diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index c3d47ed67fbfe4f63e54a0664bb3284c0da8ef29..48ae8ea11c997118b0a19a59d57a93894fd682b6 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -241,10 +241,11 @@ public class ReactomeComparison {
*
* @param result
* result to be printed
- * @throws IOException
* @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
*/
- private void printResult(MatchResult result) throws IOException, AnnotatorException {
+ private void printResult(MatchResult result) throws AnnotatorException {
String color = "#000000";
String status = "";
String error = "";
@@ -316,6 +317,9 @@ public class ReactomeComparison {
* @throws IOException
* thrown whene there are problems accessing reactome reaction
* @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
+ *
*/
private MatchResult checkReaction(String id) throws IOException, ComparatorException {
return checkReaction(model.getReactionByReactionId(id));
@@ -330,6 +334,8 @@ public class ReactomeComparison {
* @throws IOException
* thrown whene there are problems accessing reactome reaction
* @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
*/
private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index 04da1a646be703f3eee923b28fafaa2bb2f732ee..dd2aee96856c4f43a290997a283325e017ec5d61 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -96,7 +96,8 @@ 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.getElement().getClass().getSimpleName() + "[" + node.getElement().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/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index 4f9f4c5a47b62a17fc4fc2df12e8c66aa91f0e4f..b5c6af04154c775763ebbfdfede835fa08c11d0b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -5,40 +5,82 @@ import java.util.List;
import java.util.Map;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+/**
+ * This ctructure containes informationa about {@link CellDesignerElement
+ * celldesigner elements} parsed from the file. The information about this
+ * elements is used in different places in the parsing process.
+ */
public class CellDesignerElementCollection {
+ /**
+ * Element by element identifier (it's cell deigner identifier).
+ */
private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
+ /**
+ * Returns element by given identifier.
+ *
+ * @param speciesId
+ * element identifie r
+ * @return element by given identifier
+ *
+ * @param <T>
+ * type of returned object
+ */
@SuppressWarnings("unchecked")
- public <T extends CellDesignerElement<?>> T getSpeciesBySpeciesId(String speciesId) {
+ public <T extends CellDesignerElement<?>> T getElementByElementId(String speciesId) {
return (T) elementById.get(speciesId);
}
- public CellDesignerCompartment getCompartmentByCompartmentId(String compartmentId) {
- return (CellDesignerCompartment) elementById.get(compartmentId);
- }
-
- public String getElementId(Element alias) {
+ /**
+ * Returns element identifier that should be used for model element when
+ * creating cell designer xml file.
+ *
+ * @param modelElement
+ * model element for which we want to obtain identifier
+ * @return identifier of cell designer element that will be exported
+ */
+ public String getElementId(Element modelElement) {
// TODO
// silly implementation for now (if CD won't crash than we can keep it)
- return "s_id_" + alias.getElementId();
+ return "s_id_" + modelElement.getElementId();
}
+ /**
+ * Adds cell designer structures.
+ *
+ * @param elements
+ * list of objects to add
+ */
public void addElements(List<? extends CellDesignerElement<?>> elements) {
for (CellDesignerElement<?> element : elements) {
addElement(element);
}
}
+ /**
+ * Adds cell designer object.
+ *
+ * @param element
+ * object to add
+ */
public void addElement(CellDesignerElement<?> element) {
addElement(element, element.getElementId());
}
+ /**
+ * Adds celldesigner element with custom id (instead the one obtained from
+ * celldesigner structure).
+ *
+ * @param element
+ * element to be add
+ * @param id
+ * id that should be used for identifing element
+ */
private void addElement(CellDesignerElement<?> element, String id) {
if (elementById.get(id) != null) {
throw new InvalidArgumentException(
@@ -47,9 +89,18 @@ public class CellDesignerElementCollection {
elementById.put(id, element);
}
- public void addAlias(Species alias, CellDesignerElement<?> element) {
- addElement(element, getElementId(alias));
- if (getSpeciesBySpeciesId(element.getElementId()) == null) {
+ /**
+ * Adds celldesigner structure in a way that it would be accessed via
+ * identifier for model structure. Method used only for unit test.
+ *
+ * @param modelElement
+ * model element that will create identifier
+ * @param element
+ * element to be added
+ */
+ public void addModelElement(Species modelElement, CellDesignerElement<?> element) {
+ addElement(element, getElementId(modelElement));
+ if (getElementByElementId(element.getElementId()) == null) {
addElement(element);
}
}
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 1975e3d6dad8b9195f16f18baedde645818f3c99..45dfe52fb0bfb0aba3c7bc6fa5311a9f8b9b1762 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
@@ -34,6 +34,7 @@ import lcsb.mapviewer.converter.model.celldesigner.reaction.UnknownReactionClass
import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
@@ -99,6 +100,9 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
*/
private AliasCollectionXmlParser aliasCollectionParser;
+ /**
+ * Annotation parser.
+ */
private RestAnnotationParser rap = new RestAnnotationParser();
@Override
@@ -348,6 +352,9 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
* @param modelData
* object conmtaining infoirmation about species during CellDesigner
* parsing
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
* @param annotationNode
* xml node to parse
* @throws InvalidXmlSchemaException
@@ -603,6 +610,9 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
*
* @param model
* model to transform
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
* @return annotation xml string for the model
*/
private String annotationToXml(Model model, CellDesignerElementCollection elements) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
index 3ced232187f410ba236fb3bda7aad6568b7d922e..b77092450215e249adde684c5fc4fdddca6d48e4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
@@ -49,6 +50,9 @@ public class AliasCollectionXmlParser extends XmlParser {
*/
private CompartmentAliasXmlParser compartmentAliasParser = null;
+ /**
+ * Annotation parser.
+ */
private RestAnnotationParser rap = new RestAnnotationParser();
/**
@@ -59,6 +63,9 @@ public class AliasCollectionXmlParser extends XmlParser {
*
* @param model
* map model for which parsing is performed
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public AliasCollectionXmlParser(CellDesignerElementCollection elements, Model model) {
speciesAliasParser = new SpeciesAliasXmlParser(elements, model);
@@ -185,6 +192,12 @@ public class AliasCollectionXmlParser extends XmlParser {
return result;
}
+ /**
+ * Assing compartment parents for list of compartments.
