = model.getCompartmentsAliases().size();
+ int aliasSize2 = model.getCompartments().size();
assertEquals(aliasSize, aliasSize2);
} catch (Exception e) {
@@ -134,7 +134,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, levels, zoomFactor).execute();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias.getParent() == null) {
assertTrue("Alias " + alias.getElementId() + " is not visible at levels highers than " + alias.getVisibilityLevel(), alias.getVisibilityLevel() <= 1);
}
@@ -156,7 +156,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, levels, zoomFactor).execute();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
assertTrue(
"Alias " + alias.getElementId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
alias.getVisibilityLevel() <= levels);
@@ -210,13 +210,13 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
command.clean();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
assertNull(alias.getParent());
if (alias instanceof Complex) {
- assertTrue(((Complex) alias).getAliases().isEmpty());
+ assertTrue(((Complex) alias).getElements().isEmpty());
}
}
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
assertNull(alias.getParent());
assertTrue(alias.getElements().isEmpty());
}
@@ -239,7 +239,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
command.execute();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
Element parentAlias = alias.getParent();
if (parentAlias != null) {
assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
index b455827cef..9521e94745 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -41,7 +41,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
Model copy = new SubModelCommand(model, polygon).execute();
- assertEquals(2, copy.getAliases().size());
+ assertEquals(2, copy.getElements().size());
assertEquals(0, copy.getReactions().size());
} catch (Exception e) {
@@ -64,7 +64,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
Model copy = new SubModelCommand(model, polygon).execute();
- assertEquals(9, copy.getAliases().size());
+ assertEquals(9, copy.getElements().size());
assertEquals(1, copy.getReactions().size());
} catch (Exception e) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/AliasInFewParentsException.java b/model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java
similarity index 59%
rename from model/src/main/java/lcsb/mapviewer/model/map/AliasInFewParentsException.java
rename to model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java
index d99c9b7ad8..3938eb8261 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/AliasInFewParentsException.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.model.map;
-
-/**
- * Exception thrown when one alias has more then one parent.
- *
- * @author Piotr Gawron
- *
- */
-public class AliasInFewParentsException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with a message passed in the argument.
- *
- * @param message
- * text message of this exception
- */
- public AliasInFewParentsException(String message) {
- super(message);
- }
-}
+package lcsb.mapviewer.model.map;
+
+/**
+ * Exception thrown when one element has more then one parent.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementInFewParentsException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with a message passed in the argument.
+ *
+ * @param message
+ * text message of this exception
+ */
+ public ElementInFewParentsException(String message) {
+ super(message);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
index 581dc4f308..7981046d40 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.map.model.Model;
*
*/
@Entity
-@DiscriminatorValue("Bottom square Compartment Alias")
+@DiscriminatorValue("Bottom square Compartment")
public class BottomSquareCompartment extends Compartment {
/**
@@ -23,16 +23,16 @@ public class BottomSquareCompartment extends Compartment {
private static final long serialVersionUID = 1L;
/**
- * Constructor that creates an alias with the new shape but takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates an compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
* @param model
- * model object to which the alias will be assigned
+ * model object to which the compartment will be assigned
*/
- public BottomSquareCompartment(Compartment originalAlias, Model model) {
- super(originalAlias);
+ public BottomSquareCompartment(Compartment original, Model model) {
+ super(original);
setX(0.0);
setWidth(model.getWidth() * 2);
setY(0.0);
@@ -40,23 +40,33 @@ public class BottomSquareCompartment extends Compartment {
}
/**
- * Constructor that creates an alias with the new shape and takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates an compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
*/
- public BottomSquareCompartment(Compartment originalAlias) {
- super(originalAlias);
+ public BottomSquareCompartment(Compartment original) {
+ super(original);
}
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
- public BottomSquareCompartment() {
+ BottomSquareCompartment() {
super();
}
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public BottomSquareCompartment(String elementId) {
+ setElementId(elementId);
+ }
+
@Override
public BottomSquareCompartment copy() {
if (this.getClass() == BottomSquareCompartment.class) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
index 08937710b5..9381820fb6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
@@ -29,7 +29,7 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
@Entity
-@DiscriminatorValue("Compartment Alias")
+@DiscriminatorValue("Compartment")
public class Compartment extends Element {
/**
@@ -86,7 +86,7 @@ public class Compartment extends Element {
* {@link Element Elements} that are directly inside this compartment.
*/
@Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "compartmentAlias")
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "compartment")
private Set<Element> elements = new HashSet<>();
/**
@@ -181,17 +181,17 @@ public class Compartment extends Element {
if (element.equals(elementToAdd)) {
return;
} else {
- throw new InvalidArgumentException("Alias " + elementToAdd.getElementId() + " already on the list of compartment " + getElementId() + " children");
+ throw new InvalidArgumentException("Element " + elementToAdd.getElementId() + " already on the list of compartment " + getElementId() + " children");
}
}
}
elements.add(elementToAdd);
- elementToAdd.setCompartmentAlias(this);
+ elementToAdd.setCompartment(this);
}
/**
- * Return set of all {@link Element elements} inside the compartment alias
- * (not necessery directly in the compartment).
+ * Return set of all {@link Element elements} inside the compartment (not
+ * necessery directly in the compartment).
*
* @return list of all elements in the compartment
*/
@@ -280,9 +280,9 @@ public class Compartment extends Element {
*/
public void removeElement(Element element) {
elements.remove(element);
- if (element.getCompartmentAlias() != null) {
- if (element.getCompartmentAlias() == this) {
- element.setCompartmentAlias(null);
+ if (element.getCompartment() != null) {
+ if (element.getCompartment() == this) {
+ element.setCompartment(null);
} else {
logger.warn("Removing element from compartment that might not belong there");
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
index aa8860039e..e56a9c0532 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.ElementComparator;
/**
- * This class implements comparator interface for CompartmentAlias.
+ * This class implements comparator interface for {@link Compartment} objects.
*
* @author Piotr Gawron
*
@@ -23,6 +23,7 @@ import lcsb.mapviewer.model.map.species.ElementComparator;
*
*/
public class CompartmentComparator implements Comparator<Compartment> {
+
/**
* Default class logger.
*/
@@ -70,8 +71,8 @@ public class CompartmentComparator implements Comparator<Compartment> {
}
/**
- * This method compares only the fields that are defined in CompartmentAlias
- * class in inheritence tree.
+ * This method compares only the fields that are defined in
+ * {@link Compartment} class in inheritence tree.
*
* @param arg0
* first object to compare
@@ -81,8 +82,8 @@ public class CompartmentComparator implements Comparator<Compartment> {
* -1/1 is returned.
*/
private int internalCompare(Compartment arg0, Compartment arg1) {
- ElementComparator aliasComparator = new ElementComparator(epsilon);
- int result = aliasComparator.internalCompare(arg0, arg1);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ int result = elementComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
@@ -112,32 +113,32 @@ public class CompartmentComparator implements Comparator<Compartment> {
}
if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
- logger.debug("Aliases number different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
+ logger.debug("Elements number different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
}
Map<String, Element> map1 = new HashMap<>();
Map<String, Element> map2 = new HashMap<>();
- for (Element alias : arg0.getElements()) {
- if (map1.get(alias.getElementId()) != null) {
- throw new InvalidArgumentException("Few aliases with the same id: " + alias.getElementId());
+ for (Element element : arg0.getElements()) {
+ if (map1.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
}
- map1.put(alias.getElementId(), alias);
+ map1.put(element.getElementId(), element);
}
- for (Element alias : arg1.getElements()) {
- if (map2.get(alias.getElementId()) != null) {
- throw new InvalidArgumentException("Few aliases with the same id: " + alias.getElementId());
+ for (Element element : arg1.getElements()) {
+ if (map2.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
}
- map2.put(alias.getElementId(), alias);
+ map2.put(element.getElementId(), element);
}
- for (Element alias : arg0.getElements()) {
- Element alias2 = map2.get(alias.getElementId());
- int status = aliasComparator.compare(alias, alias2);
+ for (Element element : arg0.getElements()) {
+ Element element2 = map2.get(element.getElementId());
+ int status = elementComparator.compare(element, element2);
if (status != 0) {
- logger.debug("Couldn't match alias: " + alias.getElementId() + ", " + alias2);
+ logger.debug("Couldn't match element: " + element.getElementId() + ", " + element2);
return status;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
index 8df301320b..a2136ad14c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
@@ -6,7 +6,6 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.model.Model;
-
/**
* This class defines compartment that covers left part of the model up to some
* border on the right side.
@@ -15,33 +14,33 @@ import lcsb.mapviewer.model.map.model.Model;
*
*/
@Entity
-@DiscriminatorValue("Left square Compartment Alias")
+@DiscriminatorValue("Left square Compartment")
public class LeftSquareCompartment extends Compartment {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
- public LeftSquareCompartment() {
+ LeftSquareCompartment() {
super();
}
/**
- * Constructor that creates an alias with the new shape but takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
* @param model
- * model object to which the alias will be assigned
+ * model object to which the compartment will be assigned
*/
- public LeftSquareCompartment(Compartment originalAlias, Model model) {
- super(originalAlias);
+ public LeftSquareCompartment(Compartment original, Model model) {
+ super(original);
setX(0.0);
setWidth(model.getWidth() * 2);
setY(0.0);
@@ -49,14 +48,24 @@ public class LeftSquareCompartment extends Compartment {
}
/**
- * Constructor that creates an alias with the new shape and takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public LeftSquareCompartment(LeftSquareCompartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param elementId
+ * identifier of the compartment
*/
- public LeftSquareCompartment(LeftSquareCompartment originalAlias) {
- super(originalAlias);
+ public LeftSquareCompartment(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
index 23194155a7..2f5dc003cc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
@@ -6,13 +6,13 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * This class defines compartment alias with oval shape.
+ * This class defines compartment with oval shape.
*
* @author Piotr Gawron
*
*/
@Entity
-@DiscriminatorValue("Oval Compartment Alias")
+@DiscriminatorValue("Oval Compartment")
public class OvalCompartment extends Compartment {
/**
@@ -21,21 +21,21 @@ public class OvalCompartment extends Compartment {
private static final long serialVersionUID = 1L;
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
- public OvalCompartment() {
+ OvalCompartment() {
super();
}
/**
- * Constructor that creates an alias with the new shape and takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
*/
- public OvalCompartment(Compartment originalAlias) {
- super(originalAlias);
+ public OvalCompartment(Compartment original) {
+ super(original);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
index 8330145fc5..58fd5fadb6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
@Entity
-@DiscriminatorValue("Artifitial Compartment Alias")
+@DiscriminatorValue("Pathway Compartment")
public class PathwayCompartment extends Compartment {
/**
@@ -21,7 +21,7 @@ public class PathwayCompartment extends Compartment {
private static final long serialVersionUID = 1L;
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
PathwayCompartment() {
super();
@@ -30,12 +30,12 @@ public class PathwayCompartment extends Compartment {
/**
* Default constructor.
*
- * @param aliasId
+ * @param elementId
* identifier of the compartment
*/
- public PathwayCompartment(String aliasId) {
+ public PathwayCompartment(String elementId) {
super();
- setElementId(aliasId);
+ setElementId(elementId);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
index 8dd6a3f653..5e257e5881 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
@@ -16,53 +16,53 @@ import lcsb.mapviewer.model.map.model.Model;
*
*/
@Entity
-@DiscriminatorValue("Right square Compartment Alias")
+@DiscriminatorValue("Right square Compartment")
public class RightSquareCompartment extends Compartment {
/**
*
*/
- private static final long serialVersionUID = 1L;
-
+ private static final long serialVersionUID = 1L;
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RightSquareCompartment.class);
+ private static Logger logger = Logger.getLogger(RightSquareCompartment.class);
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
- public RightSquareCompartment() {
+ RightSquareCompartment() {
super();
}
/**
- * Constructor that creates an alias with the new shape but takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
* @param model
- * model object to which the alias will be assigned
+ * model object to which the compartment will be assigned
*/
- public RightSquareCompartment(Compartment originalAlias, Model model) {
- super(originalAlias);
+ public RightSquareCompartment(Compartment original, Model model) {
+ super(original);
setX(0.0);
setWidth(model.getWidth() * 2);
setY(0.0);
setHeight(model.getHeight() * 2);
}
- /**
- * Sets the CellDesigner point coordinates. In the implementation of
- * BottomSquare it should define left border.
- *
- * @param y
- * to be ignored
- * @param x
- * left border
- *
- */
+ /**
+ * Sets the CellDesigner point coordinates. In the implementation of
+ * BottomSquare it should define left border.
+ *
+ * @param y
+ * to be ignored
+ * @param x
+ * left border
+ *
+ */
public void setPoint(String x, String y) {
// set left border
setX(x);
@@ -70,14 +70,24 @@ public class RightSquareCompartment extends Compartment {
}
/**
- * Constructor that creates an alias with the new shape and takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public RightSquareCompartment(RightSquareCompartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param elementId
+ * identifier of the compartment
*/
- public RightSquareCompartment(RightSquareCompartment originalAlias) {
- super(originalAlias);
+ public RightSquareCompartment(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java
index e6dc926017..7879103bd3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java
@@ -6,13 +6,13 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * This class defines compartment alias with oval shape.
+ * This class defines compartment with oval shape.
*
* @author Piotr Gawron
*
*/
@Entity
-@DiscriminatorValue("Square Compartment Alias")
+@DiscriminatorValue("Square Compartment")
public class SquareCompartment extends Compartment {
/**
@@ -21,32 +21,32 @@ public class SquareCompartment extends Compartment {
private static final long serialVersionUID = 1L;
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
SquareCompartment() {
super();
}
/**
- * Constructor that creates an alias with the new shape and takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
*/
- public SquareCompartment(Compartment originalAlias) {
- super(originalAlias);
+ public SquareCompartment(Compartment original) {
+ super(original);
}
/**
* Default constructor.
*
- * @param aliasId
+ * @param elementId
* identifier of the compartment
*/
- public SquareCompartment(String aliasId) {
+ public SquareCompartment(String elementId) {
super();
- setElementId(aliasId);
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
index f45c36766a..03dc161d9c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.model.Model;
*/
@Entity
-@DiscriminatorValue("Top square Compartment Alias")
+@DiscriminatorValue("Top square Compartment")
public class TopSquareCompartment extends Compartment {
/**
@@ -24,23 +24,23 @@ public class TopSquareCompartment extends Compartment {
private static final long serialVersionUID = 1L;
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
- public TopSquareCompartment() {
+ TopSquareCompartment() {
super();
}
/**
- * Constructor that creates an alias with the new shape but takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param original
+ * orignal compartment where the data was kept
* @param model
- * model object to which the alias will be assigned
+ * model object to which the compartment will be assigned
*/
- public TopSquareCompartment(Compartment originalAlias, Model model) {
- super(originalAlias);
+ public TopSquareCompartment(Compartment original, Model model) {
+ super(original);
setX(0.0);
setWidth(model.getWidth() * 2);
setY(0.0);
@@ -48,14 +48,24 @@ public class TopSquareCompartment extends Compartment {
}
/**
- * Constructor that creates an alias with the new shape and takes the
- * reference data from the alias given as parameter.
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public TopSquareCompartment(TopSquareCompartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
*
- * @param originalAlias
- * orignal alias where the data was kept
+ * @param elementId
+ * identifier of the compartment
*/
- public TopSquareCompartment(TopSquareCompartment originalAlias) {
- super(originalAlias);
+ public TopSquareCompartment(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
index 9a010c87e6..d3f3b0e78a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
@@ -26,9 +26,9 @@ public class ElementGroup implements Serializable {
private String idGroup;
/**
- * List of aliases in the group.
+ * List of elements in the group.
*/
- private List<Element> aliases = new ArrayList<Element>();
+ private List<Element> elements = new ArrayList<>();
/**
* @return the idGroup
@@ -48,30 +48,30 @@ public class ElementGroup implements Serializable {
}
/**
- * @return the aliases
- * @see #aliases
+ * @return the elements
+ * @see #elements
*/
- public List<Element> getAliases() {
- return aliases;
+ public List<Element> getElements() {
+ return elements;
}
/**
- * @param aliases
- * the aliases to set
- * @see #aliases
+ * @param elements
+ * the elements to set
+ * @see #elements
*/
- public void setAliases(List<Element> aliases) {
- this.aliases = aliases;
+ public void setElements(List<Element> elements) {
+ this.elements = elements;
}
/**
- * Add alias to the group.
+ * Add element to the group.
*
- * @param alias
+ * @param element
* object to add to the group
*/
- public void addAlias(Element alias) {
- aliases.add(alias);
+ public void addElement(Element element) {
+ elements.add(element);
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java
deleted file mode 100644
index bad3304df1..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java
+++ /dev/null
@@ -1,144 +0,0 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.io.Serializable;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines connection between alias and submap (submodel). This means
- * that single alias should be "expandable" into map represented by
- * {@link SubmodelConnection#submodel} object.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ALIAS_SUBMODEL_LINK")
-public class AliasSubmodelConnection extends SubmodelConnection implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * From which alias this connection start.
- */
- @ManyToOne
- private Element fromAlias;
-
- /**
- * This object defines reference element in submodel that represents central
- * (or identical) object in reference submodel.
- */
- @ManyToOne
- private Element toAlias;
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public AliasSubmodelConnection(ModelData submodel, SubmodelType type) {
- super(submodel, type);
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param model
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public AliasSubmodelConnection(Model model, SubmodelType type) {
- super(model.getModelData(), type);
- }
-
- /**
- * Default constructor.
- */
- public AliasSubmodelConnection() {
- }
-
- /**
- * Constructor that creates copy of the {@link AliasSubmodelConnection}
- * object.
- *
- * @param original
- * original object from which copy is prepared
- */
- public AliasSubmodelConnection(AliasSubmodelConnection original) {
- super(original);
- this.setFromAlias(original.getFromAlias());
- this.setToAlias(original.getToAlias());
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- * @param name
- * {@link SubmodelConnection#name}
- */
- public AliasSubmodelConnection(Model submodel, SubmodelType type, String name) {
- super(submodel, type, name);
- }
-
- /**
- * @return the fromAlias
- * @see #fromAlias
- */
- public Element getFromAlias() {
- return fromAlias;
- }
-
- /**
- * @param fromAlias
- * the fromAlias to set
- * @see #fromAlias
- */
- public void setFromAlias(Element fromAlias) {
- this.fromAlias = fromAlias;
- }
-
- /**
- * @return the toAlias
- * @see #toAlias
- */
- public Element getToAlias() {
- return toAlias;
- }
-
- /**
- * @param toAlias
- * the toAlias to set
- * @see #toAlias
- */
- public void setToAlias(Element toAlias) {
- this.toAlias = toAlias;
- }
-
- @Override
- public AliasSubmodelConnection copy() {
- if (this.getClass() == AliasSubmodelConnection.class) {
- AliasSubmodelConnection result = new AliasSubmodelConnection();
- result.assignValuesFromOriginal(this);
- result.setFromAlias(this.getFromAlias());
- result.setToAlias(this.getToAlias());
- return result;
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java
new file mode 100644
index 0000000000..20e56a9408
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java
@@ -0,0 +1,144 @@
+package lcsb.mapviewer.model.map.model;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines connection between {@link Element} and submap (submodel).
+ * This means that single {@link Element} should be "expandable" into map
+ * represented by {@link SubmodelConnection#submodel} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ALIAS_SUBMODEL_LINK")
+public class ElementSubmodelConnection extends SubmodelConnection implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * From which {@link Element} this connection start.
+ */
+ @ManyToOne
+ private Element fromElement;
+
+ /**
+ * This object defines reference element in submodel that represents central
+ * (or identical) object in reference submodel.
+ */
+ @ManyToOne
+ private Element toElement;
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public ElementSubmodelConnection(ModelData submodel, SubmodelType type) {
+ super(submodel, type);
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param model
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public ElementSubmodelConnection(Model model, SubmodelType type) {
+ super(model.getModelData(), type);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ElementSubmodelConnection() {
+ }
+
+ /**
+ * Constructor that creates copy of the {@link ElementSubmodelConnection}
+ * object.
+ *
+ * @param original
+ * original object from which copy is prepared
+ */
+ public ElementSubmodelConnection(ElementSubmodelConnection original) {
+ super(original);
+ this.setFromElement(original.getFromElement());
+ this.setToElement(original.getToElement());
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ * @param name
+ * {@link SubmodelConnection#name}
+ */
+ public ElementSubmodelConnection(Model submodel, SubmodelType type, String name) {
+ super(submodel, type, name);
+ }
+
+ /**
+ * @return the fromElement
+ * @see #fromElement
+ */
+ public Element getFromElement() {
+ return fromElement;
+ }
+
+ /**
+ * @param fromElement
+ * the fromElement to set
+ * @see #fromElement
+ */
+ public void setFromElement(Element fromElement) {
+ this.fromElement = fromElement;
+ }
+
+ /**
+ * @return the toElement
+ * @see #toElement
+ */
+ public Element getToElement() {
+ return toElement;
+ }
+
+ /**
+ * @param toElement
+ * the toElement to set
+ * @see #toElement
+ */
+ public void setToElement(Element toElement) {
+ this.toElement = toElement;
+ }
+
+ @Override
+ public ElementSubmodelConnection copy() {
+ if (this.getClass() == ElementSubmodelConnection.class) {
+ ElementSubmodelConnection result = new ElementSubmodelConnection();
+ result.assignValuesFromOriginal(this);
+ result.setFromElement(this.getFromElement());
+ result.setToElement(this.getToElement());
+ return result;
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
similarity index 52%
rename from model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
index 5db1a1da5b..c1709b3a29 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
@@ -9,16 +9,17 @@ import lcsb.mapviewer.model.map.species.ElementComparator;
import org.apache.log4j.Logger;
/**
- * This class implements comparator interface for {@link AliasSubmodelConnection}.
+ * This class implements comparator interface for {@link ElementSubmodelConnection}.
*
* @author Piotr Gawron
*
*/
-public class AliasSubmodelConnectionComparator implements Comparator<AliasSubmodelConnection> {
+public class ElementSubmodelConnectionComparator implements Comparator<ElementSubmodelConnection> {
+
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(AliasSubmodelConnectionComparator.class);
+ private static Logger logger = Logger.getLogger(ElementSubmodelConnectionComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -31,19 +32,19 @@ public class AliasSubmodelConnectionComparator implements Comparator<AliasSubmod
* @param epsilon
* {@link #epsilon}
*/
- public AliasSubmodelConnectionComparator(double epsilon) {
+ public ElementSubmodelConnectionComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public AliasSubmodelConnectionComparator() {
+ public ElementSubmodelConnectionComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(AliasSubmodelConnection arg0, AliasSubmodelConnection arg1) {
+ public int compare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -64,7 +65,7 @@ public class AliasSubmodelConnectionComparator implements Comparator<AliasSubmod
/**
* This method compares only the fields that are defined in
- * {@link AliasSubmodelConnection} class in inheritence tree. It also calls
+ * {@link ElementSubmodelConnection} class in inheritence tree. It also calls
* the {@link SubmodelConnectionComparator} for the super class (
* {@link SubmodelConnection}).
*
@@ -75,34 +76,34 @@ public class AliasSubmodelConnectionComparator implements Comparator<AliasSubmod
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- public int internalCompare(AliasSubmodelConnection arg0, AliasSubmodelConnection arg1) {
+ public int internalCompare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
SubmodelConnectionComparator superComparator = new SubmodelConnectionComparator(epsilon);
int result = superComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
- ElementComparator aliasComparator = new ElementComparator(epsilon);
- Element alias1 = arg0.getFromAlias();
- Element alias2 = arg1.getFromAlias();
- arg0.setFromAlias(null);
- arg1.setFromAlias(null);
- int status = aliasComparator.compare(alias1, alias2);
- arg0.setFromAlias(alias1);
- arg1.setFromAlias(alias2);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ Element element1 = arg0.getFromElement();
+ Element element2 = arg1.getFromElement();
+ arg0.setFromElement(null);
+ arg1.setFromElement(null);
+ int status = elementComparator.compare(element1, element2);
+ arg0.setFromElement(element1);
+ arg1.setFromElement(element2);
if (status != 0) {
- logger.debug("from alias different: " + arg0.getFromAlias() + ", " + arg1.getFromAlias());
+ logger.debug("from element different: " + arg0.getFromElement() + ", " + arg1.getFromElement());
return status;
}
- alias1 = arg0.getToAlias();
- alias2 = arg1.getToAlias();
- arg0.setToAlias(null);
- arg1.setToAlias(null);
- status = aliasComparator.compare(alias1, alias2);
- arg0.setToAlias(alias1);
- arg1.setToAlias(alias2);
+ element1 = arg0.getToElement();
+ element2 = arg1.getToElement();
+ arg0.setToElement(null);
+ arg1.setToElement(null);
+ status = elementComparator.compare(element1, element2);
+ arg0.setToElement(element1);
+ arg1.setToElement(element2);
if (status != 0) {
- logger.debug("to alias different: " + arg0.getToAlias() + ", " + arg1.getToAlias());
+ logger.debug("to element different: " + arg0.getToElement() + ", " + arg1.getToElement());
return status;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index b29a5720fd..eaaa741a2b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -47,12 +47,12 @@ public interface Model {
void setSbgnFormat(boolean sbgnFormat);
/**
- * Adds alias to the model.
+ * Adds element to the model.
*
- * @param alias
- * alias to add
+ * @param element
+ * element to add
*/
- void addElement(Element alias);
+ void addElement(Element element);
/**
* Returns map model version.
@@ -118,10 +118,10 @@ public interface Model {
*
* @return set of all alisaes
*/
- Set<Element> getAliases();
+ Set<Element> getElements();
/**
- * Returns alias with the given alias identfier ({@link Element#aliasId}).
+ * Returns element with the given element identfier ({@link Element#elementId}).
*
* @param idElement
* element identifier
@@ -147,9 +147,9 @@ public interface Model {
Set<Reaction> getReactions();
/**
- * @return list of compartment aliases
+ * @return list of compartments
*/
- List<Compartment> getCompartmentsAliases();
+ List<Compartment> getCompartments();
/**
* Adds layer to the model.
@@ -166,12 +166,12 @@ public interface Model {
Set<Layer> getLayers();
/**
- * Adds list of aliases into model.
+ * Adds list of elements into model.
*
- * @param aliases
- * list of aliases
+ * @param elements
+ * list of elements
*/
- void addAliases(List<? extends Element> aliases);
+ void addElements(List<? extends Element> elements);
/**
* Sets new short description of the model.
@@ -207,10 +207,10 @@ public interface Model {
/**
* Adds {@link ElementGroup} to the model.
*
- * @param aliasGroup
+ * @param elementGroup
* object to add
*/
- void addAliasGroup(ElementGroup aliasGroup);
+ void addElementGroup(ElementGroup elementGroup);
/**
* Adds {@link BlockDiagram} to the model.
@@ -304,12 +304,12 @@ public interface Model {
void removeReaction(Reaction reaction);
/**
- * Removes alias from the model.
+ * Removes {@link Element} from the model.
*
- * @param alias
- * alias to remove
+ * @param element
+ * element to remove
*/
- void removeAlias(Element alias);
+ void removeElement(Element element);
/**
* Returns list of reactions sorted by reaction id.
@@ -319,9 +319,9 @@ public interface Model {
List<Reaction> getSortedReactions();
/**
- * Return list of aliases sorted by the size.
+ * Return list of elements sorted by the size.
*
- * @return list of aliases sorted by the size
+ * @return list of elements sorted by the size
*/
List<Element> getSortedSpeciesList();
@@ -421,36 +421,36 @@ public interface Model {
Calendar getCreationDate();
/**
- * Returns alias for given database identifier.
+ * Returns {@link Element} for given database identifier.
*
* @param dbId
- * alias database identifier ({@link Element#id})
- * @return alias for a given id
+ * element database identifier ({@link Element#id})
+ * @return {@link Element} for a given id
*/
- Element getAliasByDbId(Integer dbId);
+ Element getElementByDbId(Integer dbId);
/**
- * Returns reaction for given database identifier.
+ * Returns {@link Reaction} for given database identifier.
*
* @param dbId
* reaction database identifier ({@link Reaction#id})
- * @return reaction for a given id
+ * @return {@link Reaction} for a given id
*/
Reaction getReactionByDbId(Integer dbId);
/**
- * Returns sorted by size list of aliases.
+ * Returns sorted by size list of compartments.
*
- * @return list of aliases sorted by size
+ * @return list of compartment sorted by size
*/
- List<Compartment> getSortedCompartmentsAliases();
+ List<Compartment> getSortedCompartments();
/**
- * Returns list of aliases sorted by the size.
+ * Returns list of elements sorted by the size.