+ *
+ * @param compartments
+ * compartments that are looking for parents
+ */
private void assignParents(List<Compartment> compartments) {
Compartment nullParent = new Compartment("null");
nullParent.setWidth(Double.MAX_VALUE);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
index 54198db2f0808b363153e93cb18a173b794382ca..71c0aa5f0cadf4ba184ed3089c73b36e3c086cf1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
@@ -8,6 +8,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
@@ -29,18 +30,25 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class.getName());
+ private Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class.getName());
/**
* Model for which we are parsing aliases.
*/
- private Model model = null;
+ private Model model = null;
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
/**
* Default constructor.
*
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
* @param model
* model for which this parser will be used
*/
@@ -53,7 +61,7 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
Compartment parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
String compartmentId = getNodeAttr("compartment", aliasNode);
- CellDesignerCompartment compartment = elements.getCompartmentByCompartmentId(compartmentId);
+ CellDesignerCompartment compartment = elements.getElementByElementId(compartmentId);
if (compartment == null) {
throw new InvalidXmlSchemaException("Compartment does not exist in a model: " + compartmentId);
}
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 3babcfd20a73978d05cfa89aedcd485baf37e200..e3b9b91842dbc729ff6d86f03c08d8842e57f2a0 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
@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
@@ -34,14 +35,14 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ComplexAliasXmlParser.class.getName());
+ private Logger logger = Logger.getLogger(ComplexAliasXmlParser.class.getName());
/**
* Because of the CellDesigner xml model we have to store information about
* all processed Complexes. This infomrmation later on is used for connecting
* complexes in hierarchical view.
*/
- private Map<String, Complex> complexAliasesMapById = new HashMap<String, Complex>();
+ private Map<String, Complex> complexAliasesMapById = new HashMap<String, Complex>();
/**
* Because of the CellDesigner xml model we have to store information about
@@ -49,20 +50,27 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
* complexes in hierarchical view. We cannot do it immediatelly because some
* complexes doesn't exist yet.
*/
- private Map<String, String> parents = new HashMap<String, String>();
+ private Map<String, String> parents = new HashMap<String, String>();
/**
* Model for which we are parsing aliases.
*/
- private Model model = null;
+ private Model model = null;
- private CellDesignerElementCollection elements;
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
+ private CellDesignerElementCollection elements;
/**
* Default constructor with model object for which we parse data.
*
* @param model
* model for which we parse elements
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public ComplexAliasXmlParser(CellDesignerElementCollection elements, Model model) {
this.model = model;
@@ -75,7 +83,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
String aliasId = getNodeAttr("id", aliasNode);
String speciesId = getNodeAttr("species", aliasNode);
- CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) elements.getSpeciesBySpeciesId(speciesId);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) elements.getElementByElementId(speciesId);
if (species == null) {
throw new InvalidXmlSchemaException("No species with id=\"" + speciesId + "\" for complex alias \"" + aliasId + "\"");
}
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 a1bfb93987ef4421c1e1c866d48f4f5507424b45..b936673c9f4bd248161c1f01d89ba707635922c7 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
@@ -8,6 +8,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -30,8 +31,15 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
*/
private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Model for which we parse elements.
+ */
private Model model;
/**
@@ -39,9 +47,12 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
*
* @param model
* model for which we parse elements
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
- public SpeciesAliasXmlParser(CellDesignerElementCollection elementCollection, Model model) {
- this.elements = elementCollection;
+ public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.elements = elements;
this.model = model;
}
@@ -50,7 +61,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
String speciesId = getNodeAttr("species", aliasNode);
String aliasId = getNodeAttr("id", aliasNode);
- CellDesignerSpecies<?> species = elements.getSpeciesBySpeciesId(speciesId);
+ CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
if (species == null) {
throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
}
@@ -111,22 +122,22 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
result.setState(state);
String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
if (!compartmentAliasId.isEmpty()) {
- Compartment ca = model.getElementByElementId(compartmentAliasId);
- if (ca == null) {
+ Compartment compartment = model.getElementByElementId(compartmentAliasId);
+ if (compartment == null) {
throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
} else {
- result.setCompartment(ca);
- ca.addElement(result);
+ result.setCompartment(compartment);
+ compartment.addElement(result);
}
}
String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
if (!complexAliasId.isEmpty()) {
- Complex alias = (Complex) model.getElementByElementId(complexAliasId);
- if (alias == null) {
+ Complex complex = model.getElementByElementId(complexAliasId);
+ if (complex == null) {
throw new InvalidXmlSchemaException("ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
} else {
- result.setComplex(alias);
- alias.addSpecies(result);
+ result.setComplex(complex);
+ complex.addSpecies(result);
}
}
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index b488c39c4a5059802cee63a87831871a26498a04..b46d75a00ff20d1f8623ba227e437b44f9d5ce6c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -669,7 +669,13 @@ public class RestAnnotationParser extends XmlParser {
}
}
- public void processNotes(Element alias) {
- processNotes(alias.getNotes(), alias);
+ /**
+ * Process notes and assign structural information from it.
+ *
+ * @param element
+ * object with notes to be processed
+ */
+ public void processNotes(Element element) {
+ processNotes(element.getNotes(), element);
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
index fd8b7d2abfd85821f08cdd1205258adac4ac6cf2..06c84638d451d19fcb820257e5b90ee4f8898e45 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
@@ -13,6 +13,7 @@ import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.compartment.Compartment;
/**
@@ -36,6 +37,10 @@ public class CompartmentCollectionXmlParser extends XmlParser {
/**
* Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public CompartmentCollectionXmlParser(CellDesignerElementCollection elements) {
compartmentParser = new CompartmentXmlParser(elements);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
index cb86a60609cc4c0d316c01522f82ef561f16579e..958a8826f2eecf48d49f99306c56e9b239505531 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.compartment.Compartment;
/**
@@ -31,8 +32,19 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
*/
private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
public CompartmentXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
index fe8993bbdd2881905f695646a65c08dd21685594..22f483ac41c6e4a7fef5bd3717928fe252456210 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
@@ -49,14 +49,14 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
*/
private static Map<Class<? extends Element>, ICellDesignerAliasConverter<?>> elementConverters;
+ /**
+ * Class helping with transforming objectcs into meaningfull identifiers.