*
- * @return list of aliases sorted by the size
+ * @return list of elements sorted by the size
*/
- List<Element> getAliasesSortedBySize();
+ List<Element> getElementsSortedBySize();
/**
*
@@ -467,10 +467,10 @@ public interface Model {
/**
*
- * @param aliases
- * new {@link ModelData#aliases} collection
+ * @param elements
+ * new {@link ModelData#elements} collection
*/
- void setAliases(Set<Element> aliases);
+ void setElements(Set<Element> elements);
/**
* @return the modelData
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index 794fab0ab6..7c6703c3ff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -143,9 +143,9 @@ public class ModelComparator implements Comparator<Model> {
return integerComparator.compare(arg0.getTileSize(), arg1.getTileSize());
}
- int status = compareAliases(arg0.getAliases(), arg1.getAliases());
+ int status = compareElements(arg0.getElements(), arg1.getElements());
if (status != 0) {
- logger.debug("Set of aliases different");
+ logger.debug("Set of elements different");
return status;
}
@@ -335,46 +335,46 @@ public class ModelComparator implements Comparator<Model> {
}
/**
- * Compares two sets of aliases.
+ * Compares two sets of elements.
*
- * @param aliases
- * first set of aliases
- * @param aliases2
- * second set of aliases
+ * @param elements
+ * first set of elements
+ * @param elements2
+ * second set of elements
* @return if sets are equal then returns 0. If they are different then -1/1
* is returned.
*/
- private int compareAliases(Set<Element> aliases, Set<Element> aliases2) {
- ElementComparator aliasComparator = new ElementComparator(epsilon);
+ private int compareElements(Set<Element> elements, Set<Element> elements2) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
- Map<String, Element> map1 = new HashMap<String, Element>();
- Map<String, Element> map2 = new HashMap<String, Element>();
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
- if (aliases.size() != aliases2.size()) {
- logger.debug("Number of aliases different: " + aliases.size() + ", " + aliases2.size());
- return ((Integer) aliases.size()).compareTo(aliases2.size());
+ if (elements.size() != elements2.size()) {
+ logger.debug("Number of elements different: " + elements.size() + ", " + elements2.size());
+ return ((Integer) elements.size()).compareTo(elements2.size());
}
- for (Element alias : aliases) {
- map1.put(alias.getElementId(), alias);
+ for (Element element : elements) {
+ map1.put(element.getElementId(), element);
}
- for (Element alias : aliases2) {
- map2.put(alias.getElementId(), alias);
+ for (Element element : elements2) {
+ map2.put(element.getElementId(), element);
}
- for (Element alias : aliases) {
- int status = aliasComparator.compare(alias, map2.get(alias.getElementId()));
+ for (Element element : elements) {
+ int status = elementComparator.compare(element, map2.get(element.getElementId()));
if (status != 0) {
- logger.debug("Alias doesn't have a match: " + alias.getElementId() + ", " + map2.get(alias.getElementId()));
+ logger.debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
return status;
}
}
- for (Element alias : aliases2) {
- int status = aliasComparator.compare(alias, map1.get(alias.getElementId()));
+ for (Element element : elements2) {
+ int status = elementComparator.compare(element, map1.get(element.getElementId()));
if (status != 0) {
- logger.debug("Alias doesn't have a match: " + alias.getElementId() + ", " + map2.get(alias.getElementId()));
+ logger.debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
return status;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index 8fa6222607..c957eea007 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -41,7 +41,6 @@ import lcsb.mapviewer.model.map.species.Element;
* map:
* <ul>
* <li>species and compartments ({@link #elements} field)</li>
- * <li>aliases for species and compartments ({@link #aliases} field)</li>
* <li>list of reactions ({@link #reactions})</li>
* <li>layers with additional graphical objects ({@link #layers})</li>
* <li>different graphical visualizations of the whole map ({@link #layouts})
@@ -67,13 +66,13 @@ public class ModelData implements Serializable {
private static Logger logger = Logger.getLogger(ModelData.class);
/**
- * Set of all aliases in the map.
+ * Set of all elements in the map.
*
* @see Element
*/
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Element> aliases = new HashSet<Element>();
+ private Set<Element> elements = new HashSet<>();
/**
* Set of all layers in the map.
@@ -230,14 +229,14 @@ public class ModelData implements Serializable {
}
/**
- * Adds alias to model data.
+ * Adds {@link Element} to model data.
*
- * @param al
- * alias to add
+ * @param element
+ * element to add
*/
- public void addAlias(Element al) {
- al.setModelData(this);
- aliases.add(al);
+ public void addElement(Element element) {
+ element.setModelData(this);
+ elements.add(element);
}
/**
@@ -263,14 +262,14 @@ public class ModelData implements Serializable {
}
/**
- * Adds collection of {@link Element aliases} to model data.
+ * Adds collection of {@link Element elements} to model data.
*
- * @param aliases
- * aliases to add
+ * @param elements
+ * elements to add
*/
- public void addAliases(List<? extends Element> aliases) {
- for (Element alias : aliases) {
- addAlias(alias);
+ public void addElements(List<? extends Element> elements) {
+ for (Element element : elements) {
+ addElement(element);
}
}
@@ -293,11 +292,11 @@ public class ModelData implements Serializable {
/**
*
- * @param aliases
- * new {@link #aliases} collection
+ * @param elements
+ * new {@link #elements} collection
*/
- public void setAliases(Set<Element> aliases) {
- this.aliases = aliases;
+ public void setElements(Set<Element> elements) {
+ this.elements = elements;
}
/**
@@ -428,10 +427,10 @@ public class ModelData implements Serializable {
/**
* Adds {@link ElementGroup} to the model data.
*
- * @param aliasGroup
+ * @param elementGroup
* object to add
*/
- public void addAliasGroup(ElementGroup aliasGroup) {
+ public void addElementGroup(ElementGroup elementGroup) {
// for now we ignore this information
}
@@ -446,22 +445,22 @@ public class ModelData implements Serializable {
}
/**
- * Removes alias from the model.
+ * Removes {@link Element} from the model.
*
- * @param alias
- * alias to remove
+ * @param element
+ * element to remove
*/
- public void removeAlias(Element alias) {
- if (alias == null) {
+ public void removeElement(Element element) {
+ if (element == null) {
throw new InvalidArgumentException("Cannot remove null");
}
- if (!aliases.contains(alias)) {
- logger.warn("Alias doesn't exist in the map: " + alias.getElementId());
+ if (!elements.contains(element)) {
+ logger.warn("Element doesn't exist in the map: " + element.getElementId());
return;
}
- alias.setModelData(null);
- aliases.remove(alias);
+ element.setModelData(null);
+ elements.remove(element);
}
/**
@@ -634,11 +633,11 @@ public class ModelData implements Serializable {
}
/**
- * @return the aliases
- * @see #aliases
+ * @return the elements
+ * @see #elements
*/
- public Set<Element> getAliases() {
- return aliases;
+ public Set<Element> getElements() {
+ return elements;
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 72eeeed647..266d4f01cd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -28,8 +28,8 @@ import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -48,27 +48,28 @@ public class ModelFullIndexed implements Model {
private static Logger logger = Logger.getLogger(ModelFullIndexed.class);
/**
- * Object that map {@link Element#aliasId alias identifier} into {@link Element}.
+ * Object that map {@link Element#elementId element identifier} into
+ * {@link Element}.
*/
- private Map<String, Element> aliasByAliasId = new HashMap<String, Element>();
+ private Map<String, Element> elementByElementId = new HashMap<>();
/**
- * Object that map {@link Element#id alias database identifier} into
+ * Object that map {@link Element#id element database identifier} into
* {@link Element}.
*/
- private Map<Integer, Element> aliasByDbId = new HashMap<Integer, Element>();
+ private Map<Integer, Element> elementByDbId = new HashMap<>();
/**
* Object that map {@link Reaction#idReaction reaction identifier} into
* {@link Reaction}.
*/
- private Map<String, Reaction> reactionByReactionId = new HashMap<String, Reaction>();
+ private Map<String, Reaction> reactionByReactionId = new HashMap<>();
/**
* Object that map {@link Reaction#id reaction database identifier} into
* {@link Reaction}.
*/
- private Map<Integer, Reaction> reactionByDbId = new HashMap<Integer, Reaction>();
+ private Map<Integer, Reaction> reactionByDbId = new HashMap<>();
/**
* {@link ModelData} object containing "raw" data about the model.
@@ -86,9 +87,9 @@ public class ModelFullIndexed implements Model {
this.modelData = new ModelData();
} else {
this.modelData = model;
- for (Element alias : model.getAliases()) {
- aliasByAliasId.put(alias.getElementId(), alias);
- aliasByDbId.put(alias.getId(), alias);
+ for (Element element : model.getElements()) {
+ elementByElementId.put(element.getElementId(), element);
+ elementByDbId.put(element.getId(), element);
}
for (Reaction reaction : model.getReactions()) {
reactionByReactionId.put(reaction.getIdReaction(), reaction);
@@ -118,30 +119,13 @@ public class ModelFullIndexed implements Model {
if (element.getElementId() == null || element.getElementId().isEmpty()) {
throw new InvalidArgumentException("Element identifier cannot be empty");
}
- if (element instanceof Species) {
- addSpecies((Species) element);
- } else if (element instanceof Compartment) {
- addCompartmentAlias((Compartment) element);
- } else {
- throw new InvalidArgumentException("Unknown type of element: " + element);
- }
- }
-
- /**
- * Adds {@link Species} to the model.
- *
- * @param species
- * alias to add
- */
- private void addSpecies(Species species) {
- modelData.addAlias(species);
-
- Element alias2 = aliasByAliasId.get(species.getElementId());
- if (alias2 == null) {
- aliasByAliasId.put(species.getElementId(), species);
- aliasByDbId.put(species.getId(), species);
+ Element element2 = elementByElementId.get(element.getElementId());
+ if (element2 == null) {
+ modelData.addElement(element);
+ elementByElementId.put(element.getElementId(), element);
+ elementByDbId.put(element.getId(), element);
} else {
- throw new InvalidArgumentException("Species with duplicated id: " + species.getElementId());
+ throw new InvalidArgumentException("Element with duplicated id: " + element.getElementId());
}
}
@@ -186,14 +170,14 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Set<Element> getAliases() {
- return modelData.getAliases();
+ public Set<Element> getElements() {
+ return modelData.getElements();
}
@SuppressWarnings("unchecked")
@Override
- public <T extends Element> T getElementByElementId(String idAlias) {
- return (T) aliasByAliasId.get(idAlias);
+ public <T extends Element> T getElementByElementId(String elementId) {
+ return (T) elementByElementId.get(elementId);
}
@Override
@@ -208,29 +192,12 @@ public class ModelFullIndexed implements Model {
return modelData.getReactions();
}
- /**
- * Adds compartment alias.
- *
- * @param al
- * alias to add
- */
- private void addCompartmentAlias(Compartment al) {
- modelData.addAlias(al);
- Element alias2 = aliasByAliasId.get(al.getElementId());
- if (alias2 == null) {
- aliasByAliasId.put(al.getElementId(), al);
- aliasByDbId.put(al.getId(), al);
- } else {
- throw new InvalidArgumentException("Try to add CompartmentAlias with duplicated alias id: " + al.getElementId());
- }
- }
-
@Override
- public List<Compartment> getCompartmentsAliases() {
+ public List<Compartment> getCompartments() {
List<Compartment> result = new ArrayList<Compartment>();
- for (Element alias : modelData.getAliases()) {
- if (alias instanceof Compartment) {
- result.add((Compartment) alias);
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Compartment) {
+ result.add((Compartment) element);
}
}
return result;
@@ -247,9 +214,9 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addAliases(List<? extends Element> aliases) {
- for (Element alias : aliases) {
- addElement(alias);
+ public void addElements(List<? extends Element> elements) {
+ for (Element element : elements) {
+ addElement(element);
}
}
@@ -267,8 +234,8 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void setAliases(Set<Element> aliases) {
- this.modelData.setAliases(aliases);
+ public void setElements(Set<Element> elements) {
+ this.modelData.setElements(elements);
}
@Override
@@ -287,16 +254,16 @@ public class ModelFullIndexed implements Model {
}
@Override
- public List<Element> getAliasesSortedBySize() {
- List<Element> sortedAliases = new ArrayList<Element>();
- sortedAliases.addAll(getAliases());
- Collections.sort(sortedAliases, Element.SIZE_COMPARATOR);
- return sortedAliases;
+ public List<Element> getElementsSortedBySize() {
+ List<Element> sortedElements = new ArrayList<>();
+ sortedElements.addAll(getElements());
+ Collections.sort(sortedElements, Element.SIZE_COMPARATOR);
+ return sortedElements;
}
@Override
- public List<Compartment> getSortedCompartmentsAliases() {
- List<Compartment> result = getCompartmentsAliases();
+ public List<Compartment> getSortedCompartments() {
+ List<Compartment> result = getCompartments();
Collections.sort(result, Element.SIZE_COMPARATOR);
return result;
}
@@ -307,8 +274,8 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Element getAliasByDbId(Integer dbId) {
- return aliasByDbId.get(dbId);
+ public Element getElementByDbId(Integer dbId) {
+ return elementByDbId.get(dbId);
}
@Override
@@ -348,11 +315,11 @@ public class ModelFullIndexed implements Model {
@Override
public Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData) {
- Set<AnnotatedObject> result = new HashSet<AnnotatedObject>();
- for (Element alias : getAliases()) {
- for (MiriamData md : alias.getMiriamData()) {
+ Set<AnnotatedObject> result = new HashSet<>();
+ for (Element element : getElements()) {
+ for (MiriamData md : element.getMiriamData()) {
if (md.equals(miriamData)) {
- result.add(alias);
+ result.add(element);
}
}
}
@@ -377,10 +344,10 @@ public class ModelFullIndexed implements Model {
@Override
public Collection<Complex> getComplexList() {
- List<Complex> result = new ArrayList<Complex>();
- for (Element alias : modelData.getAliases()) {
- if (alias instanceof Complex) {
- result.add((Complex) alias);
+ List<Complex> result = new ArrayList<>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Complex) {
+ result.add((Complex) element);
}
}
return result;
@@ -388,10 +355,10 @@ public class ModelFullIndexed implements Model {
@Override
public Collection<Species> getNotComplexSpeciesList() {
- List<Species> result = new ArrayList<Species>();
- for (Element alias : modelData.getAliases()) {
- if (alias instanceof Species && !(alias instanceof Complex)) {
- result.add((Species) alias);
+ List<Species> result = new ArrayList<>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Species && !(element instanceof Complex)) {
+ result.add((Species) element);
}
}
return result;
@@ -407,7 +374,7 @@ public class ModelFullIndexed implements Model {
@Override
public List<Element> getSortedSpeciesList() {
List<Element> result = new ArrayList<Element>();
- result.addAll(getAliases());
+ result.addAll(getElements());
Collections.sort(result, Element.SIZE_COMPARATOR);
return result;
}
@@ -431,8 +398,8 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addAliasGroup(ElementGroup aliasGroup) {
- modelData.addAliasGroup(aliasGroup);
+ public void addElementGroup(ElementGroup elementGroup) {
+ modelData.addElementGroup(elementGroup);
}
@Override
@@ -441,33 +408,33 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void removeAlias(Element alias) {
- modelData.removeAlias(alias);
- aliasByAliasId.remove(alias.getElementId());
- aliasByDbId.remove(alias.getId());
+ public void removeElement(Element element) {
+ modelData.removeElement(element);
+ elementByElementId.remove(element.getElementId());
+ elementByDbId.remove(element.getId());
- if (alias.getParent() != null) {
- if (alias.getParent() instanceof Compartment) {
- Compartment ca = (Compartment) alias.getParent();
- ca.removeElement(alias);
- } else if (alias.getParent() instanceof Complex) {
- Complex ca = (Complex) alias.getParent();
- ca.removeAlias((Species) alias);
+ if (element.getParent() != null) {
+ if (element.getParent() instanceof Compartment) {
+ Compartment ca = (Compartment) element.getParent();
+ ca.removeElement(element);
+ } else if (element.getParent() instanceof Complex) {
+ Complex ca = (Complex) element.getParent();
+ ca.removeElement((Species) element);
} else {
- throw new InvalidArgumentException("Unknown type of alias parent: " + alias.getParent().getClass().getName());
+ throw new InvalidArgumentException("Unknown type of parent: " + element.getParent().getClass().getName());
}
}
- if (alias.getCompartmentAlias() != null) {
- Compartment ca = alias.getCompartmentAlias();
- ca.removeElement(alias);
+ if (element.getCompartment() != null) {
+ Compartment ca = element.getCompartment();
+ ca.removeElement(element);
}
- if (alias instanceof Species) {
- Species al = (Species) alias;
- if (al.getComplexAlias() != null) {
- Complex ca = ((Species) alias).getComplexAlias();
- ca.removeAlias(al);
+ if (element instanceof Species) {
+ Species al = (Species) element;
+ if (al.getComplex() != null) {
+ Complex ca = ((Species) element).getComplex();
+ ca.removeElement(al);
}
}
}
@@ -734,7 +701,7 @@ public class ModelFullIndexed implements Model {
@Override
public List<AnnotatedObject> getAnnotatedObjects() {
List<AnnotatedObject> result = new ArrayList<>();
- result.addAll(getAliases());
+ result.addAll(getElements());
result.addAll(getReactions());
return result;
}
@@ -755,7 +722,7 @@ public class ModelFullIndexed implements Model {
@Override
public List<Element> getElementsByName(String name) {
List<Element> result = new ArrayList<>();
- for (Element element : getAliases()) {
+ for (Element element : getElements()) {
if (element.getName().equalsIgnoreCase(name)) {
result.add(element);
}
@@ -766,7 +733,7 @@ public class ModelFullIndexed implements Model {
@Override
public List<Species> getSpeciesList() {
List<Species> result = new ArrayList<>();
- for (Element element : modelData.getAliases()) {
+ for (Element element : modelData.getElements()) {
if (element instanceof Species) {
result.add((Species) element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
index 3e0ef5e503..b4227814d4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
@@ -35,7 +35,7 @@ public class SubmodelConnectionComparator implements Comparator<SubmodelConnecti
public SubmodelConnectionComparator(double epsilon) {
this.epsilon = epsilon;
modelSubmodelConnectionComparator = new ModelSubmodelConnectionComparator(epsilon);
- aliasSubmodelConnectionComparator = new AliasSubmodelConnectionComparator(epsilon);
+ elementSubmodelConnectionComparator = new ElementSubmodelConnectionComparator(epsilon);
}
/**
@@ -44,9 +44,9 @@ public class SubmodelConnectionComparator implements Comparator<SubmodelConnecti
private ModelSubmodelConnectionComparator modelSubmodelConnectionComparator = null;
/**
- * Comparator used to compare {@link AliasSubmodelConnection} subclasses.
+ * Comparator used to compare {@link ElementSubmodelConnection} subclasses.
*/
- private AliasSubmodelConnectionComparator aliasSubmodelConnectionComparator = null;
+ private ElementSubmodelConnectionComparator elementSubmodelConnectionComparator = null;
/**
* Default constructor.
@@ -60,7 +60,7 @@ public class SubmodelConnectionComparator implements Comparator<SubmodelConnecti
* {@link SubmodelConnection} class in inheritence tree. It should be called
* by the super class comparators, like
* {@link ModelSubmodelConnectionComparator} and
- * {@link AliasSubmodelConnectionComparator}.
+ * {@link ElementSubmodelConnectionComparator}.
*
* @param arg0
* first object to compare
@@ -137,8 +137,8 @@ public class SubmodelConnectionComparator implements Comparator<SubmodelConnecti
if (arg0.getClass().equals(arg1.getClass())) {
if (arg0 instanceof ModelSubmodelConnection) {
return modelSubmodelConnectionComparator.compare((ModelSubmodelConnection) arg0, (ModelSubmodelConnection) arg1);
- } else if (arg0 instanceof AliasSubmodelConnection) {
- return aliasSubmodelConnectionComparator.compare((AliasSubmodelConnection) arg0, (AliasSubmodelConnection) arg1);
+ } else if (arg0 instanceof ElementSubmodelConnection) {
+ return elementSubmodelConnectionComparator.compare((ElementSubmodelConnection) arg0, (ElementSubmodelConnection) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
index 5d7b8bd08c..d5fa8d1a50 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
@@ -30,13 +30,13 @@ public class Catalysis extends Modifier {
}
/**
- * Constructor that creates Catalysis modifier for given alias and element.
+ * Constructor that creates {@link Catalysis} modifier for given element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public Catalysis(Species alias) {
- super(alias);
+ public Catalysis(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
index e38d9682b1..5eb71a10f1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
@@ -30,13 +30,13 @@ public class Inhibition extends Modifier {
}
/**
- * Constructor that creates inhibition modifier for given alias and element.
+ * Constructor that creates inhibition modifier for given element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public Inhibition(Species alias) {
- super(alias);
+ public Inhibition(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
index 5c9c4001eb..3cc706b094 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
@@ -30,13 +30,13 @@ public class Modulation extends Modifier {
}
/**
- * Constructor that creates modulation modifier for given alias and element.
+ * Constructor that creates modulation modifier for given element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public Modulation(Species alias) {
- super(alias);
+ public Modulation(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
index 24458c841f..ca7fcb28cc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
@@ -30,14 +30,13 @@ public class PhysicalStimulation extends Modifier {
}
/**
- * Constructor that creates physical stimulation modifier for given alias and
- * element.
+ * Constructor that creates physical stimulation modifier for given element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public PhysicalStimulation(Species alias) {
- super(alias);
+ public PhysicalStimulation(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
index f90175e634..642f15c1b4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
@@ -30,13 +30,13 @@ public class Trigger extends Modifier {
}
/**
- * Constructor that creates trigger modifier for given alias and element.
+ * Constructor that creates trigger modifier for given element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public Trigger(Species alias) {
- super(alias);
+ public Trigger(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
index cf6f506ea3..eba97a06f2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
@@ -30,14 +30,13 @@ public class UnknownCatalysis extends Modifier {
}
/**
- * Constructor that creates unknown catalysis modifier for given alias and
- * element.
+ * Constructor that creates unknown catalysis modifier for given element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public UnknownCatalysis(Species alias) {
- super(alias);
+ public UnknownCatalysis(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
index 7bfde19c0c..938249078a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
@@ -30,14 +30,14 @@ public class UnknownInhibition extends Modifier {
}
/**
- * Constructor that creates unknown inhibition modifier for given alias and
+ * Constructor that creates unknown inhibition modifier for given and
* element.
*
- * @param alias
- * alias object to which this modifiar is assigned
+ * @param element
+ * element object to which this modifiar is assigned
*/
- public UnknownInhibition(Species alias) {
- super(alias);
+ public UnknownInhibition(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
index cda54b65e2..d97dba4887 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
@@ -35,11 +35,11 @@ public class Modifier extends ReactionNode {
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this modifier.
*
- * @param alias
- * alias that represent this modifier
+ * @param element
+ * element that represent this modifier
*/
- public Modifier(Species alias) {
- super(alias);
+ public Modifier(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
index 9fa4bd9850..7513f79195 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
@@ -34,11 +34,11 @@ public class Product extends ReactionNode {
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this product.
*
- * @param alias
- * alias that represent this product
+ * @param element
+ * element that represent this product
*/
- public Product(Species alias) {
- super(alias);
+ public Product(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
index 1fbd827ef7..4484a4bc15 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
@@ -34,11 +34,11 @@ public class Reactant extends ReactionNode {
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this reactant.
*
- * @param alias
- * alias that represent this reactant
+ * @param element
+ * element that represent this reactant
*/
- public Reactant(Species alias) {
- super(alias);
+ public Reactant(Species element) {
+ super(element);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 8b89218bf3..c13687aaf4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -416,7 +416,7 @@ public class Reaction implements AnnotatedObject {
public int getVisibilityLevel() {
int level = 0;
for (ReactionNode node : getReactionNodes()) {
- level = Math.max(level, node.getAlias().getVisibilityLevel());
+ level = Math.max(level, node.getElement().getVisibilityLevel());
}
return level;
}
@@ -516,14 +516,14 @@ public class Reaction implements AnnotatedObject {
/**
* Check if one of the nodes reference to the element.
*
- * @param alias
+ * @param element
* element to be checked
* @return <code>true</code> if element is part of the reaction,
* <code>false</code> otherwise
*/
- public boolean containsElement(Element alias) {
+ public boolean containsElement(Element element) {
for (ReactionNode node : getReactionNodes()) {
- if (node.getAlias().equals(alias)) {
+ if (node.getElement().equals(element)) {
return true;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
index 6ed59c1df0..59d895dc48 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
@@ -8,9 +8,9 @@ import lcsb.mapviewer.model.map.species.Element;
/**
* One of two known types of nodes in the {@link Reaction}. It defines input or
- * output element of the reaction in the map model. {@link #element} and
- * {@link #alias} define which element on the map correspond to this node. There
- * are three known subclasses:
+ * output element of the reaction in the map model. {@link #element} define
+ * which element on the map correspond to this node. There are three known
+ * subclasses:
* <ul>
* <li>{@link Reactant} - input of the reaction,</li>
* <li>{@link Product} - output of the reaction,</li>
@@ -31,10 +31,10 @@ public abstract class ReactionNode extends AbstractNode {
private static final long serialVersionUID = 1L;
/**
- * {@link SpecisAlias} that represents this node in the model.
+ * {@link Element} that represents this node in the model.
*/
@ManyToOne
- private Element alias;
+ private Element element;
/**
* Default constructor.
@@ -51,35 +51,34 @@ public abstract class ReactionNode extends AbstractNode {
*/
protected ReactionNode(ReactionNode node) {
super(node);
- this.alias = node.getAlias();
+ this.element = node.getElement();
}
/**
- * Constructor that creates node for given {@link #alias} and {@link #element}
- * .
+ * Constructor that creates node for given {@link #element}.
*
- * @param alias
+ * @param element
* {@link Element} to which this node refer to
*/
- public ReactionNode(Element alias) {
- this.alias = alias;
+ public ReactionNode(Element element) {
+ this.element = element;
}
/**
- * @return the alias
- * @see #alias
+ * @return the element
+ * @see #element
*/
- public Element getAlias() {
- return alias;
+ public Element getElement() {
+ return element;
}
/**
- * @param alias
- * the alias to set
- * @see #alias
+ * @param element
+ * the element to set
+ * @see #element
*/
- public void setAlias(Element alias) {
- this.alias = alias;
+ public void setElement(Element element) {
+ this.element = element;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
index 0e2d008e73..5c22f84476 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
@@ -77,16 +77,16 @@ public class ReactionNodeComparator implements Comparator<ReactionNode> {
*/
private int internalCompare(ReactionNode arg0, ReactionNode arg1) {
AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
- ElementComparator aliasComparator = new ElementComparator(epsilon);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
int result = anComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
- if (aliasComparator.compare(arg0.getAlias(), arg1.getAlias()) != 0) {
- logger.debug("Alias different");
- return aliasComparator.compare(arg0.getAlias(), arg1.getAlias());
+ if (elementComparator.compare(arg0.getElement(), arg1.getElement()) != 0) {
+ logger.debug("Element different");
+ return elementComparator.compare(arg0.getElement(), arg1.getElement());
}
return 0;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 779352ff3a..2208709e2d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -71,12 +71,12 @@ public class AntisenseRna extends Species {
/**
* Adds {@link AntisenseRnaRegion} to the object.
*
- * @param antisenseRnaRegionAlias
+ * @param antisenseRnaRegion
* alement to be added
*/
- public void addRegion(AntisenseRnaRegion antisenseRnaRegionAlias) {
- regions.add(antisenseRnaRegionAlias);
- antisenseRnaRegionAlias.setSpecies(this);
+ public void addRegion(AntisenseRnaRegion antisenseRnaRegion) {
+ regions.add(antisenseRnaRegion);
+ antisenseRnaRegion.setSpecies(this);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
index e7dfa3ef10..e5c2a69cfb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
@@ -71,9 +71,9 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
}
/**
- * This method compares only the fields that are defined in AntisenseRnaAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in
+ * {@link AntisenseRna} class in inheritence tree. By the design it calls also
+ * comparator of the upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -83,8 +83,8 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
* -1/1 is returned.
*/
private int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
index c9d1bb5ff3..ec844f1f27 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
@@ -29,12 +29,12 @@ public class ChemicalComparator implements Comparator<Chemical> {
/**
* Comparator for {@link Ion} implementation of {@link Chemical}.
*/
- private IonComparator ionAliasComparator;
+ private IonComparator ionComparator;
/**
* Comparator for {@link SimpleMolecule} implementation of {@link Chemical}.