+ */
private static ElementUtils eu = new ElementUtils();
static {
elementConverters = new HashMap<>();
- // at the beginning lets add all implemented aliases
-
- // for alias reference
addElementConverter(GenericProtein.class, new ProteinCellDesignerAliasConverter());
addElementConverter(TruncatedProtein.class, new ProteinCellDesignerAliasConverter());
addElementConverter(ReceptorProtein.class, new ProteinCellDesignerAliasConverter());
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
index 5c76ba89b6816ce0cdf4f9e16797e8271d6b8a47..4a698ada1dcaa6fe1773fa8f40c985962581c62e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
@@ -10,7 +10,6 @@ import java.util.ArrayList;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.model.map.species.Element;
@@ -40,7 +39,10 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
*/
private static final int GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE = 10;
- private ElementUtils eu = new ElementUtils();
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
@Override
public Point2D getPointCoordinates(Protein alias, CellDesignerAnchor anchor) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
index 0bcaec942f83829e131b47e3763876ec8489a5c2..d66747545fab41d4eacab3da784a40fc817d7e3a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -43,6 +44,9 @@ public class ReactionCollectionXmlParser extends XmlParser {
* Default constructor. Model is required because some nodes require access to
* other parts of the model.
*
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
* @param model
* model that is parsed/transformed into xml
*/
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 afd11e0ff5b63acd90636e4d70fd9dcfea8b9ae8..2d08d24f64846953bab15a541fa10c2a492a4107 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
@@ -17,7 +17,6 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
@@ -133,12 +132,6 @@ public class ReactionFromXml extends XmlParser {
*/
private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
- private CellDesignerElementCollection elements;
-
- public ReactionFromXml(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
-
/**
* Returns {@link Reaction} object from CellDesigner xml node.
*
@@ -279,7 +272,7 @@ public class ReactionFromXml extends XmlParser {
Node reactantNode = reactantsNodes.item(z);
if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseReactant")) {
- parseBaseReactant(result, reactantNode, model, elements);
+ parseBaseReactant(result, reactantNode, model);
} else {
throw new ReactionParserException("Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
}
@@ -291,7 +284,7 @@ public class ReactionFromXml extends XmlParser {
Node reactantNode = reactantsNodes.item(z);
if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseProduct")) {
- parseBaseProduct(model, result, reactantNode, elements);
+ parseBaseProduct(model, result, reactantNode);
} else {
throw new ReactionParserException("Unknown element of celldesigner:baseProducts: " + node.getNodeName(), result);
}
@@ -349,10 +342,10 @@ public class ReactionFromXml extends XmlParser {
throw new ReactionParserException("Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
}
if (reactantsLinkNode != null) {
- parseReactantLinks(result, reactantsLinkNode, model, elements);
+ parseReactantLinks(result, reactantsLinkNode, model);
}
if (productsLinkNode != null) {
- parseProductLinks(result, productsLinkNode, model, elements);
+ parseProductLinks(result, productsLinkNode, model);
}
// create operators
@@ -361,7 +354,7 @@ public class ReactionFromXml extends XmlParser {
// now try to create modifiers (we must have set fixed layout data for the
// core of the reaction)
if (modifiersLinkNode != null) {
- parseReactionModification(result, modifiersLinkNode, model, elements);
+ parseReactionModification(result, modifiersLinkNode, model);
}
for (int i = 0; i < result.getModifiers().size(); i++) {
Modifier modifier = result.getModifiers().get(i);
@@ -1100,13 +1093,13 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseReactantLinks(Reaction result, Node rootNode, Model model, CellDesignerElementCollection elements) throws ReactionParserException {
+ private void parseReactantLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
NodeList list = rootNode.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:reactantLink")) {
- Reactant newReactant = getReactantLink(node, model, result, elements);
+ Reactant newReactant = getReactantLink(node, model, result);
result.addReactant(newReactant);
} else {
throw new ReactionParserException("Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
@@ -1131,7 +1124,7 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction, CellDesignerElementCollection elements) throws ReactionParserException {
+ private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
String aliasId = getNodeAttr("alias", rootNode);
Species al = (Species) model.getElementByElementId(aliasId);
if (al == null) {
@@ -1199,13 +1192,13 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseProductLinks(Reaction result, Node rootNode, Model model, CellDesignerElementCollection elements) throws ReactionParserException {
+ private void parseProductLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
NodeList list = rootNode.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:productLink")) {
- Product link = getProductLink(node, model, result, elements);
+ Product link = getProductLink(node, model, result);
result.addProduct(link);
} else {
throw new ReactionParserException("Unknown element of celldesigner:listOfProductLinks: " + node.getNodeName(), result);
@@ -1230,7 +1223,7 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private Product getProductLink(Node rootNode, Model model, Reaction reaction, CellDesignerElementCollection elements) throws ReactionParserException {
+ private Product getProductLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
String aliasId = getNodeAttr("alias", rootNode);
Species al = (Species) model.getElementByElementId(aliasId);
if (al == null) {
@@ -1332,13 +1325,13 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseReactionModification(Reaction result, Node rootNode, Model model, CellDesignerElementCollection elements) throws ReactionParserException {
+ private void parseReactionModification(Reaction result, Node rootNode, Model model) throws ReactionParserException {
NodeList nodes = rootNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
- parseModificationReaction(result, node, model, elements);
+ parseModificationReaction(result, node, model);
} else {
throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(), result);
}
@@ -1358,8 +1351,7 @@ public class ReactionFromXml extends XmlParser {
* @throws ReactionParserException
* thrown when node cannot be parsed properly
*/
- private void parseModificationReaction(Reaction reaction, Node rootNode, Model model, CellDesignerElementCollection elements)
- throws ReactionParserException {
+ private void parseModificationReaction(Reaction reaction, Node rootNode, Model model) throws ReactionParserException {
ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
String type = getNodeAttr("type", rootNode);
String modificationType = getNodeAttr("modificationType", rootNode);
@@ -1569,7 +1561,7 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseBaseReactant(Reaction result, Node reactantNode, Model model, CellDesignerElementCollection elements) throws ReactionParserException {
+ private void parseBaseReactant(Reaction result, Node reactantNode, Model model) throws ReactionParserException {
String aliasId = getNodeAttr("alias", reactantNode);
Species alias = (Species) model.getElementByElementId(aliasId);
if (alias == null) {
@@ -1605,7 +1597,7 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseBaseProduct(Model model, Reaction result, Node reactantNode, CellDesignerElementCollection elements) throws ReactionParserException {
+ private void parseBaseProduct(Model model, Reaction result, Node reactantNode) throws ReactionParserException {
String aliasId = getNodeAttr("alias", reactantNode);
Species alias = (Species) model.getElementByElementId(aliasId);
if (alias == null) {
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 1305ccd3c2f1f03bce720cabdc69f5050716e7f0..33c5670e93a1f6be9667d1b700d93742044a0822 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
@@ -21,6 +21,7 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasCon
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerLineTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
@@ -36,7 +37,6 @@ import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -66,10 +66,25 @@ public class ReactionToXml extends XmlParser {
*/
private CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
private ElementUtils eu = new ElementUtils();
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
public ReactionToXml(CellDesignerElementCollection elements) {
this.elements = elements;
}
@@ -328,7 +343,8 @@ public class ReactionToXml extends XmlParser {
*/
private String getLinkTargetXmlString(Modifier modifier) {
StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:linkTarget species=\"" + elements.getElementId(modifier.getElement()) + "\" alias=\"" + modifier.getElement().getElementId() + "\">\n");
+ 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");
@@ -387,7 +403,7 @@ public class ReactionToXml extends XmlParser {
}
parents.add(species);
}
-
+
sb.append("<speciesReference species=\"" + elements.getElementId(species) + "\">\n");
sb.append("<annotation>\n");
sb.append("<celldesigner:extension>\n");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
index 92ca7c65bc850f82712b6cd46ec73f73c0375dfc..3b5c8191763a4dcf35fc8b0be4c2a0a918af26b9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
@@ -5,6 +5,7 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -27,9 +28,17 @@ public class ReactionXmlParser extends XmlParser {
*/
private ReactionFromXml reactionFromXml;
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
public ReactionXmlParser(CellDesignerElementCollection elements) {
reactionToXml = new ReactionToXml(elements);
- reactionFromXml = new ReactionFromXml(elements);
+ reactionFromXml = new ReactionFromXml();
}
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
index 5d6268512ac181094ada756fa641f1e72fb38409..4c8449fd5e790233a81bd3c2f9387b6ba600964a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
@@ -3,6 +3,11 @@ package lcsb.mapviewer.converter.model.celldesigner.species;
import java.util.ArrayList;
import java.util.List;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -11,18 +16,15 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
/**
* Abstract class with the interface to parse element in CellDesigner file.
*
* @author Piotr Gawron
*
* @param <T>
- * type of the object to parse
+ * type of the celldesigner object to parse
+ * @param <S>
+ * type of the model object to be obtained
*/
public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>, S extends Element> extends XmlParser {
@@ -30,13 +32,13 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(AbstractElementXmlParser.class.getName());
+ private Logger logger = Logger.getLogger(AbstractElementXmlParser.class.getName());
/**
* List of special strings in CellDesigner that should be translated into some
* UTF characters.
*/
- private List<Pair<String, String>> encodedStrings = new ArrayList<Pair<String, String>>();
+ private List<Pair<String, String>> encodedStrings = new ArrayList<Pair<String, String>>();
/**
* Parser of the notes that allows to extract additional structurized data for
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
index eed59742b21683d29f5ee8ef14eb945090c1bc57..1213df96ac1b3cb495499cfb166636eb1a3ee052 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
@@ -9,6 +9,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
@@ -26,10 +27,21 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesigner
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(AntisenseRnaXmlParser.class.getName());
+ private Logger logger = Logger.getLogger(AntisenseRnaXmlParser.class.getName());
+ /**
+ * List of {@link CellDesignerElement celldesigner elements} obtained during
+ * parsing process.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * list of {@link CellDesignerElement celldesigner elements} obtained
+ * during parsing process
+ */
public AntisenseRnaXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
index 273be9a25862d99f8c3951dad61c48f67494fe1a..3813032e290fcb0a5a8632fe27ec6c362aba596e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
@@ -8,6 +8,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Gene;
@@ -27,8 +28,20 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(GeneXmlParser.class.getName());
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
public GeneXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
index 80d6eb5b25efe3158b1ee828dc850146b5f9782e..09ed6d94052da4ee93b97fa0478881480e130601 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
@@ -46,23 +46,32 @@ public enum ProteinMapping {
/**
* CellDesigner xml node type.
*/
- private String cellDesignerString;
+ private String cellDesignerString;
/**
- * Class that should be used to represent cell designer node.
+ * Model class that should be used to represent cell designer node.
*/
- private Class<? extends Protein> clazz;
+ private Class<? extends Protein> clazz;
+ /**
+ * Default class logger.
+ */
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ProteinMapping.class);
+ private static Logger logger = Logger.getLogger(ProteinMapping.class);
- private Class<? extends CellDesignerProtein<?>> cellDesignerClazz;
+ /**
+ * {@link CellDesignerProtein Celldesigner structure} used to represent the
+ * node.
+ */
+ private Class<? extends CellDesignerProtein<?>> cellDesignerClazz;
/**
* Default constructor.
*
* @param cellDesignerClazz
* {@link #clazz}
+ * @param modelClazz
+ * {@link #clazz class} in model corresponding to celldesigner object
* @param cellDesignerString
* {@link #cellDesignerString}
*/
@@ -88,6 +97,11 @@ public enum ProteinMapping {
return clazz;
}
+ /**
+ * Returns celldesigner class type that represents xml node.
+ *
+ * @return celldesigner class type that represents xml node
+ */
public Class<? extends CellDesignerProtein<?>> getCellDesignerClazz() {
return cellDesignerClazz;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
index 7d41df9d79cd0275b5897b32a7360d87c049a27a..68cd9af32aa18bae5cbbf1832c54febe80d4fef1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
@@ -8,6 +8,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Protein;
@@ -29,8 +30,20 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(ProteinXmlParser.class.getName());
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
public ProteinXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
index 04783c194b808929c8fc182ae390bd0f7e4e16ce..2febc38cc9615cff4420b7e0665521d27fe14817 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
@@ -8,6 +8,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
import lcsb.mapviewer.model.map.species.Rna;
@@ -27,8 +28,20 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(RnaXmlParser.class.getName());
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
public RnaXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
}
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 4f278118cc57d64e5e27dc59a9f675df04f9cdb3..50039742220137b42fc037bf8807605b338d1779 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
@@ -102,11 +102,19 @@ public class SpeciesCollectionXmlParser extends XmlParser {
}
};
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
/**
* Default constructor. Model is required because some CellDesigner nodes
* require access to other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public SpeciesCollectionXmlParser(CellDesignerElementCollection elements) {
sbmlSpeciesParser = new SpeciesSbmlParser(elements);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
index 35b6c49eb19fd0cfedea8774b34f6236da05ac5c..933c6486fdc3e66dc3257f5053bbf07cd8be08d9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
@@ -92,29 +92,45 @@ public enum SpeciesMapping {
/**
* CellDesigner xml node type.