*/
- private SimpleMoleculeComparator simpleMoleculeAliasComparator;
+ private SimpleMoleculeComparator simpleMoleculeComparator;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -44,8 +44,8 @@ public class ChemicalComparator implements Comparator<Chemical> {
*/
public ChemicalComparator(double epsilon) {
this.epsilon = epsilon;
- ionAliasComparator = new IonComparator(epsilon);
- simpleMoleculeAliasComparator = new SimpleMoleculeComparator(epsilon);
+ ionComparator = new IonComparator(epsilon);
+ simpleMoleculeComparator = new SimpleMoleculeComparator(epsilon);
}
/**
@@ -69,9 +69,9 @@ public class ChemicalComparator implements Comparator<Chemical> {
if (arg0.getClass().equals(arg1.getClass())) {
if (arg0.getClass().equals(Ion.class)) {
- return ionAliasComparator.compare((Ion) arg0, (Ion) arg1);
+ return ionComparator.compare((Ion) arg0, (Ion) arg1);
} else if (arg0.getClass().equals(SimpleMolecule.class)) {
- return simpleMoleculeAliasComparator.compare((SimpleMolecule) arg0, (SimpleMolecule) arg1);
+ return simpleMoleculeComparator.compare((SimpleMolecule) arg0, (SimpleMolecule) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
@@ -81,9 +81,9 @@ public class ChemicalComparator implements Comparator<Chemical> {
}
/**
- * This method compares only the fields that are defined in ChemicalAlias
+ * This method compares only the fields that are defined in {@link Chemical}
* class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -93,8 +93,8 @@ public class ChemicalComparator implements Comparator<Chemical> {
* -1/1 is returned.
*/
int internalCompare(Chemical arg0, Chemical arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
index 6d63bf94fd..c1320b9e93 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
@@ -24,7 +24,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
@Entity
-@DiscriminatorValue("Complex Species Alias")
+@DiscriminatorValue("Complex")
public class Complex extends Species {
/**
@@ -38,12 +38,12 @@ public class Complex extends Species {
private static Logger logger = Logger.getLogger(Complex.class);
/**
- * List of aliases that are in this complex alias (only aliases that lies
- * there directly).
+ * List of elements that are in this complex (only elements that lies there
+ * directly).
*/
@Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "complexAlias")
- private List<Species> aliases = new ArrayList<>();
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "complex")
+ private List<Species> elements = new ArrayList<>();
/**
* State of the complex species.
@@ -62,13 +62,13 @@ public class Complex extends Species {
* parameter.
*
* @param original
- * original alias used for initialization
+ * original complex used for initialization
*/
public Complex(Complex original) {
super(original);
- for (Species alias : original.getAliases()) {
- addAlias(alias.copy());
+ for (Species element : original.getElements()) {
+ addSpecies(element.copy());
}
this.structuralState = original.getStructuralState();
}
@@ -84,46 +84,46 @@ public class Complex extends Species {
}
/**
- * Adds alias to the complex.
+ * Adds {@link Species} to the complex.
*
- * @param alias
+ * @param species
* object to add
*/
- public void addAlias(Species alias) {
+ public void addSpecies(Species species) {
boolean contains = false;
- for (Species alias2 : aliases) {
- if (alias.getElementId().equals(alias2.getElementId())) {
+ for (Species element2 : elements) {
+ if (species.getElementId().equals(element2.getElementId())) {
contains = true;
}
}
if (!contains) {
- aliases.add(alias);
- alias.setComplexAlias(this);
+ elements.add(species);
+ species.setComplex(this);
}
}
/**
- * Returns list of aliases.
+ * Returns list of elements.
*
- * @return list of aliases insied complexAlias.
+ * @return list of element inside complex
*/
- public List<Species> getAliases() {
- return aliases;
+ public List<Species> getElements() {
+ return elements;
}
/**
- * Returns list of all aliases that lies inside complex alias (direct and
+ * Returns list of all {@link Species} that lies inside complex (direct and
* undirect).
*
- * @return list of all aliases insied complex alias.
+ * @return list of all {@link Species} inside {@link Complex}
*/
- public List<Species> getAllChildrenAliases() {
- List<Species> result = new ArrayList<Species>();
- result.addAll(aliases);
- for (Species speciesAlias : aliases) {
- if (speciesAlias instanceof Complex) {
- result.addAll(((Complex) speciesAlias).getAllChildrenAliases());
+ public List<Species> getAllChildren() {
+ List<Species> result = new ArrayList<>();
+ result.addAll(elements);
+ for (Species species : elements) {
+ if (species instanceof Complex) {
+ result.addAll(((Complex) species).getAllChildren());
}
}
return result;
@@ -140,16 +140,16 @@ public class Complex extends Species {
}
/**
- * Removes alias from the complex alias.
+ * Removes {@link Species} from the complex.
*
- * @param alias
+ * @param element
* object to remove
*/
- public void removeAlias(Species alias) {
- aliases.remove(alias);
- if (alias.getComplexAlias() != null) {
- if (alias.getComplexAlias() == this) {
- alias.setComplexAlias(null);
+ public void removeElement(Species element) {
+ elements.remove(element);
+ if (element.getComplex() != null) {
+ if (element.getComplex() == this) {
+ element.setComplex(null);
} else {
logger.warn("Removing element from complex that probably doesn't belong there");
}
@@ -181,7 +181,7 @@ public class Complex extends Species {
*/
public Set<Species> getAllSimpleChildren() {
Set<Species> result = new HashSet<>();
- for (Species element : getAliases()) {
+ for (Species element : getElements()) {
if (element instanceof Complex) {
result.addAll(((Complex) element).getAllSimpleChildren());
} else {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
index 6b005eed4a..e7a29c9ddb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
@@ -70,9 +70,9 @@ public class ComplexComparator implements Comparator<Complex> {
}
/**
- * This method compares only the fields that are defined in ComplexAlias class
- * in inheritence tree. By the design it calls also comparator of the upper
- * (SpeciesAlias) class.
+ * This method compares only the fields that are defined in {@link Complex}
+ * class in inheritence tree. By the design it calls also comparator of the
+ * upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -82,42 +82,42 @@ public class ComplexComparator implements Comparator<Complex> {
* -1/1 is returned.
*/
private int internalCompare(Complex arg0, Complex arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- ElementComparator aliasComparator = new ElementComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
IntegerComparator integerComparator = new IntegerComparator();
- if (integerComparator.compare(arg0.getAliases().size(), arg1.getAliases().size()) != 0) {
- logger.debug("children aliases size different: " + arg0.getAliases().size() + ", " + arg1.getAliases().size());
- return integerComparator.compare(arg0.getAliases().size(), arg1.getAliases().size());
+ if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
+ logger.debug("children elements size different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
+ return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
}
Map<String, Element> map1 = new HashMap<>();
Map<String, Element> map2 = new HashMap<>();
- for (Element alias : arg0.getAliases()) {
- if (map1.get(alias.getElementId()) != null) {
- throw new InvalidArgumentException("Few aliases with the same id: " + alias.getElementId());
+ for (Element element : arg0.getElements()) {
+ if (map1.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
}
- map1.put(alias.getElementId(), alias);
+ map1.put(element.getElementId(), element);
}
- for (Element alias : arg1.getAliases()) {
- if (map2.get(alias.getElementId()) != null) {
- throw new InvalidArgumentException("Few aliases with the same id: " + alias.getElementId());
+ for (Element element : arg1.getElements()) {
+ if (map2.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
}
- map2.put(alias.getElementId(), alias);
+ map2.put(element.getElementId(), element);
}
- for (Element alias : arg0.getAliases()) {
- Element alias2 = map2.get(alias.getElementId());
- int status = aliasComparator.compare(alias, alias2);
+ for (Element element : arg0.getElements()) {
+ Element element2 = map2.get(element.getElementId());
+ int status = elementComparator.compare(element, element2);
if (status != 0) {
- logger.debug("child doesn't have a match: " + alias.getElementId());
+ logger.debug("child doesn't have a match: " + element.getElementId());
return status;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
index ef33ffeb78..e716106426 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
@@ -67,9 +67,9 @@ public class DegradedComparator implements Comparator<Degraded> {
}
/**
- * This method compares only the fields that are defined in DegradedAlias
+ * This method compares only the fields that are defined in {@link Degraded}
* class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class DegradedComparator implements Comparator<Degraded> {
* -1/1 is returned.
*/
private int internalCompare(Degraded arg0, Degraded arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
index 0f64edd06d..3732d4c347 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
@@ -67,9 +67,9 @@ public class DrugComparator implements Comparator<Drug> {
}
/**
- * This method compares only the fields that are defined in DrugAlias class in
- * inheritence tree. By the design it calls also comparator of the upper
- * (SpeciesAlias) class.
+ * This method compares only the fields that are defined in {@link Drug} class
+ * in inheritence tree. By the design it calls also comparator of the upper (
+ * {@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class DrugComparator implements Comparator<Drug> {
* -1/1 is returned.
*/
private int internalCompare(Drug arg0, Drug arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index a00cdb5d9a..04308da58e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -43,7 +43,7 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -56,9 +56,9 @@ import lcsb.mapviewer.model.map.model.ModelData;
*
*/
@Entity
-@Table(name = "alias_table")
+@Table(name = "element_table")
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "alias_type_db", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorColumn(name = "element_type_db", discriminatorType = DiscriminatorType.STRING)
@DiscriminatorValue("GENERIC_ALIAS")
public abstract class Element implements AnnotatedObject, Serializable {
@@ -68,7 +68,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
private static final long serialVersionUID = 1L;
/**
- * Default font size for alias element.
+ * Default font size for element description.
*/
private static final double DEFAULT_FONT_SIZE = 12.0;
@@ -78,15 +78,15 @@ public abstract class Element implements AnnotatedObject, Serializable {
private static final int MAX_SYNONYM_LENGTH = 255;
/**
- * Comparator of aliases that takes into consideration size (width*height) of
- * aliases.
+ * Comparator of elements that takes into consideration size (width*height) of
+ * elements.
*/
public static final Comparator<Element> SIZE_COMPARATOR = new Comparator<Element>() {
@Override
- public int compare(Element alias1, Element alias2) {
+ public int compare(Element element1, Element element2) {
- double size = alias1.getWidth() * alias1.getHeight();
- double size2 = alias2.getWidth() * alias2.getHeight();
+ double size = element1.getWidth() * element1.getHeight();
+ double size2 = element2.getWidth() * element2.getHeight();
if (size < size2) {
return 1;
} else if (size > size2) {
@@ -111,34 +111,34 @@ public abstract class Element implements AnnotatedObject, Serializable {
private int id;
/**
- * This object reference to the parent alias. Parent is a ComplexAlias which
- * contains (directly) this element. When alias is not placed in a complex
- * then parent contains a reference to CompartmentAlias where the alias is
- * placed. When alias lies outside of every compartment and complexe then null
- * value is assigned.
+ * This object reference to the parent {@link Element}. Parent is a
+ * {@link Complex} which contains (directly) this element. When element is not
+ * placed in a complex then parent contains a reference to {@link Compartment}
+ * where the element is placed. When element lies outside of every compartment
+ * and complex then null value is assigned.
*/
@Cascade({ CascadeType.ALL })
@ManyToOne
private Element parent;
/**
- * Map model object to which alias belongs to.
+ * Map model object to which element belongs to.
*/
@ManyToOne(fetch = FetchType.LAZY)
private ModelData model;
/**
- * Submodel that is extension of these element alias.
+ * Submodel that is extension of these element.
*/
@ManyToOne(fetch = FetchType.LAZY, cascade = javax.persistence.CascadeType.ALL)
- private AliasSubmodelConnection submodel;
+ private ElementSubmodelConnection submodel;
/**
- * CompartmentAlias where alias is located. When alias lies outside of every
- * compartment then null value is assigned.
+ * {@link Compartment} where element is located. When element lies outside of
+ * every compartment then null value is assigned.
*/
@ManyToOne
- private Compartment compartmentAlias;
+ private Compartment compartment;
/**
* Unique string identifier within one model object (usually imported from
@@ -147,22 +147,22 @@ public abstract class Element implements AnnotatedObject, Serializable {
private String elementId;
/**
- * X coordinate on the map where alias is located (top left corner).
+ * X coordinate on the map where element is located (top left corner).
*/
private Double x;
/**
- * Y coordinate on the map where alias is located (top left corner).
+ * Y coordinate on the map where element is located (top left corner).
*/
private Double y;
/**
- * Width of the alias.
+ * Width of the element.
*/
private Double width;
/**
- * Height of the alias.
+ * Height of the element.
*/
private Double height;
@@ -177,7 +177,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
private Color color;
/**
- * From which level alias should be visible.
+ * From which level element should be visible.
*
* @see #transparencyLevel
* @see lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params#level
@@ -186,7 +186,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
private int visibilityLevel;
/**
- * From which level alias should be transparent.
+ * From which level element should be transparent.
*
* @see #visibilityLevel
* @see AbstractImageGenerator.Params#level
@@ -361,38 +361,38 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * Returns x coordinate of the alias center.
+ * Returns x coordinate of the element center.
*
- * @return x coordinate of the alias center
+ * @return x coordinate of the element center
*/
public double getCenterX() {
return getX() + getWidth() / 2;
}
/**
- * Returns y coordinate of the alias center.
+ * Returns y coordinate of the element center.
*
- * @return y coordinate of the alias center
+ * @return y coordinate of the element center
*/
public double getCenterY() {
return getY() + getHeight() / 2;
}
/**
- * Returns coordinates of the alias center point.
+ * Returns coordinates of the element center point.
*
- * @return coordinates of the alias center point
+ * @return coordinates of the element center point
*/
public Point2D getCenter() {
return new Point2D.Double(getCenterX(), getCenterY());
}
/**
- * Methods that increase size of the alias by increaseSize. It influence x, y,
- * width and height fields of the alias.
+ * Methods that increase size of the element by increaseSize. It influence x, y,
+ * width and height fields of the element.
*
* @param increaseSize
- * by how many units we want to increase size of the alias
+ * by how many units we want to increase size of the element
*/
public void increaseBorder(double increaseSize) {
x -= increaseSize;
@@ -452,12 +452,12 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * This method computes the distance between point and the alias. It assumes
- * that alias is a rectangle.
+ * This method computes the distance between point and the element. It assumes
+ * that element is a rectangle.
*
* @param point
* point from which we are looking for a distance
- * @return distance between point and this alias
+ * @return distance between point and this element
*/
public double getDistanceFromPoint(Point2D point) {
if (contains(point)) {
@@ -476,11 +476,11 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * Checks if alias contains a point. It assumes that alias is a rectangle.
+ * Checks if element contains a point. It assumes that element is a rectangle.
*
* @param point
* point to check
- * @return <i>true</i> if point belongs to the alias, <i>false</i> otherwise
+ * @return <i>true</i> if point belongs to the element, <i>false</i> otherwise
*/
public boolean contains(Point2D point) {
if (getX() <= point.getX() && getY() <= point.getY() && getX() + getWidth() >= point.getX() && getY() + getHeight() >= point.getY()) {
@@ -499,41 +499,41 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * Returns size of the alias in square units.
+ * Returns size of the element in square units.
*
- * @return size of the alias
+ * @return size of the element
*/
public double getSize() {
return getWidth() * getHeight();
}
/**
- * Checks if the alias2 (given as parameter) is placed inside this alias. This
+ * Checks if the element2 (given as parameter) is placed inside this element. This
* method should be overriden by all inheriting classes - it should properly
* handle other shapes than rectangle.
*
- * @param alias2
+ * @param element2
* object to be checked
- * @return true if alias2 lies in this object, false otherwise
- */
- public boolean contains(Element alias2) {
- if (alias2 instanceof Species) {
- Point2D p1 = new Point2D.Double(alias2.getX(), alias2.getY());
- Point2D p2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight());
- Point2D p3 = new Point2D.Double(alias2.getX() + alias2.getWidth(), alias2.getY());
- Point2D p4 = new Point2D.Double(alias2.getX() + alias2.getWidth(), alias2.getY() + alias2.getHeight());
+ * @return true if element2 lies in this object, false otherwise
+ */
+ public boolean contains(Element element2) {
+ if (element2 instanceof Species) {
+ Point2D p1 = new Point2D.Double(element2.getX(), element2.getY());
+ Point2D p2 = new Point2D.Double(element2.getX(), element2.getY() + element2.getHeight());
+ Point2D p3 = new Point2D.Double(element2.getX() + element2.getWidth(), element2.getY());
+ Point2D p4 = new Point2D.Double(element2.getX() + element2.getWidth(), element2.getY() + element2.getHeight());
return contains(p1) || contains(p2) || contains(p3) || contains(p4);
- } else if (getX() < alias2.getX() && getY() < alias2.getY() && getX() + getWidth() > alias2.getX() + alias2.getWidth()
- && getY() + getHeight() > alias2.getY() + alias2.getHeight()) {
+ } else if (getX() < element2.getX() && getY() < element2.getY() && getX() + getWidth() > element2.getX() + element2.getWidth()
+ && getY() + getHeight() > element2.getY() + element2.getHeight()) {
return true;
}
return false;
}
/**
- * Makes a copy of the alias.
+ * Makes a copy of the element.
*
- * @return copy of the alias
+ * @return copy of the element
*/
public abstract Element copy();
@@ -660,7 +660,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * @return the aliasId
+ * @return the elementId
* @see #elementId
*/
public String getElementId() {
@@ -711,20 +711,20 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * @return the compartmentAlias
- * @see #compartmentAlias
+ * @return the compartment
+ * @see #compartment
*/
- public Compartment getCompartmentAlias() {
- return compartmentAlias;
+ public Compartment getCompartment() {
+ return compartment;
}
/**
- * @param compartmentAlias
- * the compartmentAlias to set
- * @see #compartmentAlias
+ * @param compartment
+ * the compartment to set
+ * @see #compartment
*/
- public void setCompartmentAlias(Compartment compartmentAlias) {
- this.compartmentAlias = compartmentAlias;
+ public void setCompartment(Compartment compartment) {
+ this.compartment = compartment;
}
/**
@@ -821,7 +821,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
* @return the submodel
* @see #submodel
*/
- public AliasSubmodelConnection getSubmodel() {
+ public ElementSubmodelConnection getSubmodel() {
return submodel;
}
@@ -830,10 +830,10 @@ public abstract class Element implements AnnotatedObject, Serializable {
* the submodel to set
* @see #submodel
*/
- public void setSubmodel(AliasSubmodelConnection submodel) {
+ public void setSubmodel(ElementSubmodelConnection submodel) {
this.submodel = submodel;
if (submodel != null) {
- this.submodel.setFromAlias(this);
+ this.submodel.setFromElement(this);
}
}
@@ -847,11 +847,11 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * Checks if alias contains a {@link LayerText}.
+ * Checks if element contains a {@link LayerText}.
*
* @param lt
* text to check
- * @return <i>true</i> if {@link LayerText} belongs to the alias, <i>false</i>
+ * @return <i>true</i> if {@link LayerText} belongs to the element, <i>false</i>
* otherwise
*/
public boolean contains(LayerText lt) {
@@ -859,7 +859,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
}
/**
- * Adds {@link SearchIndex} to the alias.
+ * Adds {@link SearchIndex} to the element.
*
* @param searchIndex
* search index to add
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 0800590d1b..5f57312dad 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnectionComparator;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
/**
* Comparator class used for comparing {@link Element} objects.
@@ -84,7 +84,7 @@ public class ElementComparator implements Comparator<Element> {
}
/**
- * This method compares only the fields that are defined in Alias class in
+ * This method compares only the fields that are defined in {@link Element} class in
* inheritence tree. By the design it is called by subclass comparator.
*
* @param arg0
@@ -110,7 +110,7 @@ public class ElementComparator implements Comparator<Element> {
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
- logger.debug("AliasId different: " + arg0.getElementId() + ", " + arg1.getElementId());
+ logger.debug("ElementId different: " + arg0.getElementId() + ", " + arg1.getElementId());
return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
}
@@ -151,10 +151,10 @@ public class ElementComparator implements Comparator<Element> {
// this should be somehow modified, because it can create a situation where
// comparison will fall into infinite loop (in cyclic submodels)
- AliasSubmodelConnectionComparator ascc = new AliasSubmodelConnectionComparator(epsilon);
+ ElementSubmodelConnectionComparator ascc = new ElementSubmodelConnectionComparator(epsilon);
int status = ascc.compare(arg0.getSubmodel(), arg1.getSubmodel());
if (status != 0) {
- logger.debug("Alias submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ logger.debug("Element submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
return status;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
index 5ec522cc4f..044e7f059f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
@@ -71,9 +71,9 @@ public class GeneComparator implements Comparator<Gene> {
}
/**
- * This method compares only the fields that are defined in GeneAlias class in
- * inheritence tree. By the design it calls also comparator of the upper
- * (SpeciesAlias) class.
+ * This method compares only the fields that are defined in {@link Gene} class
+ * in inheritence tree. By the design it calls also comparator of the upper (
+ * {@link Species}) class.
*
* @param arg0
* first object to compare
@@ -83,8 +83,8 @@ public class GeneComparator implements Comparator<Gene> {
* -1/1 is returned.
*/
private int internalCompare(Gene arg0, Gene arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
index 4fb7a683db..ce6e0c5c2c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
@@ -80,8 +80,8 @@ public class GenericProteinComparator implements Comparator<GenericProtein> {
* -1/1 is returned.
*/
private int internalCompare(GenericProtein arg0, GenericProtein arg1) {
- ProteinComparator proteinAliasComparator = new ProteinComparator(epsilon);
- int result = proteinAliasComparator.internalCompare(arg0, arg1);
+ ProteinComparator proteinComparator = new ProteinComparator(epsilon);
+ int result = proteinComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
index 4cd44ebde6..8f6c3f4b8a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
public class IonChannelProteinComparator implements Comparator<IonChannelProtein> {
-
+
/**
* Default class logger.
*/
@@ -67,9 +67,9 @@ public class IonChannelProteinComparator implements Comparator<IonChannelProtein
}
/**
- * This method compares only the fields that are defined in IonChannelProteinAliasAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in
+ * {@link IonChannelProtein} class in inheritence tree. By the design it calls
+ * also comparator of the upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class IonChannelProteinComparator implements Comparator<IonChannelProtein
* -1/1 is returned.
*/
private int internalCompare(IonChannelProtein arg0, IonChannelProtein arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
index cddddd1b5b..365f5de9f8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
@@ -79,8 +79,8 @@ public class IonComparator implements Comparator<Ion> {
* -1/1 is returned.
*/
private int internalCompare(Ion arg0, Ion arg1) {
- ChemicalComparator speciesAliasComparator = new ChemicalComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ ChemicalComparator speciesComparator = new ChemicalComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
index b6a01629f0..8b7af90f58 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
public class PhenotypeComparator implements Comparator<Phenotype> {
-
+
/**
* Default class logger.
*/
@@ -67,9 +67,9 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
}
/**
- * This method compares only the fields that are defined in PhenotypeAlias
+ * This method compares only the fields that are defined in {@link Phenotype}
* class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
* -1/1 is returned.
*/
private int internalCompare(Phenotype arg0, Phenotype arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index 7090a9316c..53cee7bdba 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -33,22 +33,22 @@ public class ProteinComparator implements Comparator<Protein> {
/**
* Comparator for {@link GenericProtein} implementation of {@link Protein}.
*/
- private GenericProteinComparator genericProteinAliasComparator;
+ private GenericProteinComparator genericProteinComparator;
/**
* Comparator for {@link IonChannelProtein} implementation of {@link Protein}.
*/
- private IonChannelProteinComparator ionChannelProteinAliasComparator;
+ private IonChannelProteinComparator ionChannelProteinComparator;
/**
* Comparator for {@link ReceptorProtein} implementation of {@link Protein}.
*/
- private ReceptorProteinComparator receptorProteinAliasComparator;
+ private ReceptorProteinComparator receptorProteinComparator;
/**
* Comparator for {@link TruncatedProtein} implementation of {@link Protein}.
*/
- private TruncatedProteinComparator truncatedProteinAliasComparator;
+ private TruncatedProteinComparator truncatedProteinComparator;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -58,10 +58,10 @@ public class ProteinComparator implements Comparator<Protein> {
*/
public ProteinComparator(double epsilon) {
this.epsilon = epsilon;
- genericProteinAliasComparator = new GenericProteinComparator(epsilon);
- ionChannelProteinAliasComparator = new IonChannelProteinComparator(epsilon);
- receptorProteinAliasComparator = new ReceptorProteinComparator(epsilon);
- truncatedProteinAliasComparator = new TruncatedProteinComparator(epsilon);
+ genericProteinComparator = new GenericProteinComparator(epsilon);
+ ionChannelProteinComparator = new IonChannelProteinComparator(epsilon);
+ receptorProteinComparator = new ReceptorProteinComparator(epsilon);
+ truncatedProteinComparator = new TruncatedProteinComparator(epsilon);
}
/**
@@ -85,13 +85,13 @@ public class ProteinComparator implements Comparator<Protein> {
if (arg0.getClass().equals(arg1.getClass())) {
if (arg0.getClass().equals(GenericProtein.class)) {
- return genericProteinAliasComparator.compare((GenericProtein) arg0, (GenericProtein) arg1);
+ return genericProteinComparator.compare((GenericProtein) arg0, (GenericProtein) arg1);
} else if (arg0.getClass().equals(IonChannelProtein.class)) {
- return ionChannelProteinAliasComparator.compare((IonChannelProtein) arg0, (IonChannelProtein) arg1);
+ return ionChannelProteinComparator.compare((IonChannelProtein) arg0, (IonChannelProtein) arg1);
} else if (arg0.getClass().equals(ReceptorProtein.class)) {
- return receptorProteinAliasComparator.compare((ReceptorProtein) arg0, (ReceptorProtein) arg1);
+ return receptorProteinComparator.compare((ReceptorProtein) arg0, (ReceptorProtein) arg1);
} else if (arg0.getClass().equals(TruncatedProtein.class)) {
- return truncatedProteinAliasComparator.compare((TruncatedProtein) arg0, (TruncatedProtein) arg1);
+ return truncatedProteinComparator.compare((TruncatedProtein) arg0, (TruncatedProtein) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
@@ -101,9 +101,9 @@ public class ProteinComparator implements Comparator<Protein> {
}
/**
- * This method compares only the fields that are defined in ProteinAlias class
- * in inheritence tree. By the design it calls also comparator of the upper
- * (SpeciesAlias) class.
+ * This method compares only the fields that are defined in {@link Protein}
+ * class in inheritence tree. By the design it calls also comparator of the
+ * upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -113,8 +113,8 @@ public class ProteinComparator implements Comparator<Protein> {
* -1/1 is returned.
*/
int internalCompare(Protein arg0, Protein arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
index 724edc151a..186498d9fc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
public class ReceptorProteinComparator implements Comparator<ReceptorProtein> {
-
+
/**
* Default class logger.
*/
@@ -67,9 +67,9 @@ public class ReceptorProteinComparator implements Comparator<ReceptorProtein> {
}
/**
- * This method compares only the fields that are defined in ReceptorProteinAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in
+ * {@link ReceptorProtein} class in inheritence tree. By the design it calls
+ * also comparator of the upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class ReceptorProteinComparator implements Comparator<ReceptorProtein> {
* -1/1 is returned.
*/
private int internalCompare(ReceptorProtein arg0, ReceptorProtein arg1) {
- ProteinComparator proteinAliasComparator = new ProteinComparator(epsilon);
- int result = proteinAliasComparator.internalCompare(arg0, arg1);
+ ProteinComparator proteinComparator = new ProteinComparator(epsilon);
+ int result = proteinComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
index 1703a391c1..25f8e4de9b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
@@ -71,9 +71,9 @@ public class RnaComparator implements Comparator<Rna> {
}
/**
- * This method compares only the fields that are defined in RnaAlias class in
- * inheritence tree. By the design it calls also comparator of the upper
- * (SpeciesAlias) class.
+ * This method compares only the fields that are defined in {@link Rna} class
+ * in inheritence tree. By the design it calls also comparator of the upper (
+ * {@link Species}) class.
*
* @param arg0
* first object to compare
@@ -83,8 +83,8 @@ public class RnaComparator implements Comparator<Rna> {
* -1/1 is returned.
*/
private int internalCompare(Rna arg0, Rna arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
index 463b37c0b8..776941b698 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
@@ -68,8 +68,8 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
/**
* This method compares only the fields that are defined in
- * SimpleMoleculeAlias class in inheritence tree. By the design it calls also
- * comparator of the upper (SpeciesAlias) class.
+ * {@link SimpleMolecule} class in inheritence tree. By the design it calls
+ * also comparator of the upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
* -1/1 is returned.
*/
private int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
- ChemicalComparator chemicalAliasComparator = new ChemicalComparator(epsilon);
- int result = chemicalAliasComparator.internalCompare(arg0, arg1);
+ ChemicalComparator chemicalComparator = new ChemicalComparator(epsilon);
+ int result = chemicalComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index 712f212bd2..019cfd461b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -26,7 +26,7 @@ import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
*
*/
@Entity
-@DiscriminatorValue("Species Alias")
+@DiscriminatorValue("Species")
public abstract class Species extends Element {
/**
@@ -41,50 +41,50 @@ public abstract class Species extends Element {
private static Logger logger = Logger.getLogger(Species.class);
/**
- * Is the alias active.