*/
- private String cellDesignerString;
+ private String cellDesignerString;
/**
* Class that should be used to represent cell designer node.
*/
- private Class<? extends CellDesignerSpecies> cellDesignerClazz;
+ private Class<? extends CellDesignerSpecies<?>> cellDesignerClazz;
- private Class<? extends Element> modelClazz;
+ /**
+ * Model class that represent the species.
+ */
+ private Class<? extends Element> modelClazz;
/**
* Default constructor.
*
* @param cellDesignerClazz
* {@link #clazz}
+ * @param modelClazz
+ * {@link #clazz class} in model corresponding to celldesigner object
* @param cellDesignerString
* {@link #cellDesignerString}
*/
- SpeciesMapping(Class<? extends CellDesignerSpecies> cellDesignerClazz, Class<? extends Element> modelClazz, String cellDesignerString) {
+ SpeciesMapping(Class<?> cellDesignerClazz, Class<? extends Element> modelClazz, String cellDesignerString) {
this.cellDesignerString = cellDesignerString;
- this.cellDesignerClazz = cellDesignerClazz;
+ this.setCellDesignerClazz(cellDesignerClazz);
this.modelClazz = modelClazz;
}
+ /**
+ * Sets new cellDesignerClazz value.
+ *
+ * @param cellDesignerClazz2
+ * new cellDesignerClazz value
+ */
+ @SuppressWarnings("unchecked")
+ private void setCellDesignerClazz(Class<?> cellDesignerClazz2) {
+ cellDesignerClazz = (Class<? extends CellDesignerSpecies<?>>) cellDesignerClazz2;
+ }
+
/**
* @return the cellDesignerString
* @see #cellDesignerString
@@ -127,10 +143,15 @@ public enum SpeciesMapping {
* @return the clazz
* @see #clazz
*/
- public Class<? extends CellDesignerSpecies> getCellDesignerClazz() {
+ public Class<? extends CellDesignerSpecies<?>> getCellDesignerClazz() {
return cellDesignerClazz;
}
+ /**
+ * Returns model class that represent the species.
+ *
+ * @return model class that represent the species
+ */
public Class<? extends Element> getModelClazz() {
return modelClazz;
}
@@ -144,7 +165,7 @@ public enum SpeciesMapping {
* @return new instance of {@link CellDesignerSpecies} specific for this
* {@link SpeciesMapping}.
*/
- public CellDesignerSpecies createSpecies(CellDesignerSpecies result) {
+ public CellDesignerSpecies<?> createSpecies(CellDesignerSpecies<?> result) {
try {
return cellDesignerClazz.getConstructor(result.getClass()).newInstance(result);
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index 7033c094dd4fe52b3be1b2e1d1521e6862d648db..964eb33e9ae2fecbadc778429f110f563db1520d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParse
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
@@ -47,11 +48,19 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(SpeciesSbmlParser.class.getName());
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
private CellDesignerElementCollection elements;
/**
* Default constructor. Model is required because some nodes require access to
* other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public SpeciesSbmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
@@ -146,7 +155,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
species.setCharge(getNodeAttr("charge", spieciesNode));
species.setOnlySubstanceUnits(getNodeAttr("hasOnlySubstanceUnits", spieciesNode));
- CellDesignerCompartment compartment = elements.getCompartmentByCompartmentId(getNodeAttr("compartment", spieciesNode));
+ CellDesignerCompartment compartment = elements.getElementByElementId(getNodeAttr("compartment", spieciesNode));
if (compartment != null) {
species.setParent(compartment);
}
@@ -305,7 +314,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
*/
public Pair<String, CellDesignerSpecies<?>> parseSpeciesIdentity(Node rootNode) throws InvalidXmlSchemaException {
NodeList nodes = rootNode.getChildNodes();
- CellDesignerSpecies<?> result = new CellDesignerSpecies();
+ CellDesignerSpecies<?> result = new CellDesignerSpecies<Species>();
Node classNode = getNode("celldesigner:class", nodes);
if (classNode == null) {
throw new InvalidXmlSchemaException("Species node in Sbml model doesn't contain node \"celldesigner:class\".");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index 3a1c835cffe721d71f06ecadf69229d8c7cbb50a..e3456b1c883be2e35b467ce847c334b709a798fa 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -140,7 +140,7 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
@Override
public AntisenseRna createModelElement(String aliasId) {
AntisenseRna result = new AntisenseRna(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
for (CellDesignerAntisenseRnaRegion region : regions) {
result.addRegion(region.createAntisenseRegionAlias());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
index 141a50971cfeb1fd959c40abeeaf289f520ed4a2..dab97cf4b61564dee8bb3d7fede88ccc318a6e3f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
@@ -115,8 +115,8 @@ public abstract class CellDesignerChemical<T extends Chemical> extends CellDesig
}
@Override
- protected void setAliasFields(T result) {
- super.setAliasFields(result);
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
result.setInChI(inChI);
result.setInChIKey(inChIKey);
result.setSmiles(smiles);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
index 3c7bbe5ae3c80b165b177d432d3c83cd5afba39e..59a7f110ce2f147fa7a7d18a028dbe7343c796a6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
@@ -141,7 +141,7 @@ public class CellDesignerCompartment extends CellDesignerElement<Compartment> im
@Override
public Compartment createModelElement(String aliasId) {
Compartment result = new Compartment(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
if (elements.size() > 0) {
throw new NotImplementedException();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
index 1b4d7d6de12ab9ce5bc25ae29705d308dad15962..89f996caa824ef013a845b574a9ebac0507f34e3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
@@ -157,7 +157,7 @@ public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
@Override
public Complex createModelElement(String aliasId) {
Complex result = new Complex(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
if (elements.size() > 0) {
throw new NotImplementedException();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
index 76a0fe4aef1f136b6b0d11fb04b0c5f1faea745e..7ef30e6d43cb853a7ce86bfe7525630c67c95859 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
@@ -44,7 +44,7 @@ public class CellDesignerDegraded extends CellDesignerSpecies<Degraded> {
@Override
public Degraded createModelElement(String aliasId) {
Degraded result = new Degraded(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
index 3bc6b963079e9074df8e44ee5233ef3b0c3170c9..df5daabb489c0210bb5a56fa55f173ad9835df29 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
@@ -44,7 +44,7 @@ public class CellDesignerDrug extends CellDesignerSpecies<Drug> {
@Override
public Drug createModelElement(String aliasId) {
Drug result = new Drug(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
index f87b166e5ac16abf9f16652407ddb5c77629621f..c686ccb3cfb6655961373683a969c831c1d19f5b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
@@ -127,14 +127,31 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
this.notes = "";
}
+ /**
+ * Adds set of {@link MiriamData} to the object.