+ * Is the element active.
*/
private Boolean activity;
/**
- * Width of the alias border.
+ * Width of the element border.
*/
private Double lineWidth;
/**
- * State of the alias visualization (should the inside be presented in details
- * or not). TODO this should be transformed into enum
+ * State of the element visualization (should the inside be presented in
+ * details or not). TODO this should be transformed into enum
*/
private String state;
/**
- * State (free text describing alias in some way) of the alias is split into
- * {@link #aliasStatePrefix prefix} and {@link #aliasStateLabel label}. This
- * value represent the first part of the state.
+ * State (free text describing element in some way) of the element is split
+ * into {@link #statePrefix prefix} and {@link #stateLabel label}. This value
+ * represent the first part of the state.
*/
- private String aliasStatePrefix;
+ private String statePrefix;
/**
- * State (free text describing alias in some way) of the alias is split into
- * {@link #aliasStatePrefix prefix} and {@link #aliasStateLabel label}. This
- * value represent the second part of the state.
+ * State (free text describing element in some way) of the element is split
+ * into {@link #statePrefix prefix} and {@link #stateLabel label}. This value
+ * represent the second part of the state.
*/
- private String aliasStateLabel;
+ private String stateLabel;
/**
- * Complex alias to which this alias belongs to. Null if such complex alias
- * doesn't exist.
+ * Complex to which this element belongs to. Null if such complex doesn't
+ * exist.
*/
@ManyToOne
@Cascade({ CascadeType.ALL })
- @JoinColumn(name = "idComplexAliasDb")
- private Complex complexAlias;
+ @JoinColumn(name = "idcomplexdb")
+ private Complex complex;
/**
- * List of reaction nodes that point to this alias.
+ * List of reaction nodes that point to this element.
*/
@Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "alias", orphanRemoval = true)
- private Set<ReactionNode> node = new HashSet<ReactionNode>();
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "element", orphanRemoval = true)
+ private Set<ReactionNode> node = new HashSet<>();
/**
* Initial amount of species.
@@ -123,14 +123,14 @@ public abstract class Species extends Element {
private Boolean hypothetical = null;
/**
- * Cunstructor that set alias identifier.
+ * Constructor that set element identifier.
*
- * @param aliasId
- * {@link Element#aliasId}
+ * @param elementId
+ * {@link Element#elementId}
*/
- public Species(String aliasId) {
+ public Species(String elementId) {
this();
- setElementId(aliasId);
+ setElementId(elementId);
}
/**
@@ -156,9 +156,9 @@ public abstract class Species extends Element {
lineWidth = original.getLineWidth();
state = original.getState();
- complexAlias = original.getComplexAlias();
- aliasStateLabel = original.getAliasStateLabel();
- aliasStatePrefix = original.getAliasStatePrefix();
+ complex = original.getComplex();
+ stateLabel = original.getStateLabel();
+ statePrefix = original.getStatePrefix();
initialAmount = original.getInitialAmount();
charge = original.getCharge();
@@ -223,20 +223,20 @@ public abstract class Species extends Element {
}
/**
- * @return the complexAlias
- * @see #complexAlias
+ * @return the complex
+ * @see #complex
*/
- public Complex getComplexAlias() {
- return complexAlias;
+ public Complex getComplex() {
+ return complex;
}
/**
- * @param complexAlias
- * the complexAlias to set
- * @see #complexAlias
+ * @param complex
+ * the complex to set
+ * @see #complex
*/
- public void setComplexAlias(Complex complexAlias) {
- this.complexAlias = complexAlias;
+ public void setComplex(Complex complex) {
+ this.complex = complex;
}
/**
@@ -257,37 +257,37 @@ public abstract class Species extends Element {
}
/**
- * @return the aliasStatePrefix
- * @see #aliasStatePrefix
+ * @return the statePrefix
+ * @see #statePrefix
*/
- public String getAliasStatePrefix() {
- return aliasStatePrefix;
+ public String getStatePrefix() {
+ return statePrefix;
}
/**
- * @param aliasStatePrefix
- * the aliasStatePrefix to set
- * @see #aliasStatePrefix
+ * @param statePrefix
+ * the statePrefix to set
+ * @see #statePrefix
*/
- public void setAliasStatePrefix(String aliasStatePrefix) {
- this.aliasStatePrefix = aliasStatePrefix;
+ public void setStatePrefix(String statePrefix) {
+ this.statePrefix = statePrefix;
}
/**
- * @return the aliasStateLabel
- * @see #aliasStateLabel
+ * @return the stateLabel
+ * @see #stateLabel
*/
- public String getAliasStateLabel() {
- return aliasStateLabel;
+ public String getStateLabel() {
+ return stateLabel;
}
/**
- * @param aliasStateLabel
- * the aliasStateLabel to set
- * @see #aliasStateLabel
+ * @param stateLabel
+ * the stateLabel to set
+ * @see #stateLabel
*/
- public void setAliasStateLabel(String aliasStateLabel) {
- this.aliasStateLabel = aliasStateLabel;
+ public void setStateLabel(String stateLabel) {
+ this.stateLabel = stateLabel;
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
index 678e18507d..c790a81e46 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
@@ -160,8 +160,8 @@ public class SpeciesComparator implements Comparator<Species> {
* -1/1 is returned.
*/
int internalCompare(Species arg0, Species arg1) {
- ElementComparator aliasComparator = new ElementComparator(epsilon);
- int result = aliasComparator.internalCompare(arg0, arg1);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ int result = elementComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
@@ -180,14 +180,14 @@ public class SpeciesComparator implements Comparator<Species> {
return doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
}
StringComparator stringComparator = new StringComparator();
- if (stringComparator.compare(arg0.getAliasStateLabel(), arg1.getAliasStateLabel()) != 0) {
- logger.debug("state label different: " + arg0.getAliasStateLabel() + ", " + arg1.getAliasStateLabel());
- return stringComparator.compare(arg0.getAliasStateLabel(), arg1.getAliasStateLabel());
+ if (stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel()) != 0) {
+ logger.debug("state label different: " + arg0.getStateLabel() + ", " + arg1.getStateLabel());
+ return stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel());
}
- if (stringComparator.compare(arg0.getAliasStatePrefix(), arg1.getAliasStatePrefix()) != 0) {
- logger.debug("state prefix different: " + arg0.getAliasStatePrefix() + ", " + arg1.getAliasStatePrefix());
- return stringComparator.compare(arg0.getAliasStatePrefix(), arg1.getAliasStatePrefix());
+ if (stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix()) != 0) {
+ logger.debug("state prefix different: " + arg0.getStatePrefix() + ", " + arg1.getStatePrefix());
+ return stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix());
}
if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
index 39493f31f0..22483ca6f5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
@@ -68,8 +68,8 @@ public class TruncatedProteinComparator implements Comparator<TruncatedProtein>
/**
* This method compares only the fields that are defined in
- * TruncatedProteinAlias class in inheritence tree. By the design it calls
- * also comparator of the upper (SpeciesAlias) class.
+ * {@link TruncatedProtein} class in inheritence tree. By the design it calls
+ * also comparator of the upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class TruncatedProteinComparator implements Comparator<TruncatedProtein>
* -1/1 is returned.
*/
private int internalCompare(TruncatedProtein arg0, TruncatedProtein arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
index 96aea95884..96c0edce85 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
@@ -67,9 +67,9 @@ public class UnknownComparator implements Comparator<Unknown> {
}
/**
- * This method compares only the fields that are defined in UnknownAlias class
- * in inheritence tree. By the design it calls also comparator of the upper
- * (SpeciesAlias) class.
+ * This method compares only the fields that are defined in {@link Unknown}
+ * class in inheritence tree. By the design it calls also comparator of the
+ * upper ({@link Species}) class.
*
* @param arg0
* first object to compare
@@ -79,8 +79,8 @@ public class UnknownComparator implements Comparator<Unknown> {
* -1/1 is returned.
*/
private int internalCompare(Unknown arg0, Unknown arg1) {
- SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
index 5670e7eb01..3d0f487666 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
@RunWith(Suite.class)
@SuiteClasses({ AllCompartmentTests.class, //
- AliasInFewParentsExceptionTest.class, //
+ ElementInFewParentsExceptionTest.class, //
AllGraphTests.class, //
AllGraphicsTests.class, //
AllLayoutTests.class, //
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/AliasInFewParentsExceptionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java
similarity index 72%
rename from model/src/test/java/lcsb/mapviewer/model/map/AliasInFewParentsExceptionTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java
index c33431d2c0..5d4cb523ac 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AliasInFewParentsExceptionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java
@@ -5,7 +5,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-public class AliasInFewParentsExceptionTest {
+public class ElementInFewParentsExceptionTest {
@Before
public void setUp() throws Exception {
@@ -18,7 +18,7 @@ public class AliasInFewParentsExceptionTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new AliasInFewParentsException(""));
+ SerializationUtils.serialize(new ElementInFewParentsException(""));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
index cfcd1f7b1a..e0d775c942 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
@@ -36,8 +36,8 @@ public class BottomSquareCompartmentTest {
@Test
public void testConstructor1() {
try {
- BottomSquareCompartment alias = new BottomSquareCompartment(new Compartment());
- assertNotNull(alias);
+ BottomSquareCompartment compartment = new BottomSquareCompartment(new Compartment());
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -50,8 +50,8 @@ public class BottomSquareCompartmentTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- BottomSquareCompartment alias = new BottomSquareCompartment(new Compartment(), model);
- assertNotNull(alias);
+ BottomSquareCompartment compartment = new BottomSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -61,8 +61,8 @@ public class BottomSquareCompartmentTest {
@Test
public void testCopy() {
try {
- BottomSquareCompartment alias = new BottomSquareCompartment().copy();
- assertNotNull(alias);
+ BottomSquareCompartment compartment = new BottomSquareCompartment().copy();
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
index c4d2f9627d..c6888fa788 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
@@ -33,10 +33,10 @@ public class CompartmentComparatorTest {
@Test
public void testEquals() {
try {
- Compartment alias1 = createCompartmentAlias();
- Compartment alias2 = createCompartmentAlias();
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- assertEquals(0, comparator.compare(alias1, alias2));
+ assertEquals(0, comparator.compare(compartment1, compartment2));
assertEquals(0, comparator.compare(null, null));
@@ -49,9 +49,9 @@ public class CompartmentComparatorTest {
@Test
public void testDifferent2() {
try {
- Compartment alias1 = createCompartmentAlias();
+ Compartment compartment = createCompartment();
- assertTrue(comparator.compare(alias1, new PathwayCompartment()) != 0);
+ assertTrue(comparator.compare(compartment, new PathwayCompartment()) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -62,18 +62,18 @@ public class CompartmentComparatorTest {
@Test
public void testInvalid() {
try {
- Compartment alias1 = createCompartmentAlias();
- Compartment alias2 = createCompartmentAlias();
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- GenericProtein alias = new GenericProtein("1");
- alias1.getElements().add(alias);
- alias = new GenericProtein("1");
- alias1.getElements().add(alias);
+ GenericProtein protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
- alias2.getElements().add(new GenericProtein("b"));
- alias2.getElements().add(new GenericProtein("a"));
+ compartment2.getElements().add(new GenericProtein("b"));
+ compartment2.getElements().add(new GenericProtein("a"));
- comparator.compare(alias1, alias2);
+ comparator.compare(compartment1, compartment2);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -86,18 +86,18 @@ public class CompartmentComparatorTest {
@Test
public void testInvalid2() {
try {
- Compartment alias1 = createCompartmentAlias();
- Compartment alias2 = createCompartmentAlias();
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- Species alias = new GenericProtein("1");
- alias1.getElements().add(alias);
- alias = new GenericProtein("1");
- alias1.getElements().add(alias);
+ Species protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
- alias2.getElements().add(new GenericProtein("A"));
- alias2.getElements().add(new GenericProtein("B"));
+ compartment2.getElements().add(new GenericProtein("A"));
+ compartment2.getElements().add(new GenericProtein("B"));
- comparator.compare(alias2, alias1);
+ comparator.compare(compartment2, compartment1);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -107,7 +107,7 @@ public class CompartmentComparatorTest {
}
}
- private Compartment createCompartmentAlias() {
+ private Compartment createCompartment() {
Compartment result = new Compartment();
result.setElementId("asd");
@@ -123,9 +123,9 @@ public class CompartmentComparatorTest {
result.setInnerWidth(65);
result.setNamePoint(new Point2D.Double(9, 2));
- GenericProtein alias = new GenericProtein("S");
- alias.setName("a");
- result.addElement(alias);
+ GenericProtein protein = new GenericProtein("S");
+ protein.setName("a");
+ result.addElement(protein);
return result;
}
@@ -133,79 +133,79 @@ public class CompartmentComparatorTest {
@Test
public void testDifferent() {
try {
- Compartment alias1 = createCompartmentAlias();
- Compartment alias2 = createCompartmentAlias();
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- assertTrue(comparator.compare(alias1, null) != 0);
- assertTrue(comparator.compare(null, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, null) != 0);
+ assertTrue(comparator.compare(null, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.setElementId("tmp");
+ compartment1.setElementId("tmp");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.setThickness(11111);
+ compartment1.setThickness(11111);
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.setNamePoint(new Point2D.Double(9, 999));
+ compartment1.setNamePoint(new Point2D.Double(9, 999));
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.addElement(new GenericProtein("idd"));
+ compartment1.addElement(new GenericProtein("idd"));
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.getElements().iterator().next().setElementId("bnu");
+ compartment1.getElements().iterator().next().setElementId("bnu");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- Species speciesAlias = (Species) alias1.getElements().iterator().next();
- speciesAlias.setName("new namne");
+ Species species = (Species) compartment1.getElements().iterator().next();
+ species.setName("new namne");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.setOuterWidth(2);
+ compartment1.setOuterWidth(2);
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- alias1.setInnerWidth(2);
+ compartment1.setInnerWidth(2);
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- alias1 = createCompartmentAlias();
- alias2 = createCompartmentAlias();
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
index 179cb23a91..07690d2bfa 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
@@ -45,17 +45,17 @@ public class CompartmentTest {
public void testCross() throws Exception {
try {
Model model = createCrossModel();
- Element ldhbAlias1 = model.getElementByElementId("sa1115");
- Element ldhbAlias2 = model.getElementByElementId("sa1117");
- Element ldhbAlias3 = model.getElementByElementId("sa1119");
- Element ldhbAlias4 = model.getElementByElementId("sa1121");
+ Element ldhb1 = model.getElementByElementId("sa1115");
+ Element ldhb2 = model.getElementByElementId("sa1117");
+ Element ldhb3 = model.getElementByElementId("sa1119");
+ Element ldhb4 = model.getElementByElementId("sa1121");
- Compartment cytosolAlias = (Compartment) model.getElementByElementId("ca1");
+ Compartment cytosol = (Compartment) model.getElementByElementId("ca1");
- assertTrue(cytosolAlias.cross(ldhbAlias1));
- assertTrue(cytosolAlias.cross(ldhbAlias2));
- assertTrue(cytosolAlias.cross(ldhbAlias3));
- assertTrue(cytosolAlias.cross(ldhbAlias4));
+ assertTrue(cytosol.cross(ldhb1));
+ assertTrue(cytosol.cross(ldhb2));
+ assertTrue(cytosol.cross(ldhb3));
+ assertTrue(cytosol.cross(ldhb4));
} catch (Exception e) {
e.printStackTrace();
@@ -66,10 +66,10 @@ public class CompartmentTest {
@Test
public void testCrossException() throws Exception {
try {
- Compartment alias = new Compartment();
- Complex alias2 = new Complex("idd");
- alias2.setParent(alias2);
- alias.cross(alias2);
+ Compartment compartment = new Compartment();
+ Complex complex = new Complex("idd");
+ complex.setParent(complex);
+ compartment.cross(complex);
fail("Exception epxected");
} catch (InvalidStateException e) {
@@ -82,47 +82,47 @@ public class CompartmentTest {
@Test
public void testCross2() throws Exception {
try {
- Compartment alias = new Compartment();
- alias.setX(10.0);
- alias.setY(10.0);
- alias.setWidth(10.0);
- alias.setHeight(10.0);
- Complex alias2 = new Complex("idd");
- alias2.setWidth(10.0);
- alias2.setHeight(10.0);
- alias2.setX(5.0);
- alias2.setY(5.0);
- assertTrue(alias.cross(alias2));
-
- alias2.setX(15.0);
- alias2.setY(5.0);
- assertTrue(alias.cross(alias2));
-
- alias2.setX(5.0);
- alias2.setY(15.0);
- assertTrue(alias.cross(alias2));
-
- alias2.setX(15.0);
- alias2.setY(15.0);
- assertTrue(alias.cross(alias2));
-
- alias2.setWidth(100.0);
- alias2.setHeight(100.0);
- alias2.setX(-110.0);
- alias2.setY(-10.0);
- assertFalse(alias.cross(alias2));
-
- alias2.setX(-10.0);
- alias2.setY(-110.0);
- assertFalse(alias.cross(alias2));
-
- alias2.setX(40.0);
- alias2.setY(-10.0);
- assertFalse(alias.cross(alias2));
-
- alias2.setX(-10.0);
- alias2.setY(40.0);
- assertFalse(alias.cross(alias2));
+ Compartment compartment = new Compartment();
+ compartment.setX(10.0);
+ compartment.setY(10.0);
+ compartment.setWidth(10.0);
+ compartment.setHeight(10.0);
+ Complex complex = new Complex("idd");
+ complex.setWidth(10.0);
+ complex.setHeight(10.0);
+ complex.setX(5.0);
+ complex.setY(5.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setX(15.0);
+ complex.setY(5.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setX(5.0);
+ complex.setY(15.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setX(15.0);
+ complex.setY(15.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setWidth(100.0);
+ complex.setHeight(100.0);
+ complex.setX(-110.0);
+ complex.setY(-10.0);
+ assertFalse(compartment.cross(complex));
+
+ complex.setX(-10.0);
+ complex.setY(-110.0);
+ assertFalse(compartment.cross(complex));
+
+ complex.setX(40.0);
+ complex.setY(-10.0);
+ assertFalse(compartment.cross(complex));
+
+ complex.setX(-10.0);
+ complex.setY(40.0);
+ assertFalse(compartment.cross(complex));
} catch (Exception e) {
e.printStackTrace();
@@ -133,18 +133,18 @@ public class CompartmentTest {
@Test
public void testContainsIdenticalSpecies() throws Exception {
try {
- Compartment alias = new Compartment();
+ Compartment compartment = new Compartment();
- alias.setName("AS");
+ compartment.setName("AS");
- assertFalse(alias.containsIdenticalSpecies());
+ assertFalse(compartment.containsIdenticalSpecies());
- Species sAlias = new GenericProtein("idd");
- sAlias.setName("AS");
+ Species species = new GenericProtein("idd");
+ species.setName("AS");
- alias.addElement(sAlias);
+ compartment.addElement(species);
- assertTrue(alias.containsIdenticalSpecies());
+ assertTrue(compartment.containsIdenticalSpecies());
} catch (Exception e) {
e.printStackTrace();
@@ -156,66 +156,66 @@ public class CompartmentTest {
Model model = new ModelFullIndexed(null);
model.addElement(new Compartment("default"));
- model.addElement(createSpeciesAlias(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
- model.addElement(createSpeciesAlias(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
- model.addElement(createSpeciesAlias(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
- model.addElement(createSpeciesAlias(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
+ model.addElement(createSpecies(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
+ model.addElement(createSpecies(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpecies(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpecies(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
- Species alias = createSpeciesAlias(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(7804.714285714286, 11182.642857142859, 112.0, 172.0, "csa152");
- alias3.addAlias(alias);
- alias3.addAlias(alias2);
- alias.setParent(alias3);
- alias2.setParent(alias3);
+ Species species = createSpecies(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
+ Species species2 = createSpecies(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
+ Complex complex = createComplex(7804.714285714286, 11182.642857142859, 112.0, 172.0, "csa152");
+ complex.addSpecies(species);
+ complex.addSpecies(species2);
+ species.setParent(complex);
+ species2.setParent(complex);
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
+ model.addElement(species);
+ model.addElement(species2);
+ model.addElement(complex);
- model.addElement(createCompartmentAlias(1380.0, 416.0, 15893.0, 10866.0, "ca1"));
+ model.addElement(createCompartment(1380.0, 416.0, 15893.0, 10866.0, "ca1"));
return model;
}
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setElementId(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
+ private Compartment createCompartment(double x, double y, double width, double height, String elementId) {
+ Compartment compartment = new Compartment(elementId);
+ compartment.setElementId(elementId);
+ compartment.setX(x);
+ compartment.setY(y);
+ compartment.setWidth(width);
+ compartment.setHeight(height);
+ return compartment;
}
- private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- SimpleMolecule alias = new SimpleMolecule(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
+ private Species createSpecies(double x, double y, double width, double height, String elementId) {
+ SimpleMolecule simpleMolecule = new SimpleMolecule(elementId);
+ simpleMolecule.setX(x);
+ simpleMolecule.setY(y);
+ simpleMolecule.setWidth(width);
+ simpleMolecule.setHeight(height);
+ return simpleMolecule;
}
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
+ private Complex createComplex(double x, double y, double width, double height, String elementId) {
+ Complex complex = new Complex(elementId);
+ complex.setX(x);
+ complex.setY(y);
+ complex.setWidth(width);
+ complex.setHeight(height);
+ return complex;
}
@Test
public void testCrossWithComplexElements() throws Exception {
try {
Model model = createCrossModel();
- Element ldhbAlias1 = model.getElementByElementId("sa1422");
- Element ldhbAlias2 = model.getElementByElementId("sa1419");
+ Element ldhb1 = model.getElementByElementId("sa1422");
+ Element ldhb2 = model.getElementByElementId("sa1419");
- Compartment cytosolAlias = (Compartment) model.getElementByElementId("ca1");
+ Compartment cytosol = (Compartment) model.getElementByElementId("ca1");
- assertTrue(cytosolAlias.cross(ldhbAlias1));
- assertTrue(cytosolAlias.cross(ldhbAlias2));
+ assertTrue(cytosol.cross(ldhb1));
+ assertTrue(cytosol.cross(ldhb2));
} catch (Exception e) {
e.printStackTrace();
@@ -236,9 +236,9 @@ public class CompartmentTest {
@Test
public void testConstructor() {
try {
- Compartment alias = new Compartment();
- alias.addElement(new GenericProtein("idd"));
- Compartment copy = new Compartment(alias);
+ Compartment compartment = new Compartment();
+ compartment.addElement(new GenericProtein("idd"));
+ Compartment copy = new Compartment(compartment);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -295,16 +295,16 @@ public class CompartmentTest {
}
@Test
- public void testAddAlias() {
+ public void testAddElement() {
try {
- Compartment alias = new Compartment();
+ Compartment compartment = new Compartment();
Species child = new GenericProtein("id");
- alias.addElement(child);
- alias.addElement(child);
+ compartment.addElement(child);
+ compartment.addElement(child);
- assertEquals(1, alias.getElements().size());
+ assertEquals(1, compartment.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -313,15 +313,15 @@ public class CompartmentTest {
}
@Test
- public void testAddInvalidAlias() {
+ public void testAddInvalidElement() {
try {
- Compartment alias = new Compartment();
+ Compartment compartment = new Compartment();
Species child = new GenericProtein("id");
Species child2 = new GenericProtein("id");
- alias.addElement(child);
- alias.addElement(child2);
+ compartment.addElement(child);
+ compartment.addElement(child2);
fail("Exception expected");
@@ -333,16 +333,16 @@ public class CompartmentTest {
}
@Test
- public void testGetAllAlias() {
+ public void testGetAllElements() {
try {
- Compartment alias = new Compartment();
+ Compartment compartment = new Compartment();
Species child = new GenericProtein("id");
Compartment child2 = new Compartment();
child2.addElement(child);
- alias.addElement(child2);
+ compartment.addElement(child2);
- assertEquals(2, alias.getAllSubElements().size());
+ assertEquals(2, compartment.getAllSubElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -362,12 +362,12 @@ public class CompartmentTest {
}
@Test
- public void testRemoveAlias() {
+ public void testRemoveElement() {
try {
Compartment comp = new Compartment();
Species protein = new GenericProtein("idd");
comp.addElement(protein);
- protein.setCompartmentAlias(new Compartment());
+ protein.setCompartment(new Compartment());
comp.removeElement(protein);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
index 4b61f698f6..20ba0f3f69 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
@@ -36,8 +36,8 @@ public class LeftSquareCompartmentTest {
@Test
public void testConstructor1() {
try {
- LeftSquareCompartment alias = new LeftSquareCompartment(new LeftSquareCompartment());
- assertNotNull(alias);
+ LeftSquareCompartment compartment = new LeftSquareCompartment(new LeftSquareCompartment());
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -50,8 +50,8 @@ public class LeftSquareCompartmentTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- LeftSquareCompartment alias = new LeftSquareCompartment(new Compartment(), model);
- assertNotNull(alias);
+ LeftSquareCompartment compartment = new LeftSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -61,8 +61,8 @@ public class LeftSquareCompartmentTest {
@Test
public void testCopy() {
try {
- LeftSquareCompartment alias = new LeftSquareCompartment().copy();
- assertNotNull(alias);
+ LeftSquareCompartment compartment = new LeftSquareCompartment().copy();
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java
index 611b141499..eb1b298228 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java
@@ -29,10 +29,10 @@ public class PathwayCompartmentTest {
public void test() throws Exception {
try {
CompartmentComparator comparator = new CompartmentComparator();
- Compartment alias = new PathwayCompartment("id");
- Compartment copy = alias.copy();
+ Compartment pathway = new PathwayCompartment("id");
+ Compartment copy = pathway.copy();
- assertEquals(0, comparator.compare(alias, copy));
+ assertEquals(0, comparator.compare(pathway, copy));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -53,10 +53,10 @@ public class PathwayCompartmentTest {
@Test
public void testGetters() {
try {
- PathwayCompartment alias = new PathwayCompartment("id");
+ PathwayCompartment pathway = new PathwayCompartment("id");
String title = "tit27";
- alias.setName(title);
- assertEquals(title, alias.getName());
+ pathway.setName(title);
+ assertEquals(title, pathway.getName());
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
index 1135e99739..364a71fd35 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
@@ -37,8 +37,8 @@ public class RightSquareCompartmentTest {
@Test
public void testConstructor1() {
try {
- RightSquareCompartment alias = new RightSquareCompartment(new RightSquareCompartment());
- assertNotNull(alias);
+ RightSquareCompartment compartment = new RightSquareCompartment(new RightSquareCompartment());
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -51,8 +51,8 @@ public class RightSquareCompartmentTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- RightSquareCompartment alias = new RightSquareCompartment(new Compartment(), model);
- assertNotNull(alias);
+ RightSquareCompartment compartment = new RightSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -62,8 +62,8 @@ public class RightSquareCompartmentTest {
@Test
public void testCopy() {
try {
- RightSquareCompartment alias = new RightSquareCompartment().copy();
- assertNotNull(alias);
+ RightSquareCompartment compartment = new RightSquareCompartment().copy();
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -73,9 +73,9 @@ public class RightSquareCompartmentTest {
@Test
public void testSetPoint() {
try {
- RightSquareCompartment alias = new RightSquareCompartment();
- alias.setPoint("10", "10");
- assertTrue(alias.getWidth() < 0);
+ RightSquareCompartment compartment = new RightSquareCompartment();
+ compartment.setPoint("10", "10");
+ assertTrue(compartment.getWidth() < 0);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
index 244fa59044..f87750199c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
@@ -39,8 +39,8 @@ public class TopSquareCompartmentTest {
@Test
public void testConstructor1() {
try {
- TopSquareCompartment alias = new TopSquareCompartment(new TopSquareCompartment());
- assertNotNull(alias);
+ TopSquareCompartment compartment = new TopSquareCompartment(new TopSquareCompartment());