+ *
+ * @param miriamData
+ * objects to be added
+ */
public void addMiriamData(Collection<MiriamData> miriamData) {
for (MiriamData md : miriamData) {
addMiriamData(md);
}
}
+ /**
+ * Returns identifier of the species.
+ *
+ * @return identifier of the species
+ */
public abstract String getElementId();
+ /**
+ * Adds {@link MiriamData} to the element.
+ *
+ * @param md
+ * object to be added
+ */
public void addMiriamData(MiriamData md) {
if (this.miriamData.contains(md)) {
logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getElementId() + " already exists. Ignoring...");
@@ -144,6 +161,12 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
}
+ /**
+ * Sets notes about the object.
+ *
+ * @param notes
+ * new notes
+ */
public void setNotes(String notes) {
if (notes != null) {
if (notes.contains("</html>")) {
@@ -178,14 +201,30 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
}
+ /**
+ * Returns notes about the object.
+ *
+ * @return notes about the object
+ */
public String getNotes() {
return notes;
}
+ /**
+ * Returns the symbol of the element.
+ *
+ * @return the symbol of the element
+ */
public String getSymbol() {
return symbol;
}
+ /**
+ * Sets symbol of the element.
+ *
+ * @param symbol
+ * new symbol
+ */
public void setSymbol(String symbol) {
this.symbol = symbol;
}
@@ -207,6 +246,12 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
this.fullName = fullName;
}
+ /**
+ * Returns the name of the object.
+ *
+ * @return name of the object
+ *
+ */
public String getName() {
return name;
}
@@ -220,10 +265,21 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
this.name = name;
}
+ /**
+ * Get list of synonyms.
+ *
+ * @return list of synonyms
+ */
public List<String> getSynonyms() {
return synonyms;
}
+ /**
+ * Sets list of synonyms to the element.
+ *
+ * @param synonyms
+ * new list
+ */
public void setSynonyms(List<String> synonyms) {
this.synonyms = synonyms;
}
@@ -279,22 +335,49 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
this.complex = complex;
}
+ /**
+ * Returns list of {@link MiriamData annotations} for the object.
+ *
+ * @return list of {@link MiriamData annotations} for the object
+ */
public Set<MiriamData> getMiriamData() {
return miriamData;
}
+ /**
+ * Returns the abbreviation.
+ *
+ * @return the abbreviation
+ */
public String getAbbreviation() {
return abbreviation;
}
+ /**
+ * Sets abbreviation.
+ *
+ * @param abbreviation
+ * new abbreviation
+ */
public void setAbbreviation(String abbreviation) {
this.abbreviation = abbreviation;
}
+ /**
+ * Returns the formula.
+ *
+ * @return the formula
+ */
public String getFormula() {
return formula;
}
+ /**
+ * Sets formula.
+ *
+ * @param formula
+ * new formula
+ */
public void setFormula(String formula) {
this.formula = formula;
}
@@ -319,15 +402,39 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
this.formerSymbols.add(formerSymbol);
}
+ /**
+ * Sets element identifier.
+ *
+ * @param elementId
+ * element identifier
+ */
public abstract void setElementId(String elementId);
+ /**
+ * Creates model object from this celldesigner structure.
+ *
+ * @return model object from this celldesigner structure
+ */
public T createModelElement() {
return createModelElement(null);
}
+ /**
+ * Creates model object from this celldesigner structure.
+ *
+ * @param modelElementId
+ * identifier of new model object
+ * @return model object from this celldesigner structure
+ */
public abstract T createModelElement(String modelElementId);
- protected void setAliasFields(T result) {
+ /**
+ * Sets values from this cell designer structure into model object.
+ *
+ * @param result
+ * object to which values should be assigned
+ */
+ protected void setModelObjectFields(T result) {
result.setNotes(notes);
result.setSymbol(symbol);
result.setFullName(fullName);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index e053a853f13bd7969721a1e6880c6479d26493a5..efc960c93ecf0b71b58863567529b7646be24847 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -107,7 +107,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
@Override
public Gene createModelElement(String aliasId) {
Gene result = new Gene(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
for (CellDesignerModificationResidue mr : modificationResidues) {
result.addModificationResidue(mr.createModificationResidueAlias());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
index 4d12d9905728b15c50324f1783a1a3a623d5a2d5..e26903d0bd2cdafc801a90f187c2c83f76763200 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
@@ -33,6 +33,12 @@ public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProte
super(species);
}
+ /**
+ * Deafult constructor.