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -53,8 +53,8 @@ public class TopSquareCompartmentTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- TopSquareCompartment alias = new TopSquareCompartment(new Compartment(), model);
- assertNotNull(alias);
+ TopSquareCompartment compartment = new TopSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -64,8 +64,8 @@ public class TopSquareCompartmentTest {
@Test
public void testCopy() {
try {
- TopSquareCompartment alias = new TopSquareCompartment().copy();
- assertNotNull(alias);
+ TopSquareCompartment compartment = new TopSquareCompartment().copy();
+ assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java
index 2d82745194..b8673bb117 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java
@@ -39,13 +39,13 @@ public class ElementGroupTest {
try {
ElementGroup group = new ElementGroup();
String idGroup = "str";
- List<Element> aliases = new ArrayList<>();
+ List<Element> elements = new ArrayList<>();
group.setIdGroup(idGroup);
- group.setAliases(aliases);
+ group.setElements(elements);
assertEquals(idGroup, group.getIdGroup());
- assertEquals(aliases, group.getAliases());
+ assertEquals(elements, group.getElements());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -53,11 +53,11 @@ public class ElementGroupTest {
}
@Test
- public void testAddAlias() {
+ public void testAddElement() {
try {
ElementGroup group = new ElementGroup();
- group.addAlias(new GenericProtein("id"));
- assertEquals(1, group.getAliases().size());
+ group.addElement(new GenericProtein("id"));
+ assertEquals(1, group.getElements().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
index eae880a50f..b111535413 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.model.map.model;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AliasSubmodelConnectionComparatorTest.class, //
- AliasSubmodelConnectionTest.class, //
- ModelComparatorTest.class, //
- ModelDataTest.class, //
- ModelFullIndexedTest.class, //
- ModelSubmodelConnectionComparatorTest.class, //
- ModelSubmodelConnectionTest.class, //
- ModelTest.class, //
- SubmodelConnectionComparatorTest.class,//
- SubmodelTypeTest.class,//
-})
-public class AllModelTests {
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ElementSubmodelConnectionComparatorTest.class, //
+ ElementSubmodelConnectionTest.class, //
+ ModelComparatorTest.class, //
+ ModelDataTest.class, //
+ ModelFullIndexedTest.class, //
+ ModelSubmodelConnectionComparatorTest.class, //
+ ModelSubmodelConnectionTest.class, //
+ ModelTest.class, //
+ SubmodelConnectionComparatorTest.class,//
+ SubmodelTypeTest.class,//
+})
+public class AllModelTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
similarity index 63%
rename from model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
index 56b498f591..742f507357 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
@@ -15,9 +15,9 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
-public class AliasSubmodelConnectionComparatorTest {
+public class ElementSubmodelConnectionComparatorTest {
- AliasSubmodelConnectionComparator comparator = new AliasSubmodelConnectionComparator();
+ ElementSubmodelConnectionComparator comparator = new ElementSubmodelConnectionComparator();
@Before
public void setUp() throws Exception {
@@ -30,10 +30,10 @@ public class AliasSubmodelConnectionComparatorTest {
@Test
public void testEquals() throws Exception {
try {
- AliasSubmodelConnection connectionA = createConnection();
- AliasSubmodelConnection connectionB = createConnection();
+ ElementSubmodelConnection connectionA = createConnection();
+ ElementSubmodelConnection connectionB = createConnection();
- assertEquals(0, comparator.compare(new AliasSubmodelConnection(), new AliasSubmodelConnection()));
+ assertEquals(0, comparator.compare(new ElementSubmodelConnection(), new ElementSubmodelConnection()));
assertEquals(0, comparator.compare(connectionA, connectionB));
assertEquals(0, comparator.compare(connectionA, connectionA));
assertEquals(0, comparator.compare(null, null));
@@ -47,20 +47,20 @@ public class AliasSubmodelConnectionComparatorTest {
@Test
public void testDifferent() throws Exception {
try {
- AliasSubmodelConnection connectionA = createConnection();
- AliasSubmodelConnection connectionB = createConnection();
+ ElementSubmodelConnection connectionA = createConnection();
+ ElementSubmodelConnection connectionB = createConnection();
assertTrue(comparator.compare(null, connectionB) != 0);
assertTrue(comparator.compare(connectionA, null) != 0);
- connectionA.setFromAlias(null);
+ connectionA.setFromElement(null);
assertTrue(comparator.compare(connectionA, connectionB) != 0);
assertTrue(comparator.compare(connectionB, connectionA) != 0);
connectionA = createConnection();
connectionB = createConnection();
- connectionA.getFromAlias().setWidth(1234567);
+ connectionA.getFromElement().setWidth(1234567);
assertTrue(comparator.compare(connectionA, connectionB) != 0);
assertTrue(comparator.compare(connectionB, connectionA) != 0);
@@ -68,19 +68,19 @@ public class AliasSubmodelConnectionComparatorTest {
connectionA = createConnection();
connectionB = createConnection();
- connectionA.setToAlias(null);
+ connectionA.setToElement(null);
assertTrue(comparator.compare(connectionA, connectionB) != 0);
assertTrue(comparator.compare(connectionB, connectionA) != 0);
connectionA = createConnection();
connectionB = createConnection();
- connectionA.getToAlias().setWidth(1234567);
+ connectionA.getToElement().setWidth(1234567);
assertTrue(comparator.compare(connectionA, connectionB) != 0);
assertTrue(comparator.compare(connectionB, connectionA) != 0);
- assertTrue(comparator.compare(connectionB, new AliasSubmodelConnection() {
+ assertTrue(comparator.compare(connectionB, new ElementSubmodelConnection() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -98,9 +98,9 @@ public class AliasSubmodelConnectionComparatorTest {
protein.setName("ad");
model.addElement(protein);
- GenericProtein alias = new GenericProtein("a_id");
- alias.setName("ad");
- model.addElement(alias);
+ GenericProtein protein2 = new GenericProtein("a_id");
+ protein2.setName("ad");
+ model.addElement(protein2);
model.addElement(new Compartment("default"));
@@ -112,18 +112,18 @@ public class AliasSubmodelConnectionComparatorTest {
return model;
}
- private AliasSubmodelConnection createConnection() {
- AliasSubmodelConnection result = new AliasSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ private ElementSubmodelConnection createConnection() {
+ ElementSubmodelConnection result = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
result.setName("name A");
- result.setFromAlias(createAlias());
- result.setToAlias(createAlias());
+ result.setFromElement(createElement());
+ result.setToElement(createElement());
return result;
}
- private Element createAlias() {
- Element alias = new GenericProtein("alias_id");
- alias.setColor(Color.BLACK);
- return alias;
+ private Element createElement() {
+ Element protein = new GenericProtein("protein_id");
+ protein.setColor(Color.BLACK);
+ return protein;
}
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java
similarity index 65%
rename from model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java
index c07be70f0e..941aeb1dff 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class AliasSubmodelConnectionTest {
+public class ElementSubmodelConnectionTest {
@Before
public void setUp() throws Exception {
@@ -23,7 +23,7 @@ public class AliasSubmodelConnectionTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new AliasSubmodelConnection());
+ SerializationUtils.serialize(new ElementSubmodelConnection());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -33,7 +33,7 @@ public class AliasSubmodelConnectionTest {
@Test
public void testConstructor() {
try {
- AliasSubmodelConnection connection = new AliasSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS);
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS);
assertNotNull(connection);
} catch (Exception e) {
e.printStackTrace();
@@ -44,7 +44,7 @@ public class AliasSubmodelConnectionTest {
@Test
public void testConstructor2() {
try {
- AliasSubmodelConnection connection = new AliasSubmodelConnection(new AliasSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS));
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(new ElementSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS));
assertNotNull(connection);
} catch (Exception e) {
e.printStackTrace();
@@ -55,7 +55,7 @@ public class AliasSubmodelConnectionTest {
@Test
public void testConstructor3() {
try {
- AliasSubmodelConnection connection = new AliasSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "sd");
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "sd");
assertNotNull(connection);
} catch (Exception e) {
e.printStackTrace();
@@ -66,7 +66,7 @@ public class AliasSubmodelConnectionTest {
@Test
public void testCopy() {
try {
- AliasSubmodelConnection connection = new AliasSubmodelConnection().copy();
+ ElementSubmodelConnection connection = new ElementSubmodelConnection().copy();
assertNotNull(connection);
} catch (Exception e) {
e.printStackTrace();
@@ -77,7 +77,7 @@ public class AliasSubmodelConnectionTest {
@Test
public void testInvalidCopy() {
try {
- new AliasSubmodelConnection() {
+ new ElementSubmodelConnection() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
index e698bf4ad6..d8c2048b8f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
@@ -84,16 +84,16 @@ public class ModelComparatorTest {
Model model1 = getModel();
Model model2 = getModel();
- Compartment alias = new PathwayCompartment("1");
- Compartment alias2 = new PathwayCompartment("12");
- model1.addElement(alias);
- model1.addElement(alias2);
+ Compartment compartment = new PathwayCompartment("1");
+ Compartment compartment2 = new PathwayCompartment("12");
+ model1.addElement(compartment);
+ model1.addElement(compartment2);
- alias = new PathwayCompartment("1");
- alias2 = new PathwayCompartment("12");
- model2.addElement(alias);
- model2.addElement(alias2);
- alias2.setElementId("1");
+ compartment = new PathwayCompartment("1");
+ compartment2 = new PathwayCompartment("12");
+ model2.addElement(compartment);
+ model2.addElement(compartment2);
+ compartment2.setElementId("1");
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -141,11 +141,11 @@ public class ModelComparatorTest {
Model model1 = getModel();
Model model2 = getModel();
- Species mockAlias = Mockito.mock(Species.class);
- when(mockAlias.getElementId()).thenReturn("1");
- model1.addElement(mockAlias);
+ Species mockSpecies = Mockito.mock(Species.class);
+ when(mockSpecies.getElementId()).thenReturn("1");
+ model1.addElement(mockSpecies);
- model2.addElement(mockAlias);
+ model2.addElement(mockSpecies);
try {
comparator.compare(model1, model2);
@@ -188,9 +188,9 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- GenericProtein alias = new GenericProtein("SAd");
+ GenericProtein protein = new GenericProtein("SAd");
- model1.addElement(alias);
+ model1.addElement(protein);
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -198,7 +198,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.getAliases().iterator().next().setElementId("sdfsd");
+ model1.getElements().iterator().next().setElementId("sdfsd");
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -246,7 +246,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.getAliases().iterator().next().addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_HAS_PART, MiriamType.CHEBI, "c"));
+ model1.getElements().iterator().next().addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_HAS_PART, MiriamType.CHEBI, "c"));
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -382,10 +382,10 @@ public class ModelComparatorTest {
private Model getModel() {
Model model = new ModelFullIndexed(null);
model.setNotes("Some description");
- GenericProtein alias = new GenericProtein("a_id");
- alias.setName("ad");
+ GenericProtein protein = new GenericProtein("a_id");
+ protein.setName("ad");
- model.addElement(alias);
+ model.addElement(protein);
model.addElement(new Compartment("default"));
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
index e5031f22c3..aad0ee4aae 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
@@ -48,13 +48,13 @@ public class ModelDataTest {
}
@Test
- public void testAddAliases() {
+ public void testAddElements() {
try {
ModelData md = new ModelData();
- List<Element> aliases = new ArrayList<>();
- aliases.add(new GenericProtein("unk_id"));
- md.addAliases(aliases);
- assertEquals(1, md.getAliases().size());
+ List<Element> elements = new ArrayList<>();
+ elements.add(new GenericProtein("unk_id"));
+ md.addElements(elements);
+ assertEquals(1, md.getElements().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -65,9 +65,9 @@ public class ModelDataTest {
public void testAddReactions() {
try {
ModelData md = new ModelData();
- List<Reaction> aliases = new ArrayList<>();
- aliases.add(new Reaction());
- md.addReactions(aliases);
+ List<Reaction> reactions = new ArrayList<>();
+ reactions.add(new Reaction());
+ md.addReactions(reactions);
assertEquals(1, md.getReactions().size());
} catch (Exception e) {
e.printStackTrace();
@@ -79,9 +79,9 @@ public class ModelDataTest {
public void testAddLayers() {
try {
ModelData md = new ModelData();
- List<Layer> aliases = new ArrayList<>();
- aliases.add(new Layer());
- md.addLayers(aliases);
+ List<Layer> layers = new ArrayList<>();
+ layers.add(new Layer());
+ md.addLayers(layers);
assertEquals(1, md.getLayers().size());
} catch (Exception e) {
e.printStackTrace();
@@ -90,10 +90,10 @@ public class ModelDataTest {
}
@Test
- public void testAddAliasGroup() {
+ public void testAddElementGroup() {
try {
ModelData md = new ModelData();
- md.addAliasGroup(null);
+ md.addElementGroup(null);
// not implemented for now
} catch (Exception e) {
e.printStackTrace();
@@ -141,10 +141,10 @@ public class ModelDataTest {
}
@Test
- public void testRemoveAlias1() {
+ public void testRemoveElement1() {
try {
ModelData md = new ModelData();
- md.removeAlias(null);
+ md.removeElement(null);
fail("Exception expected");
} catch (InvalidArgumentException e) {
} catch (Exception e) {
@@ -154,10 +154,10 @@ public class ModelDataTest {
}
@Test
- public void testRemoveAlias2() {
+ public void testRemoveElement2() {
try {
ModelData md = new ModelData();
- md.removeAlias(new GenericProtein("unk_id"));
+ md.removeElement(new GenericProtein("unk_id"));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -165,14 +165,14 @@ public class ModelDataTest {
}
@Test
- public void testRemoveAlias3() {
+ public void testRemoveElement3() {
try {
ModelData md = new ModelData();
- Element alias = new GenericProtein("unk_id");
- md.addAlias(alias);
- assertEquals(1, md.getAliases().size());
- md.removeAlias(alias);
- assertEquals(0, md.getAliases().size());
+ Element protein = new GenericProtein("unk_id");
+ md.addElement(protein);
+ assertEquals(1, md.getElements().size());
+ md.removeElement(protein);
+ assertEquals(0, md.getElements().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -194,10 +194,10 @@ public class ModelDataTest {
public void testRemoveReaction3() {
try {
ModelData md = new ModelData();
- Reaction alias = new Reaction();
- md.addReaction(alias);
+ Reaction reaction = new Reaction();
+ md.addReaction(reaction);
assertEquals(1, md.getReactions().size());
- md.removeReaction(alias);
+ md.removeReaction(reaction);
assertEquals(0, md.getReactions().size());
} catch (Exception e) {
e.printStackTrace();
@@ -323,7 +323,7 @@ public class ModelDataTest {
public void testGetters() {
try {
ModelData md = new ModelData();
- Set<Element> aliases = new HashSet<>();
+ Set<Element> elements = new HashSet<>();
List<Layout> layouts = new ArrayList<>();
Set<Layer> layers = new HashSet<>();
Set<Reaction> reactions = new HashSet<>();
@@ -352,8 +352,8 @@ public class ModelDataTest {
md.setId(id);
assertEquals(id, md.getId());
- md.setAliases(aliases);
- assertEquals(aliases, md.getAliases());
+ md.setElements(elements);
+ assertEquals(elements, md.getElements());
md.setProject(project);
assertEquals(project, md.getProject());
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index ca457e1bc4..4dd1b0b7a7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -59,23 +59,23 @@ public class ModelFullIndexedTest {
public void testConstructor() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Species proteinAlias = new GenericProtein("1a");
- Species proteinAlias2 = new GenericProtein("f");
- Species proteinAlias3 = new GenericProtein("fa");
-
- Element compartmentAlias = new Compartment("aaa");
- Element compartmentAlias3 = new Compartment("aaa3");
- Element compartmentAlias2 = new PathwayCompartment("aaa2");
- model.addElement(proteinAlias);
- model.addElement(proteinAlias2);
- model.addElement(proteinAlias3);
- model.addElement(compartmentAlias);
- model.addElement(compartmentAlias2);
- model.addElement(compartmentAlias3);
+ Species protein = new GenericProtein("1a");
+ Species protein2 = new GenericProtein("f");
+ Species protein3 = new GenericProtein("fa");
+
+ Element compartment = new Compartment("aaa");
+ Element compartment3 = new Compartment("aaa3");
+ Element compartment2 = new PathwayCompartment("aaa2");
+ model.addElement(protein);
+ model.addElement(protein2);
+ model.addElement(protein3);
+ model.addElement(compartment);
+ model.addElement(compartment2);
+ model.addElement(compartment3);
Reaction reaction = new TransportReaction();
- reaction.addReactant(new Reactant(proteinAlias));
- reaction.addProduct(new Product(proteinAlias2));
+ reaction.addReactant(new Reactant(protein));
+ reaction.addProduct(new Product(protein2));
model.addReaction(reaction);
model.setProject(new Project());
@@ -163,11 +163,11 @@ public class ModelFullIndexedTest {
}
@Test
- public void testAddInvalidAlias() {
+ public void testAddInvalidElement6() {
try {
- Element alias = Mockito.mock(Element.class);
+ Element elementMock = Mockito.mock(Element.class);
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addElement(alias);
+ model.addElement(elementMock);
new ModelFullIndexed(model.getModelData());
@@ -181,15 +181,15 @@ public class ModelFullIndexedTest {
}
@Test
- public void testAddInvalidSpeciesAlias5() {
+ public void testAddInvalidElement5() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Complex alias = new Complex("1");
+ Complex complex = new Complex("1");
- model.addElement(alias);
+ model.addElement(complex);
try {
- model.addElement(alias);
+ model.addElement(complex);
fail("Exception expected");
} catch (InvalidArgumentException e) {
}
@@ -215,23 +215,23 @@ public class ModelFullIndexedTest {
}
@Test
- public void testAddSpeciesAliasWithParent() {
+ public void testAddSpeciesWithParent() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
model.addElement(new Compartment("default"));
- Complex alias = new Complex("1");
+ Complex complex = new Complex("1");
- Element proteinAlias = new GenericProtein("asd");
- proteinAlias.setElementId("zz");
- proteinAlias.setParent(alias);
+ Element protein = new GenericProtein("asd");
+ protein.setElementId("zz");
+ protein.setParent(complex);
- model.addElement(alias);
+ model.addElement(complex);
- model.addElement(proteinAlias);
+ model.addElement(protein);
- assertEquals(3, model.getAliases().size());
+ assertEquals(3, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -240,25 +240,25 @@ public class ModelFullIndexedTest {
}
@Test
- public void testAddSpeciesAliasWithParentWithCompartment() {
+ public void testAddSpeciesWithParentWithCompartment() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Compartment compAlias = new Compartment("default");
- model.addElement(compAlias);
+ Compartment compartment = new Compartment("default");
+ model.addElement(compartment);
- Complex alias = new Complex("1");
- alias.setParent(compAlias);
+ Complex complex = new Complex("1");
+ complex.setParent(compartment);
- Element proteinAlias = new GenericProtein("asd");
- proteinAlias.setElementId("zz");
- proteinAlias.setParent(alias);
+ Element protein = new GenericProtein("asd");
+ protein.setElementId("zz");
+ protein.setParent(complex);
- model.addElement(alias);
+ model.addElement(complex);
- model.addElement(proteinAlias);
+ model.addElement(protein);
- assertEquals(3, model.getAliases().size());
+ assertEquals(3, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -267,15 +267,15 @@ public class ModelFullIndexedTest {
}
@Test
- public void testGetAliasByAliasId() {
+ public void testGetElementByElementId() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
assertNull(model.getElementByElementId("id"));
- Species alias = new GenericProtein("asd");
- alias.setElementId("id");
+ Species protein = new GenericProtein("asd");
+ protein.setElementId("id");
- model.addElement(alias);
+ model.addElement(protein);
assertNotNull(model.getElementByElementId("id"));
@@ -286,16 +286,16 @@ public class ModelFullIndexedTest {
}
@Test
- public void testAddCompartmentAlias2() {
+ public void testAddCompartment2() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Compartment alias = new Compartment("1");
+ Compartment compartment = new Compartment("1");
- assertEquals(0, model.getCompartmentsAliases().size());
- model.addElement(alias);
- assertEquals(1, model.getCompartmentsAliases().size());
- model.addElement(alias);
+ assertEquals(0, model.getCompartments().size());
+ model.addElement(compartment);
+ assertEquals(1, model.getCompartments().size());
+ model.addElement(compartment);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -340,15 +340,15 @@ public class ModelFullIndexedTest {
}
@Test
- public void testGetAliasByDbId() {
+ public void testGetElementByDbId() {
try {
- int aliasId = 12;
+ int elementId = 12;
ModelFullIndexed model = new ModelFullIndexed(null);
- Element alias = new GenericProtein("1");
- alias.setId(aliasId);
- assertNull(model.getAliasByDbId(aliasId));
- model.addElement(alias);
- assertEquals(alias, model.getAliasByDbId(aliasId));
+ Element protein = new GenericProtein("1");
+ protein.setId(elementId);
+ assertNull(model.getElementByDbId(elementId));
+ model.addElement(protein);
+ assertEquals(protein, model.getElementByDbId(elementId));
} catch (Exception e) {
e.printStackTrace();
@@ -357,26 +357,26 @@ public class ModelFullIndexedTest {
}
@Test
- public void testGetSortedCompartmentAliases() {
+ public void testGetSortedCompartments() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Compartment alias = new Compartment("a1");
- alias.setWidth(12);
- alias.setHeight(12);
- model.addElement(alias);
- alias = new Compartment("a2");
- alias.setWidth(14);
- alias.setHeight(14);
- model.addElement(alias);
- alias = new Compartment("a3");
- alias.setWidth(13);
- alias.setHeight(13);
- model.addElement(alias);
+ Compartment compartment = new Compartment("a1");
+ compartment.setWidth(12);
+ compartment.setHeight(12);
+ model.addElement(compartment);
+ compartment = new Compartment("a2");
+ compartment.setWidth(14);
+ compartment.setHeight(14);
+ model.addElement(compartment);
+ compartment = new Compartment("a3");
+ compartment.setWidth(13);
+ compartment.setHeight(13);
+ model.addElement(compartment);
- List<Compartment> aliases = model.getSortedCompartmentsAliases();
- assertEquals(196.0, aliases.get(0).getSize(), Configuration.EPSILON);
- assertEquals(169.0, aliases.get(1).getSize(), Configuration.EPSILON);
- assertEquals(144.0, aliases.get(2).getSize(), Configuration.EPSILON);
+ List<Compartment> compartments = model.getSortedCompartments();
+ assertEquals(196.0, compartments.get(0).getSize(), Configuration.EPSILON);
+ assertEquals(169.0, compartments.get(1).getSize(), Configuration.EPSILON);
+ assertEquals(144.0, compartments.get(2).getSize(), Configuration.EPSILON);
} catch (Exception e) {
e.printStackTrace();
@@ -385,22 +385,22 @@ public class ModelFullIndexedTest {
}
@Test
- public void testRemoveCompartmentAliases() {
+ public void testRemoveCompartment2() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Compartment alias = new Compartment("a1");
- alias.setWidth(12);
- alias.setHeight(12);
- model.addElement(alias);
+ Compartment compartment = new Compartment("a1");
+ compartment.setWidth(12);
+ compartment.setHeight(12);
+ model.addElement(compartment);
- alias = new Compartment("a2");
- alias.setWidth(14);
- alias.setHeight(14);
- model.addElement(alias);
- assertEquals(2, model.getAliases().size());
+ compartment = new Compartment("a2");
+ compartment.setWidth(14);
+ compartment.setHeight(14);
+ model.addElement(compartment);
+ assertEquals(2, model.getElements().size());
- model.removeAlias(alias);
- assertEquals(1, model.getAliases().size());
+ model.removeElement(compartment);
+ assertEquals(1, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -409,37 +409,37 @@ public class ModelFullIndexedTest {
}
@Test
- public void testAddAliases() {
+ public void testAddElements() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Compartment alias = new Compartment("1");
- alias.setWidth(100);
- alias.setHeight(100);
- List<Element> aliases = new ArrayList<>();
- aliases.add(alias);
+ Compartment compartment = new Compartment("1");
+ compartment.setWidth(100);
+ compartment.setHeight(100);
+ List<Element> elements = new ArrayList<>();
+ elements.add(compartment);
- Complex cAlias = new Complex("ca1");
- aliases.add(cAlias);
- cAlias.setWidth(10);
- cAlias.setHeight(10);
+ Complex complex = new Complex("ca1");
+ elements.add(complex);
+ complex.setWidth(10);
+ complex.setHeight(10);
- Species sAlias = new GenericProtein("a1");
- aliases.add(sAlias);
- sAlias.setWidth(20);
- sAlias.setHeight(20);
+ Species species = new GenericProtein("a1");
+ elements.add(species);
+ species.setWidth(20);
+ species.setHeight(20);
- assertEquals(0, model.getCompartmentsAliases().size());
- model.addAliases(aliases);
- assertEquals(1, model.getCompartmentsAliases().size());
+ assertEquals(0, model.getCompartments().size());
+ model.addElements(elements);
+ assertEquals(1, model.getCompartments().size());
assertEquals(1, model.getComplexList().size());
assertEquals(1, model.getNotComplexSpeciesList().size());
- List<Element> sortedAliases = model.getSortedSpeciesList();
+ List<Element> sortedSpecies = model.getSortedSpeciesList();
- assertEquals(alias, sortedAliases.get(0));
- assertEquals(sAlias, sortedAliases.get(1));
- assertEquals(cAlias, sortedAliases.get(2));
+ assertEquals(compartment, sortedSpecies.get(0));
+ assertEquals(species, sortedSpecies.get(1));
+ assertEquals(complex, sortedSpecies.get(2));
} catch (Exception e) {
e.printStackTrace();
@@ -488,10 +488,10 @@ public class ModelFullIndexedTest {
model.addElement(compartment);
- assertEquals(1, model.getAliases().size());
+ assertEquals(1, model.getElements().size());
- model.removeAlias(compartment);
- assertEquals(0, model.getAliases().size());
+ model.removeElement(compartment);
+ assertEquals(0, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -500,28 +500,28 @@ public class ModelFullIndexedTest {
}
@Test
- public void testRemoveComplexAlias() {
+ public void testRemoveComplex() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
model.addElement(new Compartment("default"));
- Complex parentAlias = new Complex("a");
+ Complex parentComplex = new Complex("a");
- Complex alias = new Complex("b");
- alias.setParent(parentAlias);
- alias.setElementId("1");
+ Complex childComplex = new Complex("b");
+ childComplex.setParent(parentComplex);
+ childComplex.setElementId("1");
- alias.setCompartmentAlias(new Compartment("comp_alias"));
- alias.setComplexAlias(new Complex("d"));
+ childComplex.setCompartment(new Compartment("comp_id"));
+ childComplex.setComplex(new Complex("d"));
- model.addElement(alias);
+ model.addElement(childComplex);
- assertEquals(2, model.getAliases().size());
+ assertEquals(2, model.getElements().size());
- alias.setComplexAlias(new Complex("xxx"));
+ childComplex.setComplex(new Complex("xxx"));
- model.removeAlias(alias);
- assertEquals(1, model.getAliases().size());
+ model.removeElement(childComplex);
+ assertEquals(1, model.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -530,14 +530,14 @@ public class ModelFullIndexedTest {
}
@Test
- public void testRemoveInvalidAlias2() {
+ public void testRemoveInvalidElement2() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Element alias = new GenericProtein("id");
- alias.setParent(Mockito.mock(Element.class));
+ Element protein = new GenericProtein("id");
+ protein.setParent(Mockito.mock(Element.class));
- model.removeAlias(alias);
+ model.removeElement(protein);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -669,7 +669,7 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addAliasGroup(null);
+ model.addElementGroup(null);
model.addBlockDiagream(null);
} catch (Exception e) {
@@ -831,7 +831,7 @@ public class ModelFullIndexedTest {
Double height = 13.0;
String heightStr = "13.0";
int heightInt = 13;
- Set<Element> aliases = new HashSet<>();
+ Set<Element> elements = new HashSet<>();
List<Layout> layouts = new ArrayList<>();
int zoomLevels = 98;
int tileSize = 1024;
@@ -866,8 +866,8 @@ public class ModelFullIndexedTest {
model.setMapVersion(mapVersion);
assertEquals(mapVersion, model.getMapVersion());
- model.setAliases(aliases);
- assertEquals(aliases, model.getAliases());
+ model.setElements(elements);
+ assertEquals(elements, model.getElements());
model.setLayouts(layouts);
assertEquals(layouts, model.getLayouts());
model.setZoomLevels(zoomLevels);
@@ -903,8 +903,8 @@ public class ModelFullIndexedTest {
Reaction reaction = new Reaction();
reaction.setIdReaction(reactionId);
model.addReaction(reaction);
- Species alias = new GenericProtein("2");
- model.addElement(alias);
+ Species protein = new GenericProtein("2");
+ model.addElement(protein);
Collection<AnnotatedObject> obj = model.getAnnotatedObjects();
assertEquals(2, obj.size());
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
index 39759fa416..daeeda9fcc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
@@ -86,9 +86,9 @@ public class ModelSubmodelConnectionComparatorTest {
model.setNotes("Some description");
- Species alias = new GenericProtein("a_id");
- alias.setName("ad");
- model.addElement(alias);
+ Species species = new GenericProtein("a_id");
+ species.setName("ad");
+ model.addElement(species);