+ *
+ * @param id
+ * identifier of the protein
+ */
public CellDesignerGenericProtein(String id) {
setElementId(id);
}
@@ -46,9 +52,10 @@ public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProte
}
}
+ @Override
public GenericProtein createModelElement(String aliasId) {
GenericProtein result = new GenericProtein(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
index 7a828e6790800e75b25a37e1027b7cdb1431f4b0..31eb0cf621a5d2d86a08bdfd244facf0ad683196 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
@@ -45,7 +45,7 @@ public class CellDesignerIon extends CellDesignerChemical<Ion> {
@Override
public Ion createModelElement(String aliasId) {
Ion result = new Ion(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
index 8a7fbc97a8b0550392419d1db4b1f0fe3a20d80a..2a1da5d74367f703c0f807563f54cecbf41257a4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
@@ -45,7 +45,7 @@ public class CellDesignerIonChannelProtein extends CellDesignerProtein<IonChanne
@Override
public IonChannelProtein createModelElement(String aliasId) {
IonChannelProtein result = new IonChannelProtein(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
index a27e5fe6bd0b8dd7d4b838ca480b51303f6e10d6..8ee7a94bce41eaeff8e51f16f7d8527515d7d9a3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
@@ -45,7 +45,7 @@ public class CellDesignerPhenotype extends CellDesignerSpecies<Phenotype> {
@Override
public Phenotype createModelElement(String aliasId) {
Phenotype result = new Phenotype(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index 35f08309b1760c71125a3bc6444272ed4d172167..d94a1dc5381972c8515bccb8a85325e9e152da04 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -142,8 +142,8 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
}
@Override
- protected void setAliasFields(T result) {
- super.setAliasFields(result);
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
result.setStructuralState(structuralState);
for (CellDesignerModificationResidue mr : modificationResidues) {
result.addModificationResidue(mr.createModificationResidueAlias());
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
index 0416953bc0b77633dd4aa5cb7fee8d323dc7d030..f838567d0bd56393a0182cd1f719bf885964e4b4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
@@ -45,7 +45,7 @@ public class CellDesignerReceptorProtein extends CellDesignerProtein<ReceptorPro
@Override
public ReceptorProtein createModelElement(String aliasId) {
ReceptorProtein result = new ReceptorProtein(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index e2b75d38162e3892bfb02eee228b0482dc58b4cc..a1d476c3f02c9681fed20b53cf0bbd62b8d869ef 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -136,7 +136,7 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
@Override
public Rna createModelElement(String aliasId) {
Rna result = new Rna(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
for (CellDesignerRnaRegion region : regions) {
result.addRegion(region.createRnaRegionAlias());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
index ccc562159f2c62890f6a6b8181862c1e4e0b4534..cdbf286113a9c918eb1e5ec23bc803704981d5d0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
@@ -52,7 +52,7 @@ public class CellDesignerSimpleMolecule extends CellDesignerChemical<SimpleMolec
@Override
public SimpleMolecule createModelElement(String aliasId) {
SimpleMolecule result = new SimpleMolecule(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index 66acec7dce75536aaf67e1f0bdd9890bb6cd7a55..693bd4dba045f4266115b4df0dc547c8214edce7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -465,8 +465,8 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
}
@Override
- protected void setAliasFields(T result) {
- super.setAliasFields(result);
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
result.setInitialAmount(initialAmount);
result.setCharge(charge);
result.setInitialConcentration(initialConcentration);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
index e30481b3980abb53dd7fb9e1c80238604b268bfc..f3484fcbd4411a0fd35039fbed225d0734b787b1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
@@ -45,7 +45,7 @@ public class CellDesignerTruncatedProtein extends CellDesignerProtein<TruncatedP
@Override
public TruncatedProtein createModelElement(String aliasId) {
TruncatedProtein result = new TruncatedProtein(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
index e2c47cc817db2604da542fde81cf3d211d150707..5253b209d0b27d201eceb86bd50f4e08d702d82c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
@@ -43,7 +43,7 @@ public class CellDesignerUnknown extends CellDesignerSpecies<Unknown> {
@Override
public Unknown createModelElement(String aliasId) {
Unknown result = new Unknown(aliasId);
- super.setAliasFields(result);
+ super.setModelObjectFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
index 4861bdbb14a68ee56775f4c709569486857b5efc..36decddc98a49f81ef86a92f4431a0349825d4c2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
@@ -25,40 +25,40 @@ public class CellDesignerAntisenseRnaRegion implements Serializable {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default size of the object (in graphical representation).
*/
- private static final double DEFAULT_SIZE = 0.1;
+ private static final double DEFAULT_SIZE = 0.1;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerAntisenseRnaRegion.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerAntisenseRnaRegion.class.getName());
/**
* Unique identifier in the database.
*/
- private int id;
+ private int id;
/**
* String identifier of the element. Unique in the model.
*/
- private String idAntisenseRnaRegion = "";
+ private String idAntisenseRnaRegion = "";
/**
* Name of the region.
*/
- private String name = "";
+ private String name = "";
/**
* Defines a state of the region (for instance ubiquitinated etc).
*
* @see ModificationState
*/
- private ModificationState state = null;
+ private ModificationState state = null;
/**
* Type of the region in the rna. There are three possible values:
@@ -68,22 +68,22 @@ public class CellDesignerAntisenseRnaRegion implements Serializable {
* <li>Modification site.</li>
* </ul>
*/
- private AntisenseRnaRegionType type;
+ private AntisenseRnaRegionType type;
/**
* Size of the region in the graphic representation.
*/
- private double size = DEFAULT_SIZE;
+ private double size = DEFAULT_SIZE;
/**
* Position on the species in graphic representation.
*/
- private Double pos;
+ private Double pos;
/**
* Defines a species where the region belongs to.
*/
- private CellDesignerAntisenseRna species;
+ private CellDesignerAntisenseRna species;
/**
* Default constructor.
@@ -316,6 +316,11 @@ public class CellDesignerAntisenseRnaRegion implements Serializable {
this.id = id;
}
+ /**
+ * Creates model representation of {@link AntisenseRnaRegion}.
+ *
+ * @return {@link AntisenseRnaRegion} representing this object in a model
+ */
public AntisenseRnaRegion createAntisenseRegionAlias() {
AntisenseRnaRegion result = new AntisenseRnaRegion();
result.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index abd1d0416685a280dedb072074e1bbbad8fd028c..ba82b6567d1672bdee106fcb78030553b7ceaac8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -88,6 +88,12 @@ public class CellDesignerModificationResidue implements Serializable {
this.state = mr.state;
}
+ /**
+ * Constructor that creates object from model representation of modification.
+ *
+ * @param mr
+ * model represnation of {@link ModificationResidue}
+ */
public CellDesignerModificationResidue(ModificationResidue mr) {
this.idModificationResidue = mr.getIdModificationResidue();
this.name = mr.getName();
@@ -297,6 +303,11 @@ public class CellDesignerModificationResidue implements Serializable {
this.species = species;
}
+ /**
+ * Creates model representation of {@link ModificationResidue}.
+ *
+ * @return {@link ModificationResidue} representing this object in a model
+ */
public ModificationResidue createModificationResidueAlias() {
ModificationResidue result = new ModificationResidue();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
index 926263ee13ef4af287e31b619714ff4e84f9a2d5..bbb44414758cd125082930ee1f9f62f290b94edd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
@@ -12,7 +12,8 @@ import lcsb.mapviewer.model.map.species.field.RnaRegion;
/**
* This structure contains information about rna region (rna fragment of
* interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna Rna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna
+ * Rna}.
*
* @author Piotr Gawron
*
@@ -76,7 +77,7 @@ public class CellDesignerRnaRegion implements Serializable {
/**
* Defines a species where the region belongs to.
*/
- private CellDesignerRna species;
+ private CellDesignerRna species;
/**
* Default constructor.
@@ -135,7 +136,8 @@ public class CellDesignerRnaRegion implements Serializable {
* region.