model.addElement(new Compartment("default"));
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
index 2325cd8ab9..93808c4c64 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
@@ -21,26 +21,26 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class ModelTest {
- Logger logger = Logger.getLogger(ModelTest.class);
+ Logger logger = Logger.getLogger(ModelTest.class);
- private Species alias;
+ private Species species;
- private Complex cAlias;
- private Model model;
+ private Complex complex;
+ private Model model;
@Before
public void setUp() throws Exception {
model = new ModelFullIndexed(null);
- alias = new GenericProtein("sa1");
+ species = new GenericProtein("sa1");
- cAlias = new Complex("sa2");
+ complex = new Complex("sa2");
}
@@ -49,13 +49,13 @@ public class ModelTest {
}
@Test
- public void testAddAlias() {
+ public void testAddElement() {
try {
- model.addElement(alias);
- Element sAlias = model.getElementByElementId(alias.getElementId());
- assertNotNull(sAlias);
- sAlias = model.getElementByElementId(alias.getElementId() + "blbla");
- assertNull(sAlias);
+ model.addElement(species);
+ Element element = model.getElementByElementId(species.getElementId());
+ assertNotNull(element);
+ element = model.getElementByElementId(species.getElementId() + "blbla");
+ assertNull(element);
} catch (Exception e) {
e.printStackTrace();
@@ -64,25 +64,25 @@ public class ModelTest {
}
@Test
- public void testGetAliasList() {
+ public void testGetElements() {
try {
- Set<Element> aliases = model.getAliases();
- assertEquals(0, aliases.size());
- model.addElement(alias);
- assertEquals(1, aliases.size());
+ Set<Element> elements = model.getElements();
+ assertEquals(0, elements.size());
+ model.addElement(species);
+ assertEquals(1, elements.size());
- Element sAlias = model.getElementByElementId(alias.getElementId());
- assertNotNull(sAlias);
- sAlias = model.getElementByElementId(alias.getElementId() + "blbla");
- assertNull(sAlias);
+ Element element = model.getElementByElementId(species.getElementId());
+ assertNotNull(element);
+ element = model.getElementByElementId(species.getElementId() + "blbla");
+ assertNull(element);
- sAlias = model.getElementByElementId(cAlias.getElementId());
- assertNull(sAlias);
+ element = model.getElementByElementId(complex.getElementId());
+ assertNull(element);
- model.addElement(cAlias);
- assertEquals(2, aliases.size());
- sAlias = model.getElementByElementId(cAlias.getElementId());
- assertNotNull(sAlias);
+ model.addElement(complex);
+ assertEquals(2, elements.size());
+ element = model.getElementByElementId(complex.getElementId());
+ assertNotNull(element);
} catch (Exception e) {
e.printStackTrace();
@@ -153,28 +153,28 @@ public class ModelTest {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- Species proteinAlias = new GenericProtein("sa1");
- proteinAlias.setName("s1");
- model.addElement(proteinAlias);
+ Species protein = new GenericProtein("sa1");
+ protein.setName("s1");
+ model.addElement(protein);
- Species proteinAlias2 = new GenericProtein("sa2");
- proteinAlias2.setName("s1");
- model.addElement(proteinAlias2);
+ Species protein2 = new GenericProtein("sa2");
+ protein2.setName("s1");
+ model.addElement(protein2);
- Species proteinAlias3 = new GenericProtein("sa3");
- proteinAlias3.setName("s1");
- model.addElement(proteinAlias3);
+ Species protein3 = new GenericProtein("sa3");
+ protein3.setName("s1");
+ model.addElement(protein3);
- Species proteinAlias4 = new GenericProtein("sa4");
- proteinAlias4.setName("s5");
- proteinAlias4.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
- model.addElement(proteinAlias4);
+ Species protein4 = new GenericProtein("sa4");
+ protein4.setName("s5");
+ protein4.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
+ model.addElement(protein4);
- Compartment compartmentAlias = new Compartment("cca");
- compartmentAlias.setName("c1");
- compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12"));
+ Compartment compartment = new Compartment("cca");
+ compartment.setName("c1");
+ compartment.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12"));
- model.addElement(compartmentAlias);
+ model.addElement(compartment);
return model;
}
@@ -184,40 +184,40 @@ public class ModelTest {
try {
Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("2");
- alias.setWidth(100);
- alias.setHeight(100);
- model.addElement(alias);
-
- alias = new GenericProtein("3");
- alias.setWidth(10);
- alias.setHeight(10);
- model.addElement(alias);
-
- alias = new GenericProtein("4");
- alias.setWidth(200);
- alias.setHeight(100);
- model.addElement(alias);
-
- Compartment cAlias = new Compartment("5");
- cAlias.setWidth(10);
- cAlias.setHeight(20);
- model.addElement(cAlias);
-
- cAlias = new Compartment("6");
- cAlias.setWidth(100);
- cAlias.setHeight(200);
- model.addElement(cAlias);
-
- cAlias = new Compartment("7");
- cAlias.setWidth(20);
- cAlias.setHeight(30);
- model.addElement(cAlias);
-
- List<Element> sortedAliases = model.getAliasesSortedBySize();
- if (sortedAliases.size() > 0) {
- double last = (sortedAliases.get(0)).getHeight() * (sortedAliases.get(0)).getWidth();
- for (Element a : sortedAliases) {
+ Species species = new GenericProtein("2");
+ species.setWidth(100);
+ species.setHeight(100);
+ model.addElement(species);
+
+ species = new GenericProtein("3");
+ species.setWidth(10);
+ species.setHeight(10);
+ model.addElement(species);
+
+ species = new GenericProtein("4");
+ species.setWidth(200);
+ species.setHeight(100);
+ model.addElement(species);
+
+ Compartment compartment = new Compartment("5");
+ compartment.setWidth(10);
+ compartment.setHeight(20);
+ model.addElement(compartment);
+
+ compartment = new Compartment("6");
+ compartment.setWidth(100);
+ compartment.setHeight(200);
+ model.addElement(compartment);
+
+ compartment = new Compartment("7");
+ compartment.setWidth(20);
+ compartment.setHeight(30);
+ model.addElement(compartment);
+
+ List<Element> sortedElements = model.getElementsSortedBySize();
+ if (sortedElements.size() > 0) {
+ double last = (sortedElements.get(0)).getHeight() * (sortedElements.get(0)).getWidth();
+ for (Element a : sortedElements) {
assertTrue(last >= a.getHeight() * a.getWidth());
}
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
index 2351aa6a17..e4598a4f02 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
@@ -33,7 +33,7 @@ public class SubmodelConnectionComparatorTest {
SubmodelConnection connectionA = createConnection();
SubmodelConnection connectionB = createConnection();
- assertEquals(0, comparator.compare(new AliasSubmodelConnection(), new AliasSubmodelConnection()));
+ assertEquals(0, comparator.compare(new ElementSubmodelConnection(), new ElementSubmodelConnection()));
assertEquals(0, comparator.compare(new ModelSubmodelConnection(), new ModelSubmodelConnection()));
assertEquals(0, comparator.compare(connectionA, connectionB));
assertEquals(0, comparator.compare(connectionA, connectionA));
@@ -147,8 +147,8 @@ public class SubmodelConnectionComparatorTest {
@Test
public void testDifferent2() throws Exception {
try {
- AliasSubmodelConnection connectionA = new AliasSubmodelConnection();
- AliasSubmodelConnection connectionB = new AliasSubmodelConnection();
+ ElementSubmodelConnection connectionA = new ElementSubmodelConnection();
+ ElementSubmodelConnection connectionB = new ElementSubmodelConnection();
connectionB.setSubmodel(new ModelFullIndexed(null));
assertTrue(comparator.compare(connectionA, connectionB) != 0);
@@ -165,10 +165,10 @@ public class SubmodelConnectionComparatorTest {
model.setNotes("Some description");
- Species alias = new GenericProtein("a_id");
- alias.setName("ad");
- alias.setElementId("a_id");
- model.addElement(alias);
+ Species protein = new GenericProtein("a_id");
+ protein.setName("ad");
+ protein.setElementId("a_id");
+ model.addElement(protein);
model.addElement(new Compartment("default"));
@@ -180,8 +180,8 @@ public class SubmodelConnectionComparatorTest {
return model;
}
- private AliasSubmodelConnection createConnection() {
- AliasSubmodelConnection result = new AliasSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ private ElementSubmodelConnection createConnection() {
+ ElementSubmodelConnection result = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
result.setName("name A");
return result;
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
index 208cf3e900..080daf0321 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
@@ -74,7 +74,7 @@ public class NodeOperatorComparatorTest {
operator2 = createNodeOperator();
Reactant reactant = (Reactant) operator1.getInputs().get(0);
- reactant.setAlias(new GenericProtein("id666"));
+ reactant.setElement(new GenericProtein("id666"));
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
@@ -82,7 +82,7 @@ public class NodeOperatorComparatorTest {
operator2 = createNodeOperator();
Product product= (Product) operator1.getOutputs().get(0);
- product.setAlias(new GenericProtein("id666"));
+ product.setElement(new GenericProtein("id666"));
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
@@ -90,7 +90,7 @@ public class NodeOperatorComparatorTest {
operator2 = createNodeOperator();
reactant = (Reactant) operator1.getInputs().get(0);
- reactant.getAlias().setName("bla");
+ reactant.getElement().setName("bla");
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
@@ -108,36 +108,36 @@ public class NodeOperatorComparatorTest {
private NodeOperator createNodeOperator() {
AndOperator result = new AndOperator();
- Species alias0 = new GenericProtein("id0");
- alias0.setName("protein a");
- alias0.setX(12.0);
- alias0.setY(1.0);
- alias0.setWidth(2.0);
- alias0.setHeight(3.0);
+ Species protein0 = new GenericProtein("id0");
+ protein0.setName("protein a");
+ protein0.setX(12.0);
+ protein0.setY(1.0);
+ protein0.setWidth(2.0);
+ protein0.setHeight(3.0);
- Product product = new Product(alias0);
+ Product product = new Product(protein0);
result.addOutput(product);
- Species alias1 = new GenericProtein("id1");
- alias1.setName("protein b");
- alias1.setX(120.0);
- alias1.setY(10.0);
- alias1.setWidth(20.0);
- alias1.setHeight(30.0);
+ Species protein1 = new GenericProtein("id1");
+ protein1.setName("protein b");
+ protein1.setX(120.0);
+ protein1.setY(10.0);
+ protein1.setWidth(20.0);
+ protein1.setHeight(30.0);
- Reactant reactant = new Reactant(alias1);
+ Reactant reactant = new Reactant(protein1);
result.addInput(reactant);
- Species alias2 = new Gene("id2");
- alias2.setName("gene b");
- alias2.setX(320.0);
- alias2.setY(30.0);
- alias2.setWidth(30.0);
- alias2.setHeight(40.0);
+ Species protein2 = new Gene("id2");
+ protein2.setName("gene b");
+ protein2.setX(320.0);
+ protein2.setY(30.0);
+ protein2.setWidth(30.0);
+ protein2.setHeight(40.0);
- Modifier modifier = new Modifier(alias2);
+ Modifier modifier = new Modifier(protein2);
result.addInput(modifier);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index db8a868e06..fbd1794bde 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -194,7 +194,7 @@ public class ReactionComparatorTest {
reaction1 = createReaction();
reaction2 = createReaction();
- reaction1.getModifiers().get(0).getAlias().setElementId("dfshkj");
+ reaction1.getModifiers().get(0).getElement().setElementId("dfshkj");
assertTrue(comparator.compare(reaction1, reaction2) != 0);
assertTrue(comparator.compare(reaction2, reaction1) != 0);
@@ -208,7 +208,7 @@ public class ReactionComparatorTest {
reaction1 = createReaction();
reaction2 = createReaction();
- reaction1.getReactants().get(0).getAlias().setElementId("dfshkj");
+ reaction1.getReactants().get(0).getElement().setElementId("dfshkj");
assertTrue(comparator.compare(reaction1, reaction2) != 0);
assertTrue(comparator.compare(reaction2, reaction1) != 0);
@@ -222,7 +222,7 @@ public class ReactionComparatorTest {
reaction1 = createReaction();
reaction2 = createReaction();
- reaction1.getProducts().get(0).getAlias().setElementId("dfshkj");
+ reaction1.getProducts().get(0).getElement().setElementId("dfshkj");
assertTrue(comparator.compare(reaction1, reaction2) != 0);
assertTrue(comparator.compare(reaction2, reaction1) != 0);
@@ -248,21 +248,21 @@ public class ReactionComparatorTest {
private Reaction createReaction() {
Reaction reaction = new Reaction();
- Species alias = new GenericProtein("id1");
- alias.setName("ASD");
- Reactant reactant = new Reactant(alias);
+ Species protein = new GenericProtein("id1");
+ protein.setName("ASD");
+ Reactant reactant = new Reactant(protein);
- Species alias2 = new GenericProtein("id2");
- alias2.setName("ASD2");
- Reactant reactant2 = new Reactant(alias2);
+ Species protein2 = new GenericProtein("id2");
+ protein2.setName("ASD2");
+ Reactant reactant2 = new Reactant(protein2);
- Species moelculeAlias = new SimpleMolecule("id3");
- moelculeAlias.setName("mol");
- Product product = new Product(moelculeAlias);
+ Species simpleMolecule = new SimpleMolecule("id3");
+ simpleMolecule.setName("mol");
+ Product product = new Product(simpleMolecule);
- Species unknownAlias = new Unknown("id4");
- unknownAlias.setName("unk");
- Modifier modifier = new Catalysis(unknownAlias);
+ Species unknown = new Unknown("id4");
+ unknown.setName("unk");
+ Modifier modifier = new Catalysis(unknown);
AndOperator operator = new AndOperator();
operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
index c317a22021..5328d0a7ea 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
@@ -73,14 +73,14 @@ public class ReactionNodeComparatorTest {
operator1 = createNodeOperator();
operator2 = createNodeOperator();
- operator1.setAlias(new GenericProtein("new_id"));
+ operator1.setElement(new GenericProtein("new_id"));
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
operator1 = createNodeOperator();
operator2 = createNodeOperator();
- operator1.getAlias().setName("bla");
+ operator1.getElement().setName("bla");
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
@@ -94,14 +94,14 @@ public class ReactionNodeComparatorTest {
private ReactionNode createNodeOperator() {
- Species alias2 = new Gene("id_1");
- alias2.setName("gene b");
- alias2.setX(320.0);
- alias2.setY(30.0);
- alias2.setWidth(30.0);
- alias2.setHeight(40.0);
+ Species species = new Gene("id_1");
+ species.setName("gene b");
+ species.setX(320.0);
+ species.setY(30.0);
+ species.setWidth(30.0);
+ species.setHeight(40.0);
- Modifier modifier = new Modifier(alias2);
+ Modifier modifier = new Modifier(species);
PolylineData pd = new PolylineData();
pd.addPoint(new Point2D.Double(1, 2));
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index 12a353ab6b..94cd14d33a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -39,11 +39,11 @@ public class ReactionTest extends ModelTestFunctions {
Logger logger = Logger.getLogger(ReactantTest.class);
- private Species alias;
+ private Species species;
@Before
public void setUp() throws Exception {
- alias = new GenericProtein("sa1");
+ species = new GenericProtein("sa1");
}
@After
@@ -54,10 +54,10 @@ public class ReactionTest extends ModelTestFunctions {
public void testContainsElement() {
try {
Reaction reaction = new Reaction();
- assertFalse(reaction.containsElement(alias));
- Modifier modifier = new Catalysis(alias);
+ assertFalse(reaction.containsElement(species));
+ Modifier modifier = new Catalysis(species);
reaction.addModifier(modifier);
- assertTrue(reaction.containsElement(alias));
+ assertTrue(reaction.containsElement(species));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -235,9 +235,9 @@ public class ReactionTest extends ModelTestFunctions {
assertEquals(0, reaction1.getVisibilityLevel());
Reactant reactant = new Reactant();
- Element alias = new GenericProtein("id_xyz");
- alias.setVisibilityLevel(2);
- reactant.setAlias(alias);
+ Element protein = new GenericProtein("id_xyz");
+ protein.setVisibilityLevel(2);
+ reactant.setElement(protein);
reaction1.addReactant(reactant);
assertEquals(2, reaction1.getVisibilityLevel());
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
index 295600e2ca..25f93cb5c3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
@@ -32,10 +32,10 @@ public class ComplexComparatorTest {
@Test
public void testEquals() {
try {
- Complex alias1 = createComplexAlias();
- Complex alias2 = createComplexAlias();
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
- assertEquals(0, comparator.compare(alias1, alias2));
+ assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(null, null));
@@ -45,7 +45,7 @@ public class ComplexComparatorTest {
}
}
- private Complex createComplexAlias() {
+ private Complex createComplex2() {
Complex result = new Complex();
result.setName("complex");
@@ -58,9 +58,9 @@ public class ComplexComparatorTest {
result.setColor(Color.BLUE);
result.setVisibilityLevel(14);
- Species alias = new GenericProtein("S");
- alias.setName("a");
- result.addAlias(alias);
+ Species protein = new GenericProtein("S");
+ protein.setName("a");
+ result.addSpecies(protein);
return result;
}
@@ -68,52 +68,52 @@ public class ComplexComparatorTest {
@Test
public void testDifferent() {
try {
- Complex alias1 = createComplexAlias();
- Complex alias2 = createComplexAlias();
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
- assertTrue(comparator.compare(alias1, null) != 0);
- assertTrue(comparator.compare(null, alias1) != 0);
+ assertTrue(comparator.compare(complex1, null) != 0);
+ assertTrue(comparator.compare(null, complex1) != 0);
- alias1 = createComplexAlias();
- alias2 = createComplexAlias();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- alias1.setElementId("tmp");
+ complex1.setElementId("tmp");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- alias1 = createComplexAlias();
- alias2 = createComplexAlias();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- alias1.addAlias(new GenericProtein("id"));
+ complex1.addSpecies(new GenericProtein("id"));
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- alias1 = createComplexAlias();
- alias2 = createComplexAlias();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- alias1.getAliases().iterator().next().setElementId("bnu");
+ complex1.getElements().iterator().next().setElementId("bnu");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- alias1 = createComplexAlias();
- alias2 = createComplexAlias();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- Species speciesAlias = (Species) alias1.getAliases().iterator().next();
- speciesAlias.setName("new namne");
+ Species species = (Species) complex1.getElements().iterator().next();
+ species.setName("new namne");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- alias1 = createComplexAlias();
- alias2 = createComplexAlias();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- alias1.setName("new namne");
+ complex1.setName("new namne");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -124,18 +124,18 @@ public class ComplexComparatorTest {
@Test
public void testInvalid() {
try {
- Complex alias1 = createComplexAlias();
- Complex alias2 = createComplexAlias();
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
- GenericProtein alias = new GenericProtein("1");
- alias1.getAliases().add(alias);
- alias = new GenericProtein("1");
- alias1.getAliases().add(alias);
+ GenericProtein protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
- alias2.getAliases().add(new GenericProtein("b"));
- alias2.getAliases().add(new GenericProtein("a"));
+ complex2.getElements().add(new GenericProtein("b"));
+ complex2.getElements().add(new GenericProtein("a"));
- comparator.compare(alias1, alias2);
+ comparator.compare(complex1, complex2);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -163,18 +163,18 @@ public class ComplexComparatorTest {
@Test
public void testInvalid2() {
try {
- Complex alias1 = createComplexAlias();
- Complex alias2 = createComplexAlias();
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
- Species alias = new GenericProtein("1");
- alias1.getAliases().add(alias);
- alias = new GenericProtein("1");
- alias1.getAliases().add(alias);
+ Species protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
- alias2.getAliases().add(new GenericProtein("A"));
- alias2.getAliases().add(new GenericProtein("B"));
+ complex2.getElements().add(new GenericProtein("A"));
+ complex2.getElements().add(new GenericProtein("B"));
- comparator.compare(alias2, alias1);
+ comparator.compare(complex2, complex1);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -195,8 +195,8 @@ public class ComplexComparatorTest {
assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(complex2, complex1));
- complex2.addAlias(new GenericProtein("test"));
- complex1.addAlias(new GenericProtein("test"));
+ complex2.addSpecies(new GenericProtein("test"));
+ complex1.addSpecies(new GenericProtein("test"));
assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(complex2, complex1));
} catch (Exception e) {
@@ -213,8 +213,8 @@ public class ComplexComparatorTest {
Species mock = Mockito.mock(Species.class);
when(mock.getElementId()).thenReturn("id");
- complex1.addAlias(mock);
- complex2.addAlias(mock);
+ complex1.addSpecies(mock);
+ complex2.addSpecies(mock);
comparator.compare(complex1, complex2);
comparator.compare(complex2, complex1);
fail("Exception expected");
@@ -233,13 +233,13 @@ public class ComplexComparatorTest {
Complex complex2 = createComplex();
GenericProtein c = new GenericProtein("test");
c.setName("a");
- complex2.addAlias(c);
+ complex2.addSpecies(c);
c.setName("");
- complex1.addAlias(new GenericProtein("test"));
+ complex1.addSpecies(new GenericProtein("test"));
Species mock = Mockito.mock(Species.class);
when(mock.getElementId()).thenReturn("id");
- complex1.addAlias(mock);
- complex2.addAlias(mock);
+ complex1.addSpecies(mock);
+ complex2.addSpecies(mock);
comparator.compare(complex2, complex1);
fail("Exception expected");
} catch (NotImplementedException e) {
@@ -261,13 +261,13 @@ public class ComplexComparatorTest {
complex1 = createComplex();
complex2 = createComplex();
- complex1.getAliases().iterator().next().setNotes("bla");
+ complex1.getElements().iterator().next().setNotes("bla");
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
complex1 = createComplex();
complex2 = createComplex();
- complex1.getAliases().clear();
+ complex1.getElements().clear();
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -279,8 +279,8 @@ public class ComplexComparatorTest {
complex1 = createComplex();
complex2 = createComplex();
- Complex child = (Complex) complex1.getAliases().iterator().next();
- child.getAliases().iterator().next().setNotes("grand child notes");
+ Complex child = (Complex) complex1.getElements().iterator().next();
+ child.getElements().iterator().next().setNotes("grand child notes");
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -288,7 +288,7 @@ public class ComplexComparatorTest {
complex2 = createComplex();
Protein prot = new GenericProtein();
prot.setElementId("test");
- complex1.addAlias(prot);
+ complex1.addSpecies(prot);
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -313,10 +313,10 @@ public class ComplexComparatorTest {
Complex complex2 = createComplex();
GenericProtein prot = new GenericProtein();
prot.setElementId("test");
- complex1.addAlias(prot);
+ complex1.addSpecies(prot);
prot = new GenericProtein();
prot.setElementId("test2");
- complex2.addAlias(prot);
+ complex2.addSpecies(prot);
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -333,14 +333,14 @@ public class ComplexComparatorTest {
Complex complex2 = createComplex();
GenericProtein c = new GenericProtein("test");
c.setName("a");
- complex2.addAlias(c);
- complex2.addAlias(new GenericProtein("test"));
+ complex2.addSpecies(c);
+ complex2.addSpecies(new GenericProtein("test"));
c.setName("");
- complex1.addAlias(new GenericProtein("test"));
+ complex1.addSpecies(new GenericProtein("test"));
GenericProtein d = new GenericProtein("test2");
d.setName("a");
- complex1.addAlias(d);
+ complex1.addSpecies(d);
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -357,8 +357,8 @@ public class ComplexComparatorTest {
Complex complex2 = createComplex();
GenericProtein comp = new GenericProtein("test");
comp.setFullName("X");
- complex1.addAlias(comp);
- complex2.addAlias(new GenericProtein("test"));
+ complex1.addSpecies(comp);
+ complex2.addSpecies(new GenericProtein("test"));
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -375,13 +375,13 @@ public class ComplexComparatorTest {
result.setHomodimer(3);
Complex child = new Complex();
- result.addAlias(child);
+ result.addSpecies(child);
child.setCharge(12);
child.setName("buu");
child.setNotes("hey, hi, hello");
Complex grandChild = new Complex();
- child.addAlias(grandChild);
+ child.addSpecies(grandChild);
child.setCharge(123);
child.setName("buus");
child.setNotes("hey, hi, hello !!");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
index 34a28408e0..3990f8888e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
@@ -36,7 +36,7 @@ public class ComplexTest {
public void testConstructor() {
try {
Complex complex = new Complex();
- complex.addAlias(new GenericProtein());
+ complex.addSpecies(new GenericProtein());
Complex copy = new Complex(complex);
assertNotNull(copy);
@@ -47,17 +47,17 @@ public class ComplexTest {
}
@Test
- public void testAddAlias() {
+ public void testAddElement() {
try {
Complex complex = new Complex();
- Species alias = new GenericProtein("id1");
- complex.addAlias(alias);
- assertEquals(1, complex.getAllChildrenAliases().size());
- complex.addAlias(alias);
- assertEquals(1, complex.getAllChildrenAliases().size());
- Species alias2 = new GenericProtein("s");
- complex.addAlias(alias2);
- assertEquals(2, complex.getAllChildrenAliases().size());
+ Species species = new GenericProtein("id1");
+ complex.addSpecies(species);
+ assertEquals(1, complex.getAllChildren().size());
+ complex.addSpecies(species);
+ assertEquals(1, complex.getAllChildren().size());
+ Species protein2 = new GenericProtein("s");
+ complex.addSpecies(protein2);
+ assertEquals(2, complex.getAllChildren().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -69,15 +69,15 @@ public class ComplexTest {
try {
Complex complex = new Complex();
- complex.addAlias(new GenericProtein("1"));
+ complex.addSpecies(new GenericProtein("1"));
Complex complex2 = new Complex("c3");
- complex2.addAlias(new GenericProtein("2"));
- complex2.addAlias(new GenericProtein("4"));
+ complex2.addSpecies(new GenericProtein("2"));
+ complex2.addSpecies(new GenericProtein("4"));
- complex.addAlias(complex2);
+ complex.addSpecies(complex2);
- assertEquals(4, complex.getAllChildrenAliases().size());
- assertEquals(2, complex.getAliases().size());
+ assertEquals(4, complex.getAllChildren().size());
+ assertEquals(2, complex.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -86,20 +86,20 @@ public class ComplexTest {
}
@Test
- public void testRemoveAlias() {
+ public void testRemoveElement() {
try {
Complex complex = new Complex();
- Species alias = new GenericProtein("1");
- complex.addAlias(alias);
- complex.addAlias(new GenericProtein("2"));
- complex.addAlias(new GenericProtein("4"));
+ Species protein = new GenericProtein("1");
+ complex.addSpecies(protein);
+ complex.addSpecies(new GenericProtein("2"));
+ complex.addSpecies(new GenericProtein("4"));
- assertEquals(3, complex.getAliases().size());
- complex.removeAlias(alias);
- assertEquals(2, complex.getAliases().size());
- complex.removeAlias(alias);
- assertEquals(2, complex.getAliases().size());
+ assertEquals(3, complex.getElements().size());
+ complex.removeElement(protein);
+ assertEquals(2, complex.getElements().size());
+ complex.removeElement(protein);
+ assertEquals(2, complex.getElements().size());
} catch (Exception e) {
e.printStackTrace();
@@ -134,11 +134,11 @@ public class ComplexTest {
public void testGetAllSimpleChildren() {
try {
Complex child = new Complex();
- child.addAlias(new GenericProtein("id2"));
+ child.addSpecies(new GenericProtein("id2"));
Complex original = new Complex();
- original.addAlias(child);
- original.addAlias(new Complex());
- original.addAlias(new GenericProtein("id"));
+ original.addSpecies(child);
+ original.addSpecies(new Complex());
+ original.addSpecies(new GenericProtein("id"));
assertEquals(2, original.getAllSimpleChildren().size());
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
index 43cbdec5fc..7a6bdc24d0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
@@ -18,7 +18,7 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
@@ -99,21 +99,21 @@ public class ElementComparatorTest {
@Test
public void testCompareSubmodel() throws Exception {
try {
- Element alias1 = createAlias();
- Element alias2 = createAlias();
- assertEquals(0, comparator.compare(alias1, alias2));
+ Element element1 = createElement();
+ Element element2 = createElement();
+ assertEquals(0, comparator.compare(element1, element2));
- alias1.setSubmodel(null);
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ element1.setSubmodel(null);
+ assertTrue(comparator.compare(element1, element2) != 0);
+ assertTrue(comparator.compare(element2, element1) != 0);
- alias1 = createAlias();
- alias2 = createAlias();
+ element1 = createElement();
+ element2 = createElement();
- alias1.getSubmodel().setName("Na");
+ element1.getSubmodel().setName("Na");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(element1, element2) != 0);
+ assertTrue(comparator.compare(element2, element1) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -121,9 +121,9 @@ public class ElementComparatorTest {
}
}
- private Element createAlias() {
+ private Element createElement() {
Element result = new GenericProtein("id2");
- AliasSubmodelConnection submodel = new AliasSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ ElementSubmodelConnection submodel = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
result.setSubmodel(submodel);
return result;
}
@@ -136,9 +136,9 @@ public class ElementComparatorTest {
protein.setName("ad");
model.addElement(protein);
- Protein alias = new GenericProtein("a_id");
- alias.setName("ad");
- model.addElement(alias);
+ Protein protein2 = new GenericProtein("a_id");
+ protein2.setName("ad");
+ model.addElement(protein2);
model.addElement(new Compartment("default"));
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
index 32260105d0..78ee89782a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
@@ -26,7 +26,7 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -45,71 +45,66 @@ public class ElementTest extends ModelTestFunctions {
@Test
public void testDistance1() {
- Species alias;
- alias = new GenericProtein();
- alias.setWidth(10);
- alias.setHeight(20);
- alias.setX(100.0);
- alias.setY(200.0);
- double distance = alias.getDistanceFromPoint(alias.getCenter());
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(species.getCenter());
assertEquals(0, distance, EPSILON);
}
@Test
public void testDistance2() {
- Species alias;
- alias = new GenericProtein();
- alias.setWidth(10);
- alias.setHeight(20);
- alias.setX(100.0);
- alias.setY(200.0);
- double distance = alias.getDistanceFromPoint(new Point2D.Double(100, 205));
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(100, 205));
assertEquals(0, distance, EPSILON);
}
@Test
public void testDistance6() {
- Species alias;
- alias = new GenericProtein();
- alias.setWidth(10);
- alias.setHeight(20);
- alias.setX(100.0);
- alias.setY(200.0);
- double distance = alias.getDistanceFromPoint(new Point2D.Double(105, 95));
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(105, 95));
assertEquals(105, distance, EPSILON);
}
@Test
public void testDistance3() {
- Species alias;
- alias = new GenericProtein();
- alias.setWidth(10);
- alias.setHeight(20);
- alias.setX(100.0);
- alias.setY(200.0);
- double distance = alias.getDistanceFromPoint(new Point2D.Double(50, 205));
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(50, 205));
assertEquals(50, distance, EPSILON);
}
@Test
public void testDistance4() {
- Species alias;
- alias = new GenericProtein();
- alias.setWidth(10);
- alias.setHeight(20);
- alias.setX(100.0);
- alias.setY(200.0);
- double distance = alias.getDistanceFromPoint(new Point2D.Double(120, 230));
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(120, 230));
assertEquals(Math.sqrt(200), distance, EPSILON);
}
@Test
public void testConstructor() {
try {
- GenericProtein alias = new GenericProtein();
- alias.addSearchIndex(new SearchIndex());
- alias.setSubmodel(new AliasSubmodelConnection());
- Element copy = new GenericProtein(alias);
+ GenericProtein protein = new GenericProtein();
+ protein.addSearchIndex(new SearchIndex());
+ protein.setSubmodel(new ElementSubmodelConnection());
+ Element copy = new GenericProtein(protein);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -120,10 +115,10 @@ public class ElementTest extends ModelTestFunctions {
@Test
public void testIncreaseBorder() {
try {
- Species alias = new GenericProtein();
- assertEquals(0.0, alias.getSize(), Configuration.EPSILON);
- alias.increaseBorder(2);
- assertEquals(16.0, alias.getSize(), Configuration.EPSILON);
+ Species protein = new GenericProtein();
+ assertEquals(0.0, protein.getSize(), Configuration.EPSILON);
+ protein.increaseBorder(2);
+ assertEquals(16.0, protein.getSize(), Configuration.EPSILON);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -148,7 +143,7 @@ public class ElementTest extends ModelTestFunctions {
Double height = 4.0;
ModelData modelData = new ModelData();
Set<MiriamData> miriamData = new HashSet<>();
- Compartment compartmentAlias = new Compartment("idd");
+ Compartment compartment = new Compartment("idd");
int id = 72;
int transparencyLevel = 2;
Model model = new ModelFullIndexed(modelData);
@@ -157,7 +152,7 @@ public class ElementTest extends ModelTestFunctions {
element.setMiriamData(miriamData);
assertEquals(miriamData, element.getMiriamData());
-
+
element.setX(xStr);
assertEquals(x, element.getX(), Configuration.EPSILON);
element.setX(nullDouble);
@@ -207,8 +202,8 @@ public class ElementTest extends ModelTestFunctions {
} catch (InvalidArgumentException e) {
}
- element.setCompartmentAlias(compartmentAlias);
- assertEquals(compartmentAlias, element.getCompartmentAlias());
+ element.setCompartment(compartment);
+ assertEquals(compartment, element.getCompartment());
element.setId(id);
assertEquals(id, element.getId());
element.setTransparencyLevel(transparencyLevel);
@@ -244,60 +239,60 @@ public class ElementTest extends ModelTestFunctions {
}
@Test
- public void testContainsAlias() {
+ public void testContainsElement() {
try {
- Species alias = new GenericProtein();
- alias.setWidth(100);
- alias.setHeight(100);
- Species alias2 = new GenericProtein();
- alias2.setX(-2);
- alias2.setY(-2);
- alias2.setWidth(100);
- alias2.setHeight(100);
-
- assertTrue(alias.contains(alias2));
- alias2.setX(2);
- alias2.setY(2);
- assertTrue(alias.contains(alias2));
- alias2.setX(-2);
- alias2.setY(2);
- assertTrue(alias.contains(alias2));
- alias2.setX(2);
- alias2.setY(-2);
- assertTrue(alias.contains(alias2));
-
- alias2.setX(-2);
- alias2.setY(-2);
- alias2.setWidth(200);
- alias2.setHeight(200);
- assertFalse(alias.contains(alias2));
-
- Compartment alias3 = new Compartment("idd");
- alias3.setX(2);
- alias3.setY(2);
- alias3.setWidth(10);
- alias3.setHeight(100);
- assertFalse(alias.contains(alias3));
-
- alias3.setWidth(100);
- alias3.setHeight(10);
- assertFalse(alias.contains(alias3));
-
- alias3.setWidth(10);
- alias3.setHeight(10);
- assertTrue(alias.contains(alias3));
-
- alias3.setWidth(100);
- alias3.setHeight(100);
- alias3.setX(-2);
- alias3.setY(2);
- assertFalse(alias.contains(alias3));
- alias3.setX(2);
- alias3.setY(-2);
- assertFalse(alias.contains(alias3));
- alias3.setX(-2);
- alias3.setY(-2);
- assertFalse(alias.contains(alias3));
+ Species element = new GenericProtein();
+ element.setWidth(100);
+ element.setHeight(100);
+ Species element2 = new GenericProtein();
+ element2.setX(-2);
+ element2.setY(-2);
+ element2.setWidth(100);
+ element2.setHeight(100);
+
+ assertTrue(element.contains(element2));
+ element2.setX(2);
+ element2.setY(2);
+ assertTrue(element.contains(element2));
+ element2.setX(-2);
+ element2.setY(2);
+ assertTrue(element.contains(element2));
+ element2.setX(2);
+ element2.setY(-2);
+ assertTrue(element.contains(element2));
+
+ element2.setX(-2);
+ element2.setY(-2);
+ element2.setWidth(200);
+ element2.setHeight(200);
+ assertFalse(element.contains(element2));
+
+ Compartment compartment = new Compartment("idd");
+ compartment.setX(2);
+ compartment.setY(2);
+ compartment.setWidth(10);
+ compartment.setHeight(100);
+ assertFalse(element.contains(compartment));
+
+ compartment.setWidth(100);
+ compartment.setHeight(10);
+ assertFalse(element.contains(compartment));
+
+ compartment.setWidth(10);
+ compartment.setHeight(10);
+ assertTrue(element.contains(compartment));
+
+ compartment.setWidth(100);
+ compartment.setHeight(100);
+ compartment.setX(-2);
+ compartment.setY(2);
+ assertFalse(element.contains(compartment));
+ compartment.setX(2);
+ compartment.setY(-2);
+ assertFalse(element.contains(compartment));
+ compartment.setX(-2);
+ compartment.setY(-2);
+ assertFalse(element.contains(compartment));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -307,19 +302,19 @@ public class ElementTest extends ModelTestFunctions {
@Test
public void testContainsLayerText() {
try {
- Species alias = new GenericProtein();
- alias.setWidth(100);
- alias.setHeight(100);
- LayerText alias2 = new LayerText();
- alias2.setX(2.0);
- alias2.setY(2.0);
- alias2.setWidth(100.0);
- alias2.setHeight(100.0);
-
- assertFalse(alias.contains(alias2));
- alias2.setWidth(10.0);
- alias2.setHeight(10.0);
- assertTrue(alias.contains(alias2));
+ Species protein = new GenericProtein();
+ protein.setWidth(100);
+ protein.setHeight(100);
+ LayerText layerText = new LayerText();
+ layerText.setX(2.0);
+ layerText.setY(2.0);
+ layerText.setWidth(100.0);
+ layerText.setHeight(100.0);
+
+ assertFalse(protein.contains(layerText));
+ layerText.setWidth(10.0);
+ layerText.setHeight(10.0);
+ assertTrue(protein.contains(layerText));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
index acbe0f722f..68c0c063da 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
@@ -32,10 +32,10 @@ public class SpeciesComparatorTest {
@Test
public void testEquals() {
try {
- Species alias1 = createSpeciesAlias();
- Species alias2 = createSpeciesAlias();
+ Species species1 = createSpecies();
+ Species species2 = createSpecies();
- assertEquals(0, comparator.compare(alias1, alias2));
+ assertEquals(0, comparator.compare(species1, species2));
assertEquals(0, comparator.compare(null, null));
@@ -51,8 +51,8 @@ public class SpeciesComparatorTest {
public void testCompareInvalid() {
try {
- Species alias = Mockito.mock(Species.class);
- comparator.compare(alias, alias);
+ Species speciesMock = Mockito.mock(Species.class);
+ comparator.compare(speciesMock, speciesMock);
fail("Exception expected");
} catch (NotImplementedException e) {
@@ -62,7 +62,7 @@ public class SpeciesComparatorTest {
}
}
- private Species createSpeciesAlias() {
+ private Species createSpecies() {
GenericProtein result = new GenericProtein();
result.setName("a");
@@ -74,8 +74,8 @@ public class SpeciesComparatorTest {
result.setFontSize(9.0);
result.setColor(Color.BLUE);
result.setVisibilityLevel(14);
- result.setAliasStateLabel("123");
- result.setAliasStatePrefix("1234");
+ result.setStateLabel("123");
+ result.setStatePrefix("1234");
return result;
}
@@ -83,61 +83,61 @@ public class SpeciesComparatorTest {
@Test
public void testDifferent() throws Exception {
try {
- Species alias1 = createSpeciesAlias();
- Species alias2 = createSpeciesAlias();
+ Species species1 = createSpecies();
+ Species species2 = createSpecies();
- assertTrue(comparator.compare(alias1, null) != 0);
- assertTrue(comparator.compare(null, alias1) != 0);
+ assertTrue(comparator.compare(species1, null) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
- assertTrue(comparator.compare(new Complex(), alias1) != 0);
+ assertTrue(comparator.compare(new Complex(), species1) != 0);
- alias1 = createSpeciesAlias();
- alias2 = createSpeciesAlias();
+ species1 = createSpecies();
+ species2 = createSpecies();
- alias1.setElementId("tmp");
+ species1.setElementId("tmp");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- alias1 = createSpeciesAlias();
- alias2 = createSpeciesAlias();
+ species1 = createSpecies();
+ species2 = createSpecies();
- alias1.setAliasStateLabel("tmp");
+ species1.setStateLabel("tmp");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- alias1 = createSpeciesAlias();
- alias2 = createSpeciesAlias();
+ species1 = createSpecies();
+ species2 = createSpecies();
- alias1.setAliasStatePrefix("tmp");
+ species1.setStatePrefix("tmp");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- alias1 = createSpeciesAlias();
- alias2 = createSpeciesAlias();
+ species1 = createSpecies();
+ species2 = createSpecies();
- alias1.setName("new namne");
+ species1.setName("new namne");
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- alias1 = createSpeciesAlias();
- alias2 = createSpeciesAlias();
+ species1 = createSpecies();
+ species2 = createSpecies();
- alias1.setActivity(true);
+ species1.setActivity(true);
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- alias1 = createSpeciesAlias();
- alias2 = createSpeciesAlias();
+ species1 = createSpecies();
+ species2 = createSpecies();
- alias1.setLineWidth(453.75);
+ species1.setLineWidth(453.75);
- assertTrue(comparator.compare(alias1, alias2) != 0);
- assertTrue(comparator.compare(alias2, alias1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
index a19acb8b2c..2568aed9e8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
@@ -26,14 +26,14 @@ public class SpeciesTest {
@Test
public void testGetter() {
try {
- Species alias = new GenericProtein("id");
+ Species species = new GenericProtein("id");
String state = "as";
Set<ReactionNode> node = new HashSet<>();
- alias.setState(state);
- alias.setNode(node);
+ species.setState(state);
+ species.setNode(node);
- assertEquals(state, alias.getState());
- assertEquals(node, alias.getNode());
+ assertEquals(state, species.getState());
+ assertEquals(node, species.getNode());
} catch (Exception e) {
e.printStackTrace();
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 40d498bf84..5c70f1b4f6 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -564,8 +564,8 @@ public class ModelContructor {
if (species instanceof Species) {
Species speciesAlias = (Species) species;
- speciesAlias.setComplexAlias(complexSpecies);
- complexSpecies.addAlias(speciesAlias);
+ speciesAlias.setComplex(complexSpecies);
+ complexSpecies.addSpecies(speciesAlias);
if (speciesAlias.getParent() == null) {
speciesAlias.setParent(complexSpecies);
@@ -633,12 +633,12 @@ public class ModelContructor {
PolylineData pdsecondpart = pair.getRight();
Reactant reactant = new Reactant();
- reactant.setAlias(data.id2alias.get(interaction.getStart()));
+ reactant.setElement(data.id2alias.get(interaction.getStart()));
reactant.setLine(pdfirstpart);
reaction.addReactant(reactant);
Product product = new Product();
- product.setAlias(data.id2alias.get(interaction.getEnd()));
+ product.setElement(data.id2alias.get(interaction.getEnd()));
product.setLine(pdsecondpart);
reaction.addProduct(product);
@@ -765,7 +765,7 @@ public class ModelContructor {
}
Reactant reac = new Reactant();
- reac.setAlias(data.id2alias.get(id));
+ reac.setElement(data.id2alias.get(id));
reac.setLine(e.getLine());
// if somebody drew the reaction in reverse order (starting from reaction
@@ -797,7 +797,7 @@ public class ModelContructor {
throw new InvalidStateException("This product is invalid");
}
Product pro = new Product();
- pro.setAlias(data.id2alias.get(id));
+ pro.setElement(data.id2alias.get(id));
pro.setLine(e.getLine());
// if somebody drew the reaction in reverse order (starting from reaction
// and going to the product) then reverse the order of points: order should
@@ -963,11 +963,11 @@ public class ModelContructor {
* model where aliases will be modifed
*/
private void putAliasesIntoCompartments(Model model) {
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias.getParent() == null) {
if (alias instanceof Species) {
Compartment selectedAlias = null;
- for (Compartment cAlias : model.getCompartmentsAliases()) {
+ for (Compartment cAlias : model.getCompartments()) {
if (cAlias.cross(alias)) {
if (selectedAlias == null) {
selectedAlias = cAlias;
@@ -994,15 +994,15 @@ public class ModelContructor {
Set<Element> aliasesInReaction = new HashSet<>();
for (Reaction reaction : model.getReactions()) {
for (ReactionNode node : reaction.getReactionNodes()) {
- aliasesInReaction.add(node.getAlias());
+ aliasesInReaction.add(node.getElement());
}
}
List<Element> toRemove = new ArrayList<>();
ElementUtils eu = new ElementUtils();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Complex) {
Complex cAlias = (Complex) alias;
- if (cAlias.getSize() <= EPSILON && cAlias.getAllChildrenAliases().size() == 0) {
+ if (cAlias.getSize() <= EPSILON && cAlias.getAllChildren().size() == 0) {
if (aliasesInReaction.contains(alias)) {
logger.warn(eu.getElementTag(alias) + "Empty element is invalid, but it's a part of reaction.");
} else {
@@ -1013,7 +1013,7 @@ public class ModelContructor {
}
}
for (Element alias : toRemove) {
- model.removeAlias(alias);
+ model.removeElement(alias);
}
}
@@ -1025,7 +1025,7 @@ public class ModelContructor {
* model where complexes are placed
*/
private void assignNamesToComplexes(Model model) {
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Complex) {
if (alias.getName() == null || (alias.getName().isEmpty())) {
for (Layer layer : model.getLayers()) {
@@ -1055,7 +1055,7 @@ public class ModelContructor {
* model where compartments are placed
*/
private void assignNamesToCompartments(Model model) {
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Compartment) {
if (alias.getName() == null || alias.getName().isEmpty()) {
for (Layer layer : model.getLayers()) {
@@ -1100,16 +1100,16 @@ public class ModelContructor {
* model where assignments are fixed.
*/
private void fixCompartmentAliases(Model model) {
- List<Compartment> aliases = model.getCompartmentsAliases();
+ List<Compartment> aliases = model.getCompartments();
// clear all assignments
for (Compartment compartmentAlias : aliases) {
compartmentAlias.getElements().clear();
}
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
// elements inside complexes shouldn't be considered
if (alias instanceof Species) {
- if (((Species) alias).getComplexAlias() != null) {
+ if (((Species) alias).getComplex() != null) {
continue;
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 412b0124d6..b63e8970ef 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -150,11 +150,11 @@ public class ModelToGPML {
if (alias instanceof Complex) {
Complex ca = (Complex) alias;
- if (ca.getAliases().size() == 0) {
+ if (ca.getElements().size() == 0) {
res = (Rectangle2D) ca.getBorder().clone();
} else {
- res = getRectangle(ca.getAliases().get(0));
- for (Element al : ca.getAliases()) {
+ res = getRectangle(ca.getElements().get(0));
+ for (Element al : ca.getElements()) {
Rectangle2D.union(res, getRectangle(al), res);
}
res = new Rectangle2D.Double(
@@ -186,7 +186,7 @@ public class ModelToGPML {
PolylineData startLine = start.getLine();
Point2D ps = startLine.getBeginPoint();
- Rectangle2D rec1 = getRectangle(start.getAlias());
+ Rectangle2D rec1 = getRectangle(start.getElement());
double dis1 = Geo.distance(ps, rec1);
if (dis1 > DIS_FOR_REP) {
@@ -203,7 +203,7 @@ public class ModelToGPML {
PolylineData endLine = end.getLine();
Point2D pe = endLine.getEndPoint();
- Rectangle2D rec2 = getRectangle(end.getAlias());
+ Rectangle2D rec2 = getRectangle(end.getElement());
double dis2 = Geo.distance(pe, rec2);
for (Point2D p2d : endLine.getPoints()) {
@@ -230,7 +230,7 @@ public class ModelToGPML {
PolylineData line = rn.getLine();
Point2D ps = line.getBeginPoint();
Point2D pe = line.getEndPoint();
- Rectangle2D rec = getRectangle(rn.getAlias());
+ Rectangle2D rec = getRectangle(rn.getElement());
if (rn instanceof Reactant || rn instanceof Modifier) {
double dis = Geo.distance(ps, rec);
@@ -294,7 +294,7 @@ public class ModelToGPML {
*/
private String getComparments(Model model) {
StringBuilder comparments = new StringBuilder("");
- for (Compartment ca : model.getCompartmentsAliases()) {
+ for (Compartment ca : model.getCompartments()) {
double x = ca.getCenterX(), y = ca.getCenterY(), h = ca.getHeight(), w = ca.getWidth();
String shape;
@@ -351,7 +351,7 @@ public class ModelToGPML {
if (rn instanceof Reactant) {
for (Point2D p2d : line.getPoints()) {
if (p2d.equals(ps)) {
- interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + rn.getAlias().getElementId() + "\"/>\n");
+ interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + rn.getElement().getElementId() + "\"/>\n");
} else if (p2d.equals(pe)) {
interaction.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
} else {
@@ -364,7 +364,7 @@ public class ModelToGPML {
interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
} else if (p2d.equals(pe)) {
interaction.append(
- " <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + rn.getAlias().getElementId() + "\" ArrowHead=\"mim-conversion\"/>\n");
+ " <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + rn.getElement().getElementId() + "\" ArrowHead=\"mim-conversion\"/>\n");
} else {
interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
}
@@ -372,7 +372,7 @@ public class ModelToGPML {
} else if (rn instanceof Modifier) {
for (Point2D p2d : line.getPoints()) {
if (p2d.equals(ps)) {
- interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + rn.getAlias().getElementId() + "\"/>\n");
+ interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + rn.getElement().getElementId() + "\"/>\n");
} else if (p2d.equals(pe)) {
interaction.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId + "\" ArrowHead=\"mim-catalysis\"/>\n");
} else {
@@ -414,8 +414,8 @@ public class ModelToGPML {
for (Species sa : model.getNotComplexSpeciesList()) {
if (!(sa instanceof Complex)) {
dataNodes.append(" <DataNode TextLabel=\"" + sa.getName() + "\" GraphId=\"" + sa.getElementId() + "\" Type=\"" + getType(sa) + "\"");
- if (sa.getComplexAlias() != null) {
- dataNodes.append(" GroupRef=\"" + sa.getComplexAlias().getElementId() + "\"");
+ if (sa.getComplex() != null) {
+ dataNodes.append(" GroupRef=\"" + sa.getComplex().getElementId() + "\"");
}
dataNodes.append(">\n");
@@ -448,10 +448,10 @@ public class ModelToGPML {
/** Special Case for empty Complexes **/
for (Complex ca : model.getComplexList()) {
- if (ca.getAliases().size() == 0) {
+ if (ca.getElements().size() == 0) {
dataNodes.append(" <DataNode TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\" Type=\"Complex\"");
- if (ca.getComplexAlias() != null) {
- dataNodes.append(" GroupRef=\"" + ca.getComplexAlias().getElementId() + "\"");
+ if (ca.getComplex() != null) {
+ dataNodes.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
}
dataNodes.append(">\n");
@@ -481,10 +481,10 @@ public class ModelToGPML {
StringBuilder groups = new StringBuilder("");
for (Complex ca : model.getComplexList()) {
- if (ca.getAliases().size() > 0) {
+ if (ca.getElements().size() > 0) {
groups.append(" <Group GroupId=\"" + ca.getElementId() + "\" GraphId=\"" + ca.getElementId() + "\"");
- if (ca.getComplexAlias() != null) {
- groups.append(" GroupRef=\"" + ca.getComplexAlias().getElementId() + "\"");
+ if (ca.getComplex() != null) {
+ groups.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
}
groups.append("/>\n");
}
@@ -523,8 +523,8 @@ public class ModelToGPML {
PolylineData line = getPolyline(start, end);
Point2D ps = line.getBeginPoint();
Point2D pe = line.getEndPoint();
- String sid = start.getAlias().getElementId();
- String eid = end.getAlias().getElementId();
+ String sid = start.getElement().getElementId();
+ String eid = end.getElement().getElementId();
for (Point2D p2d : line.getPoints()) {
if (p2d.equals(ps)) {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 5aaa91d06c..e7c8ca2773 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -453,7 +453,7 @@ public class GPMLToModelTest {
try {
String fileName = "testFiles/compartment/compartment_name.gpml";
Model model = new GPMLToModel().getModel(fileName);
- for (Compartment compartment : model.getCompartmentsAliases()) {
+ for (Compartment compartment : model.getCompartments()) {
assertEquals("Compartment parsed from gpml should have a valid name", "Label", compartment.getName());
}
assertEquals(0, model.getCreationWarnings().size());
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index 0232a42c1d..80442db55b 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -45,7 +45,7 @@ public class BugTest extends WikipathwaysTestFunctions {
assertEquals(7, model1.getCreationWarnings().size());
int complexes = 0;
- for (Element alias : model1.getAliases()) {
+ for (Element alias : model1.getElements()) {
if (alias instanceof Complex) {
complexes++;
}
diff --git a/persist/src/db/10.0.3/fix_db_20161005.sql b/persist/src/db/10.0.3/fix_db_20161005.sql
new file mode 100644
index 0000000000..4f9b15d5d9
--- /dev/null
+++ b/persist/src/db/10.0.3/fix_db_20161005.sql
@@ -0,0 +1,24 @@
+alter table submodel_connection_table rename fromalias_iddb to fromelement_iddb;
+alter table submodel_connection_table rename toalias_iddb to toelement_iddb;
+
+alter table alias_table rename to element_table;
+
+update element_table set alias_type_db ='Bottom square Compartment' where alias_type_db = 'Bottom square Compartment Alias';
+update element_table set alias_type_db ='Left square Compartment' where alias_type_db = 'Left square Compartment Alias';
+update element_table set alias_type_db ='Oval Compartment' where alias_type_db = 'Oval Compartment Alias';
+update element_table set alias_type_db ='Compartment' where alias_type_db = 'Compartment Alias';
+update element_table set alias_type_db ='Pathway Compartment' where alias_type_db = 'Artifitial Compartment Alias';
+update element_table set alias_type_db ='Right square Compartment' where alias_type_db = 'Right square Compartment Alias';
+update element_table set alias_type_db ='Square Compartment' where alias_type_db = 'Square Compartment Alias';
+update element_table set alias_type_db ='Top square Compartment' where alias_type_db = 'Top square Compartment Alias';
+
+alter table node_table rename alias_iddb to element_iddb;
+
+update element_table set alias_type_db ='Complex' where alias_type_db = 'Complex Species Alias';
+update element_table set alias_type_db ='Species' where alias_type_db = 'Species Alias';
+
+alter table element_table rename alias_type_db to element_type_db;
+alter table element_table rename idcomplexaliasdb to idcomplexdb;
+
+alter table element_table rename aliasstatelabel to statelabel;
+alter table element_table rename aliasstateprefix to stateprefix;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
index ba1eb26bf8..b961cbc625 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -179,8 +179,8 @@ public class ProjectDaoTest extends PersistTestFunctions {
Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addAlias(alias);
- alias3.addAlias(alias2);
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
alias.setParent(alias3);
alias2.setParent(alias3);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index 856380cd3f..180c0711a1 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -114,8 +114,8 @@ public class CommentDaoTest extends PersistTestFunctions {
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addAlias(alias);
- alias3.addAlias(alias2);
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
alias.setParent(alias3);
alias2.setParent(alias3);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
index 0e48ff8d14..ce6a9bed27 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
@@ -161,8 +161,8 @@ public class LayoutDaoTest extends PersistTestFunctions {
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addAlias(alias);
- alias3.addAlias(alias2);
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
alias.setParent(alias3);
alias2.setParent(alias3);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index b7cd79ee28..ecfb1f3bb3 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -73,7 +73,7 @@ public class ModelDaoTest extends PersistTestFunctions {
assertNotNull(model2);
assertFalse(model2 == model);
- assertEquals(model.getAliases().size(), model2.getAliases().size());
+ assertEquals(model.getElements().size(), model2.getElements().size());
assertEquals(model.getLayers().size(), model2.getLayers().size());
assertEquals(model.getReactions().size(), model2.getReactions().size());
@@ -99,21 +99,21 @@ public class ModelDaoTest extends PersistTestFunctions {
Model fullModel = new ModelFullIndexed(model2);
assertNotNull(model2);
- assertEquals(model.getAliases().size(), model2.getAliases().size());
+ assertEquals(model.getElements().size(), model2.getElements().size());
assertEquals(model.getLayers().size(), model2.getLayers().size());
assertEquals(model.getReactions().size(), model2.getReactions().size());
// check if we really performed a test
boolean test = false;
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
test = true;
}
assertTrue(test);
test = false;
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Compartment) {
assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
test = true;
@@ -341,8 +341,8 @@ public class ModelDaoTest extends PersistTestFunctions {
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addAlias(alias);
- alias3.addAlias(alias2);
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
alias.setParent(alias3);
alias2.setParent(alias3);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
index a0d5a976a2..5f4fc73a85 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
@@ -79,8 +79,8 @@ public class AliasDaoTest extends PersistTestFunctions {
Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addAlias(alias);
- alias3.addAlias(alias2);
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
alias.setParent(alias3);
alias2.setParent(alias3);
@@ -128,7 +128,7 @@ public class AliasDaoTest extends PersistTestFunctions {
Model model = createModel();
Model model1 = createModel();
Element alias = model.getElementByElementId("sa2");
- AliasSubmodelConnection submodel = new AliasSubmodelConnection(model1, SubmodelType.UNKNOWN);
+ ElementSubmodelConnection submodel = new ElementSubmodelConnection(model1, SubmodelType.UNKNOWN);
alias.setSubmodel(submodel);
project.addModel(model);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
index 4faae67b56..02c33a2fc3 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
@@ -56,10 +56,10 @@ public class AntisenseRnaTest extends PersistTestFunctions {
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
- Element sp = model.getAliases().iterator().next();
+ Element sp = model.getElements().iterator().next();
AntisenseRna ar = (AntisenseRna) sp;
- Element sp2 = model2.getAliases().iterator().next();
+ Element sp2 = model2.getElements().iterator().next();
AntisenseRna ar2 = (AntisenseRna) sp2;
projectDao.delete(project2);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
index 723b4dd75c..04da77ac6f 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
@@ -55,10 +55,10 @@ public class RnaTest extends PersistTestFunctions {
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
- Element sp = model.getAliases().iterator().next();
+ Element sp = model.getElements().iterator().next();
Rna ar = (Rna) sp;
- Element sp2 = model2.getAliases().iterator().next();
+ Element sp2 = model2.getElements().iterator().next();
Rna ar2 = (Rna) sp2;
projectDao.delete(project2);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
index 1ec4d89ac5..c6e710375c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
@@ -63,7 +63,7 @@ public class ReactionComparator {
}
for (ReactionNode node : reaction.getReactionNodes()) {
- if (node.getAlias() instanceof Phenotype) {
+ if (node.getElement() instanceof Phenotype) {
result.setStatus(MatchStatus.INVALID_REACTION_WITH_PHEONTYPE);
return result;
}
@@ -80,7 +80,7 @@ public class ReactionComparator {
for (ReactionNode node : reaction.getModifiers()) {
boolean verified = false;
- Element species = node.getAlias();
+ Element species = node.getElement();
for (ReactomeCatalystActivity catalystActivity : reactomeReaction.getCatalystActivities()) {
if (nc.compareNodes(species, catalystActivity)) {
@@ -95,7 +95,7 @@ public class ReactionComparator {
}
}
for (ReactionNode node : reaction.getReactants()) {
- Element species = node.getAlias();
+ Element species = node.getElement();
boolean verified = false;
for (ReactomePhysicalEntity input : reactomeReaction.getInputs()) {
if (nc.compareNodes(species, input)) {
@@ -110,7 +110,7 @@ public class ReactionComparator {
}
}
for (ReactionNode node : reaction.getProducts()) {
- Element species = node.getAlias();
+ Element species = node.getElement();
boolean verified = false;
for (ReactomePhysicalEntity input : reactomeReaction.getOutputs()) {
if (nc.compareNodes(species, input)) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
index 36b03907ce..2a7c77ff90 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
@@ -628,7 +628,7 @@ public class ReactomeQueryUtil {
public ReactomeReactionlikeEvent getSimilarReaction(Reaction reaction) {
List<Element> list = new ArrayList<>();
for (ReactionNode node : reaction.getReactionNodes()) {
- list.add(node.getAlias());
+ list.add(node.getElement());
}
List<ReactomeReactionlikeEvent> reactions = getReactionsBetweenSpecies(list, true);
// logger.debug("Reactions: " + reactions.size());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
index eb6f7539a2..19400e3cc9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -294,7 +294,7 @@ public class CommentService implements ICommentService {
logger.warn("Invalid reaction dbID: " + comment.getTableId() + ". Table: " + comment.getTableName().getName());
}
} else {
- Element alias = model.getAliasByDbId(comment.getTableId());
+ Element alias = model.getElementByDbId(comment.getTableId());
if (alias != null) {
identifier = ((Species) alias).getElementId();
} else {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java b/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
index 691a276741..7313dd7d14 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
@@ -162,7 +162,7 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
if (geneName == null) {
return result;
}
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
Collection<DataMining> set = missingConnectionDao.getMissingConnectionForElement(element);
for (DataMining dataMining : set) {
for (MiriamData md : dataMining.getSuggestedConnections()) {
@@ -243,7 +243,7 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
@Override
public void removeConnectionsForModel(ModelData model) {
- Collection<Element> nodes = model.getAliases();
+ Collection<Element> nodes = model.getElements();
dbUtils.setAutoFlush(false);
for (Element node : nodes) {
@@ -489,8 +489,8 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
List<ReactionNode> rNodes = reaction.getReactionNodes();
for (int i = 0; i < rNodes.size(); i++) {
for (int j = i + 1; j < rNodes.size(); j++) {
- for (MiriamData md1 : rNodes.get(i).getAlias().getMiriamData()) {
- for (MiriamData md2 : rNodes.get(j).getAlias().getMiriamData()) {
+ for (MiriamData md1 : rNodes.get(i).getElement().getMiriamData()) {
+ for (MiriamData md2 : rNodes.get(j).getElement().getMiriamData()) {
if (md1.compareTo(md2) < 0) {
reactionsHash.add(new Pair<MiriamData, MiriamData>(md1, md2));
} else {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
index 8de8004743..d1172615b3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
@@ -91,7 +91,7 @@ public class ExporterService implements IExporterService {
}
builder.append("\n");
for (Model model : parameters.getModels()) {
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Species) {
Species speciesAlias = (Species) alias;
boolean toBeProcessed = false;
@@ -199,10 +199,10 @@ public class ExporterService implements IExporterService {
line.append(species.getModelData().getName());
} else if (column == ExportColumn.COMPLEX) {
String complex = null;
- if (species.getComplexAlias() != null) {
- complex = species.getComplexAlias().getName();
+ if (species.getComplex() != null) {
+ complex = species.getComplex().getName();
- complex += " [id=" + getId(species.getComplexAlias()) + "]";
+ complex += " [id=" + getId(species.getComplex()) + "]";
}
line.append(complex);
} else {
@@ -242,7 +242,7 @@ public class ExporterService implements IExporterService {
Compartment smallestAlias = null;
List<Compartment> compartmentAliases = new ArrayList<Compartment>();
- for (Compartment alias : element.getModel().getCompartmentsAliases()) {
+ for (Compartment alias : element.getModel().getCompartments()) {
if (alias.cross(element)) {
if (!(alias instanceof PathwayCompartment)) {
compartmentAliases.add(alias);
@@ -272,7 +272,7 @@ public class ExporterService implements IExporterService {
Model model = element.getModel();
List<Compartment> aliases = new ArrayList<Compartment>();
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
if (alias instanceof PathwayCompartment) {
if (alias.cross(element)) {
aliases.add(alias);
@@ -368,7 +368,7 @@ public class ExporterService implements IExporterService {
for (Reaction reaction : model.getReactions()) {
int counter = 0;
for (ReactionNode node : reaction.getReactionNodes()) {
- Element element = node.getAlias();
+ Element element = node.getElement();
for (Class<?> type : parameters.getTypes()) {
if (type.isAssignableFrom(element.getClass())) {
counter++;
@@ -383,7 +383,7 @@ public class ExporterService implements IExporterService {
}
if (parameters.isMoleculeEdges()) {
for (Model model : parameters.getModels()) {
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (element instanceof Species) {
if (element instanceof SimpleMolecule) {
boolean ok = false;
@@ -446,8 +446,8 @@ public class ExporterService implements IExporterService {
for (Reaction reaction : model.getReactions()) {
boolean goodReaction = false;
for (ReactionNode node : reaction.getReactionNodes()) {
- if (node.getAlias() instanceof SimpleMolecule) {
- Element species2 = node.getAlias();
+ if (node.getElement() instanceof SimpleMolecule) {
+ Element species2 = node.getElement();
if (species.getName().equalsIgnoreCase(species2.getName())) {
goodReaction = true;
}
@@ -462,19 +462,19 @@ public class ExporterService implements IExporterService {
ok = true;
}
for (Compartment alias2 : parameters.getIncludedAliases()) {
- if (alias2.cross(node.getAlias())) {
+ if (alias2.cross(node.getElement())) {
ok = true;
break;
}
}
for (Compartment alias2 : parameters.getExcludedAliases()) {
- if (alias2.cross(node.getAlias())) {
+ if (alias2.cross(node.getElement())) {
ok = false;
break;
}
}
if (ok) {
- Element element = node.getAlias();
+ Element element = node.getElement();
for (Class<?> type : parameters.getTypes()) {
if (type.isAssignableFrom(element.getClass())) {
if (element instanceof Complex) {
@@ -530,19 +530,19 @@ public class ExporterService implements IExporterService {
ok = true;
}
for (Compartment alias2 : parameters.getIncludedAliases()) {
- if (alias2.cross(node.getAlias())) {
+ if (alias2.cross(node.getElement())) {
ok = true;
break;
}
}
for (Compartment alias2 : parameters.getExcludedAliases()) {
- if (alias2.cross(node.getAlias())) {
+ if (alias2.cross(node.getElement())) {
ok = false;
break;
}
}
if (ok) {
- Element element = node.getAlias();
+ Element element = node.getElement();
if (parameters.getTypes().size() == 0) {
elements.add(element);
} else {
@@ -628,13 +628,13 @@ public class ExporterService implements IExporterService {
for (Reactant reactant : reaction.getReactants()) {
result.append("REACTANT");
result.append("\t");
- result.append(getExportSingleSpecies((Species) reactant.getAlias(), parameters));
+ result.append(getExportSingleSpecies((Species) reactant.getElement(), parameters));
result.append("\t");
}
for (Product product : reaction.getProducts()) {
result.append("PRODUCT");
result.append("\t");
- result.append(getExportSingleSpecies((Species) product.getAlias(), parameters));
+ result.append(getExportSingleSpecies((Species) product.getElement(), parameters));
result.append("\t");
}
for (Modifier modifier : reaction.getModifiers()) {
@@ -642,7 +642,7 @@ public class ExporterService implements IExporterService {
result.append("\t");
result.append("type=" + modifier.getClass().getSimpleName());
result.append("\t");
- result.append(getExportSingleSpecies((Species) modifier.getAlias(), parameters));
+ result.append(getExportSingleSpecies((Species) modifier.getElement(), parameters));
result.append("\t");
}
return result.toString();
@@ -703,33 +703,33 @@ public class ExporterService implements IExporterService {
Set<Element> inputs = new HashSet<Element>();
Set<Element> outputs = new HashSet<Element>();
for (Reactant reactant : reaction.getReactants()) {
- if (!isAssignable(parameters, reactant.getAlias())) {
+ if (!isAssignable(parameters, reactant.getElement())) {
continue;
}
- if (reactant.getAlias() instanceof Complex) {
- inputs.addAll(((Complex) (reactant.getAlias())).getAllChildrenAliases());
+ if (reactant.getElement() instanceof Complex) {
+ inputs.addAll(((Complex) (reactant.getElement())).getAllChildren());
} else {
- inputs.add(reactant.getAlias());
+ inputs.add(reactant.getElement());
}
}
for (Product product : reaction.getProducts()) {
- if (!isAssignable(parameters, product.getAlias())) {
+ if (!isAssignable(parameters, product.getElement())) {
continue;
}
- if (product.getAlias() instanceof Complex) {
- outputs.addAll(((Complex) (product.getAlias())).getAllChildrenAliases());
+ if (product.getElement() instanceof Complex) {
+ outputs.addAll(((Complex) (product.getElement())).getAllChildren());
} else {
- outputs.add(product.getAlias());
+ outputs.add(product.getElement());
}
}
for (Modifier modifier : reaction.getModifiers()) {
- if (!isAssignable(parameters, modifier.getAlias())) {
+ if (!isAssignable(parameters, modifier.getElement())) {
continue;
}
- if (modifier.getAlias() instanceof Complex) {
- inputs.addAll(((Complex) (modifier.getAlias())).getAllChildrenAliases());
+ if (modifier.getElement() instanceof Complex) {
+ inputs.addAll(((Complex) (modifier.getElement())).getAllChildren());
} else {
- inputs.add(modifier.getAlias());
+ inputs.add(modifier.getElement());
}
}
for (Element input : inputs) {
@@ -747,36 +747,36 @@ public class ExporterService implements IExporterService {
} else {
for (Reactant reactant : reaction.getReactants()) {
- if (!isAssignable(parameters, reactant.getAlias())) {
+ if (!isAssignable(parameters, reactant.getElement())) {
continue;
}
counter++;
builder.append("REACTANT");
builder.append("\t");
- builder.append(getId(reactant.getAlias()));
+ builder.append(getId(reactant.getElement()));
builder.append("\t");
}
for (Product product : reaction.getProducts()) {
- if (!isAssignable(parameters, product.getAlias())) {
+ if (!isAssignable(parameters, product.getElement())) {
continue;
}
counter++;
builder.append("PRODUCT");
builder.append("\t");
- builder.append(getId(product.getAlias()));
+ builder.append(getId(product.getElement()));
builder.append("\t");
}
for (Modifier modifier : reaction.getModifiers()) {
- if (!isAssignable(parameters, modifier.getAlias())) {
+ if (!isAssignable(parameters, modifier.getElement())) {
continue;
}
counter++;
builder.append("MODIFIER");
builder.append("\t");
- builder.append(getId(modifier.getAlias()));
+ builder.append(getId(modifier.getElement()));
builder.append("\t");
}
if (counter > 1) {
@@ -835,8 +835,8 @@ public class ExporterService implements IExporterService {
sb.append("compartment=" + compartment);
sb.append("\t");
String complexId = null;
- if (alias.getComplexAlias() != null) {
- complexId = getId(alias.getComplexAlias());
+ if (alias.getComplex() != null) {
+ complexId = getId(alias.getComplex());
}
sb.append("complex=" + complexId);
sb.append("\t");
@@ -975,7 +975,7 @@ public class ExporterService implements IExporterService {
Set<String> uniqeLines = new HashSet<>();
StringBuilder builder = new StringBuilder();
for (Model model : parameters.getModels()) {
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
// check where it lays
boolean toBeProcessed = (parameters.getIncludedAliases().size() == 0);
@@ -1066,7 +1066,7 @@ public class ExporterService implements IExporterService {
models.addAll(model.getSubmodels());
Set<MiriamData> miriamDatas = new HashSet<>();
for (Model m : models) {
- for (Element element : m.getAliases()) {
+ for (Element element : m.getElements()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.PUBMED.equals(md.getDataType())) {
miriamDatas.add(md);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 4752653eec..65b0ce3877 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -180,7 +180,7 @@ public class ModelService implements IModelService {
if (model != null) {
Set<Integer> pubmedIds = new HashSet<>();
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.PUBMED.equals(md.getDataType())) {
try {
@@ -344,7 +344,7 @@ public class ModelService implements IModelService {
if (model != null) {
Set<MiriamData> pubmedIds = new HashSet<MiriamData>();
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
pubmedIds.addAll(element.getMiriamData());
}
for (Reaction reaction : model.getReactions()) {
@@ -439,7 +439,7 @@ public class ModelService implements IModelService {
for (Model model2 : models) {
Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
if (set != null) {
- for (Element alias : model2.getAliases()) {
+ for (Element alias : model2.getElements()) {
if (set.contains(alias.getId())) {
result.add(alias);
set.remove(alias.getId());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 2668362530..d011bcb456 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -784,9 +784,9 @@ public class ProjectService implements IProjectService {
try {
Logger.getRootLogger().addAppender(appender);
Set<Element> nodes = new HashSet<>();
- nodes.addAll(model.getAliases());
+ nodes.addAll(model.getElements());
for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- nodes.addAll(connection.getSubmodel().getAliases());
+ nodes.addAll(connection.getSubmodel().getElements());
}
Set<Reaction> reactions = new HashSet<Reaction>();
reactions.addAll(model.getReactions());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 0f555b798b..cec3c35b2c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -238,7 +238,7 @@ public class SearchService implements ISearchService {
} else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
result.add(fullAliasViewFactory.create(model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""))));
} else {
- Set<Element> aliases = model.getAliases();
+ Set<Element> aliases = model.getElements();
List<SearchResult> sortedResults = new ArrayList<SearchService.SearchResult>();
for (Element alias : aliases) {
@@ -324,7 +324,7 @@ public class SearchService implements ISearchService {
List<IHeavyView> result = new ArrayList<>();
result.add(fullReactionViewFactory.create(reaction));
for (ReactionNode node : reaction.getReactionNodes()) {
- result.add(fullAliasViewFactory.create(node.getAlias()));
+ result.add(fullAliasViewFactory.create(node.getElement()));
}
return result;
}
@@ -336,7 +336,7 @@ public class SearchService implements ISearchService {
List<Object> results = new ArrayList<Object>();
- Set<Element> aliases = params.getModel().getAliases();
+ Set<Element> aliases = params.getModel().getElements();
Point2D point = new Point2D.Double(params.getX(), params.getY());
for (Element alias : aliases) {
if (alias instanceof Species) {
@@ -422,7 +422,7 @@ public class SearchService implements ISearchService {
return true;
}
for (ReactionNode node : reaction.getReactionNodes()) {
- if (isVisible(node.getAlias(), params)) {
+ if (isVisible(node.getElement(), params)) {
return true;
}
}
@@ -537,7 +537,7 @@ public class SearchService implements ISearchService {
for (Reaction reaction : model.getReactions()) {
tmpList.add(new DistanceToObject(reaction, point));
}
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Species) {
tmpList.add(new DistanceToObject(alias, point));
}
@@ -660,13 +660,13 @@ public class SearchService implements ISearchService {
Map<String, List<String>> result = new HashMap<String, List<String>>();
Set<String> possibilities = new HashSet<String>();
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (alias instanceof Species) {
possibilities.addAll(getSearchPossibilitiesForAlias(alias));
}
}
for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- for (Element alias : connection.getSubmodel().getModel().getAliases()) {
+ for (Element alias : connection.getSubmodel().getModel().getElements()) {
if (alias instanceof Species) {
possibilities.addAll(getSearchPossibilitiesForAlias(alias));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
index 83af2d42fc..1895e4acd5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
@@ -122,7 +122,7 @@ public interface IExporterService {
for (Model modelElement : models) {
includedAliases.clear();
for (String string : included) {
- for (Compartment alias : modelElement.getCompartmentsAliases()) {
+ for (Compartment alias : modelElement.getCompartments()) {
if (alias.getName().equalsIgnoreCase(string)) {
includedAliases.add(alias);
}
@@ -131,7 +131,7 @@ public interface IExporterService {
excludedAliases.clear();
for (String string : excluded) {
- for (Compartment alias : modelElement.getCompartmentsAliases()) {
+ for (Compartment alias : modelElement.getCompartments()) {
if (alias.getName().equalsIgnoreCase(string)) {
excludedAliases.add(alias);
}
@@ -153,7 +153,7 @@ public interface IExporterService {
if (models.size() > 0) {
for (Model model : models) {
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
if (alias.getName().equalsIgnoreCase(included)) {
includedAliases.add(alias);
}
@@ -189,7 +189,7 @@ public interface IExporterService {
if (models.size() > 0) {
for (Model model : models) {
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
if (alias.getName().equalsIgnoreCase(excluded)) {
excludedAliases.add(alias);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index 080f82df06..ec5c533a35 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -87,7 +87,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
return null;
} else if (ElementIdentifierType.ALIAS.getJsName().equalsIgnoreCase(element.getType())) {
Model m = model.getSubmodelById(element.getModelId());
- Element alias = m.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ Element alias = m.getElementByDbId(Integer.valueOf(element.getObjectId()));
if (alias == null) {
logger.warn("Alias with object id = " + element.getObjectId() + " is unknown.");
return null;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionViewFactory.java
index 357b09b686..ee4da49f1f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionViewFactory.java
@@ -63,7 +63,7 @@ public class FullReactionViewFactory extends ElementViewFactory<Reaction, FullRe
result.setReferences(annotationViewFactory.createList(reaction.getMiriamData()));
for (ReactionNode node : reaction.getReactionNodes()) {
- FullAliasView fav = fullAliasViewFactory.create(node.getAlias());
+ FullAliasView fav = fullAliasViewFactory.create(node.getElement());
if (node instanceof Reactant) {
fav.addOther("NodeType", "Reactant");
} else if (node instanceof Product) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
index f475b4cbfa..5754dcac66 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
@@ -177,7 +177,7 @@ public class ChemicalViewFactory extends SearchResultFactory<Chemical, ChemicalV
for (Model model : models) {
for (TargetView target : chemical.getTargetRows()) {
if (target.getSelected() && target.getIcon() != null) {
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (elementMatch(target, element)) {
result.add(new ElementIdentifier(element, target.getIcon()));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java
index 8ed19f9a96..cbf58c412a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java
@@ -169,7 +169,7 @@ public class DrugViewFactory extends SearchResultFactory<Drug, DrugView> {
List<ElementIdentifier> result = new ArrayList<>();
for (Model m : models) {
- for (Element element : m.getAliases()) {
+ for (Element element : m.getElements()) {
if (elementMatch(complexTarget, element)) {
result.add(new ElementIdentifier(element, complexTarget.getIcon()));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
index 595ec33ca5..235a3a6824 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
@@ -102,7 +102,7 @@ public class MiRNAViewFactory extends SearchResultFactory<MiRNA, MiRNAView> {
for (Model model : models) {
for (TargetView target : searchResult.getTargetRows()) {
if (target.getSelected() && target.getIcon() != null) {
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (elementMatch(target, element)) {
result.add(new ElementIdentifier(element, target.getIcon()));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
index a16772c76b..f3cf4961cd 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
@@ -78,7 +78,7 @@ public class CommentViewFactory extends AbstractViewFactory<Comment, CommentView
}
} else {
- Element alias = model.getAliasByDbId(comment.getTableId());
+ Element alias = model.getElementByDbId(comment.getTableId());
if (alias != null) {
title = alias.getName();
coordinates = alias.getCenter();
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
index 2d984725fa..df6d60a4f6 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
@@ -47,7 +47,7 @@ public class CommentServiceTest extends ServiceTestFunctions {
model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
model.setMapVersion("tes");
model.setTileSize(128);
- Set<Element> aliases = model.getAliases();
+ Set<Element> aliases = model.getElements();
alias = null;
alias2 = null;
for (Element nAlias : aliases) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
index 7c94ef9f11..1831ffa26e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
@@ -54,7 +54,7 @@ public class DataMiningServiceTest extends ServiceTestFunctions {
project.addModel(model);
projectDao.add(project);
modelDao.add(model);
- nodes = model.getAliases();
+ nodes = model.getElements();
node = nodes.iterator().next();
createUser();
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
index cc5c205c6d..b3ff181821 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
@@ -174,7 +174,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
try {
Model model = getModelForFile("testFiles/export/reaction.xml", false);
Set<Compartment> aliases = new HashSet<>();
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
aliases.add(alias);
}
@@ -274,7 +274,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
strings.add(ReactionLineData.getByReactionType(reaction.getClass()).getCellDesignerString());
strings.add(reaction.getIdReaction());
for (ReactionNode node : reaction.getReactionNodes()) {
- strings.add(node.getAlias().getName());
+ strings.add(node.getElement().getName());
}
for (String string : strings) {
@@ -463,7 +463,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
try {
Model model = getModelForFile("testFiles/export/reaction.xml", false);
Set<Compartment> aliases = new HashSet<>();
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
aliases.add(alias);
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
index 2049084f81..7fc816df52 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
@@ -42,7 +42,7 @@ public class LogServiceTest extends ServiceTestFunctions {
project.addModel(model);
projectDao.add(project);
modelDao.add(model);
- nodes = model.getAliases();
+ nodes = model.getElements();
node = nodes.iterator().next();
mc = new DataMining();
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
index f6cfdb028f..07b4937096 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
@@ -84,7 +84,7 @@ public class ModelServiceTest extends ServiceTestFunctions {
Model model = getModelForFile("testFiles/sample.xml", false);
int counter = 0;
Element alias0 = null;
- for (Element alias : model.getAliases()) {
+ for (Element alias : model.getElements()) {
if (counter == 0) {
alias0 = alias;
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index f79c6e0da8..18674a4d47 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -645,7 +645,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
boolean dmFound = false;
- for (Element element : model.getAliases()) {
+ for (Element element : model.getElements()) {
if (dataMiningService.getMissingConnections(element).size() > 0) {
dmFound = true;
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index cbe8096960..5e7afaf635 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -125,7 +125,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
try {
createFullModel();
MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
- model.getAliases().iterator().next().addMiriamData(md);
+ model.getElements().iterator().next().addMiriamData(md);
SearchElementResult global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
assertNotNull(global);
assertEquals(1, global.size());
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java
index 14bcf86a90..e14cc30512 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java
@@ -112,7 +112,7 @@ public class DrugViewFactoryTest extends ServiceTestFunctions {
Element alias = model.getElementByElementId("sa9");
alias.setName("M");
alias.setId(12);
- model.removeAlias(alias);
+ model.removeElement(alias);
model.addElement(alias);
ElementIdentifier ei = new ElementIdentifier(alias, null);
model.setTileSize(256);
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java
index d6b812bb0e..aa1ef78519 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java
@@ -37,7 +37,7 @@ public class MissingConnectionDaoTest extends ServiceTestFunctions {
project.addModel(model);
modelDao.add((Model) model);
- nodes = model.getAliases();
+ nodes = model.getElements();
}
@After
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java b/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
index a0a0fd6a43..709a0bf310 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
@@ -239,7 +239,7 @@ public class ChemicalBean extends AbstractMarkerManagerBean<ChemicalView> implem
Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
- Element alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ Element alias = model.getElementByDbId(Integer.valueOf(element.getObjectId()));
List<Element> list = new ArrayList<>();
list.add(alias);
List<ChemicalView> chemicals = chemicalService
diff --git a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
index dbd1bb3205..41e848d6b1 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
@@ -138,7 +138,7 @@ public class DrugBean extends AbstractMarkerManagerBean<DrugView> implements Ser
// polygon
SubModelCommand subModelCommand = new SubModelCommand(model, awtPolygon);
Model partModel = subModelCommand.execute();
- suggestedDrugs.addAll(drugService.getForTargets(partModel.getAliases(), new DbSearchCriteria().organisms(mapBean.getOrganism())));
+ suggestedDrugs.addAll(drugService.getForTargets(partModel.getElements(), new DbSearchCriteria().organisms(mapBean.getOrganism())));
}
/**
@@ -338,7 +338,7 @@ public class DrugBean extends AbstractMarkerManagerBean<DrugView> implements Ser
Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
- Element alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ Element alias = model.getElementByDbId(Integer.valueOf(element.getObjectId()));
List<Element> list = new ArrayList<>();
list.add(alias);
List<DrugView> drugs = drugService.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()));
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
index 1f7734ae50..9650be2c4d 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
@@ -289,7 +289,7 @@ public class ExportBean extends AbstractManagedBean {
annotations.put(mt, 0);
}
for (Model model2 : models) {
- for (Element alias : model2.getAliases()) {
+ for (Element alias : model2.getElements()) {
for (MiriamData md : alias.getMiriamData()) {
Integer amount = annotations.get(md.getDataType());
amount += 1;
@@ -699,11 +699,11 @@ public class ExportBean extends AbstractManagedBean {
}
Set<String> components = new HashSet<String>();
- for (Compartment alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartments()) {
components.add(alias.getName());
}
for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- for (Compartment alias : submodel.getSubmodel().getModel().getCompartmentsAliases()) {
+ for (Compartment alias : submodel.getSubmodel().getModel().getCompartments()) {
components.add(alias.getName());
}
}
@@ -1149,7 +1149,7 @@ public class ExportBean extends AbstractManagedBean {
// if it's clean then remove coloring
new ColorModelCommand(colorModel, new HashSet<>()).execute();
}
- for (Element alias : colorModel.getAliases()) {
+ for (Element alias : colorModel.getElements()) {
alias.setVisibilityLevel(0);
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
index 9932115018..aefdf5dc47 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
@@ -303,7 +303,7 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
if (feedbackElement.equals(getDescription(object))) {
String result = "Reactants: ";
for (Reactant reactant : reaction.getReactants()) {
- result += reactant.getAlias().getName() + ", ";
+ result += reactant.getElement().getName() + ", ";
}
return result;
}
@@ -328,7 +328,7 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
if (feedbackElement.equals(getDescription(object))) {
String result = "Products: ";
for (Product product : reaction.getProducts()) {
- result += product.getAlias().getName() + ", ";
+ result += product.getElement().getName() + ", ";
}
return result;
}
@@ -353,7 +353,7 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
if (feedbackElement.equals(getDescription(object))) {
String result = "Modifiers: ";
for (Modifier modifier : reaction.getModifiers()) {
- result += modifier.getAlias().getName() + ", ";
+ result += modifier.getElement().getName() + ", ";
}
return result;
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java b/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
index 6915f552c1..ba1d8260d5 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
@@ -186,7 +186,7 @@ public class MiRNABean extends AbstractMarkerManagerBean<MiRNAView> implements S
Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
- Element alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ Element alias = model.getElementByDbId(Integer.valueOf(element.getObjectId()));
List<Element> list = new ArrayList<>();
list.add(alias);
List<MiRNAView> mirnas = miRNAService.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()));
--
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