*
* @param mr
- * {@link CellDesignerRnaRegion} from which data will be used to update
+ * {@link CellDesignerRnaRegion} from which data will be used to
+ * update
*/
public void update(CellDesignerRnaRegion mr) {
if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
@@ -280,6 +282,11 @@ public class CellDesignerRnaRegion implements Serializable {
this.species = species;
}
+ /**
+ * Creates model representation of {@link RnaRegion}.
+ *
+ * @return {@link RnaRegion} representing this object in a model
+ */
public RnaRegion createRnaRegionAlias() {
RnaRegion result = new RnaRegion();
result.setIdRnaRegion(this.idRnaRegion);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..aeacb0eda133269ffa24ea15b451f7ded862852d
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java
@@ -0,0 +1,5 @@
+/**
+ * This package contains internal CellDesigner structures describing some fields
+ * of the Species elements.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java
index 227adf6ee7b9cc32bbeaa6b981b6b2e6dbd90fe5..2248a314c6741f9748e9936d2bf76e002c568a2a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java
@@ -1,7 +1,6 @@
-/**
- * This package contains internal CellDesigner structures used in the xml to
- * store some data. Structures from this package should be used only during
- * convertion from/to CellDEsigner format.
- */
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
+/**
+ * This package contains internal CellDesigner structures used in the xml to
+ * store some data. Structures from this package should be used only during
+ * convertion from/to CellDEsigner format.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.structure;
\ No newline at end of file
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
index cc85c6f0e78271b8c71997230d171bc500191881..cb6b24155d85b63768cde78a311549c07a50a367 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
@@ -454,7 +454,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
try {
// test situation when createProperTypeReaction returns reaction of
// unknown type
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
return result;
}
@@ -484,7 +484,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
}
}
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
return new NewReactionType(result);
}
@@ -506,7 +506,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoProductReaction encounter
// reaction with two many base reactants
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addReactant(new Reactant());
@@ -530,7 +530,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoProductReaction encounter
// reaction with two many base products
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addProduct(new Product());
@@ -562,7 +562,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
}
}
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
return new NewReactionType(result);
}
@@ -584,7 +584,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoReactantReaction encounter
// reaction with two many base reactants
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addReactant(new Reactant());
@@ -608,7 +608,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoReactantReaction encounter
// reaction with two many base products
- ReactionFromXml parser = new ReactionFromXml(elements) {
+ ReactionFromXml parser = new ReactionFromXml() {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addProduct(new Product());
@@ -629,7 +629,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
@Test
public void testParseInvalidEditPointsString() throws Exception {
try {
- ReactionFromXml parser = new ReactionFromXml(elements);
+ ReactionFromXml parser = new ReactionFromXml();
parser.parseEditPointsString("1");
fail("Exception expected");
@@ -644,7 +644,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
@Test
public void testParseInvalidEditPointsString2() throws Exception {
try {
- ReactionFromXml parser = new ReactionFromXml(elements);
+ ReactionFromXml parser = new ReactionFromXml();
parser.parseEditPointsString("1,Infinity");
fail("Exception expected");
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 b9b22b09e354dc56e86fc8ef05da06457ad4d53c..ff062411c0acd1cb89e20ffa79d4f063c59705e3 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
@@ -1551,7 +1551,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa1.setWidth(300.0);
sa1.setHeight(400.0);
model.addElement(sa1);
- elements.addAlias(sa1, new CellDesignerGenericProtein("s1"));
+ elements.addModelElement(sa1, new CellDesignerGenericProtein("s1"));
Species sa2 = new GenericProtein("sa2");
sa2.setX(1050.0);
@@ -1559,7 +1559,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa2.setWidth(300.0);
sa2.setHeight(450.0);
model.addElement(sa2);
- elements.addAlias(sa2, new CellDesignerGenericProtein("s2"));
+ elements.addModelElement(sa2, new CellDesignerGenericProtein("s2"));
Species sa3 = new GenericProtein("sa3");
sa3.setX(600.0);
@@ -1567,7 +1567,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa3.setWidth(300.0);
sa3.setHeight(400.0);
model.addElement(sa3);
- elements.addAlias(sa3, new CellDesignerGenericProtein("s3"));
+ elements.addModelElement(sa3, new CellDesignerGenericProtein("s3"));
Species sa4 = new GenericProtein("sa4");
sa4.setX(550.0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
index c4a253098856018d5846816ee826b439d61602f2..2b76440dfc2b212ff4a10001562bac1ade80187f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
@@ -51,7 +51,7 @@ public class SpeciesMappingTest {
// mopdify one of the elements of SpeciesMapping so it will have invalid
// implementation
SpeciesMapping typeToModify = SpeciesMapping.ANTISENSE_RNA;
- Class<? extends CellDesignerSpecies> clazz = typeToModify.getCellDesignerClazz();
+ Class<? extends CellDesignerSpecies<?>> clazz = typeToModify.getCellDesignerClazz();
try {
Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
index 6e000c3bcafb3af831fb2ceb967c282fe1cb9cc4..214e436b0aa4dd9bf87e50ac0081c78e0a93d6b8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
@@ -18,8 +18,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
public class ElementTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ElementTest.class);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
index 0ab3558eea0c50e343686212fe213a7dbffa29e4..8894d14ba9a3f1ef55304feb81f00affef9148a2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
@@ -16,7 +16,6 @@ import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
public class ProteinTest {
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 f4664073978d6befb82847bd3014f59fec118336..c408b252ec46ad4dbd0e6197bca23debb212647c 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
@@ -80,6 +80,9 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class SbgnmlXmlExporter {
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
private ElementUtils eu = new ElementUtils();
/**
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 913e639749cf5a4171f13e879a67fe6c81b1c28d..f5dbf5eb9b96740e642987e4913e189aeb92b807 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
@@ -60,7 +60,6 @@ import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction
import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Gene;
@@ -637,27 +636,27 @@ public class SbgnmlXmlParser {
* @param model
* model to be updated
*/
- private void parseAlias(Glyph g, Species newAlias, Model model) {
- newAlias.setHeight(new Double(g.getBbox().getH()));
- newAlias.setWidth(new Double(g.getBbox().getW()));
- newAlias.setX(new Double(g.getBbox().getX()));
- newAlias.setY(new Double(g.getBbox().getY()));
+ private void parseAlias(Glyph g, Species newSpecies, Model model) {
+ newSpecies.setHeight(new Double(g.getBbox().getH()));
+ newSpecies.setWidth(new Double(g.getBbox().getW()));
+ newSpecies.setX(new Double(g.getBbox().getX()));
+ newSpecies.setY(new Double(g.getBbox().getY()));
if (g.getCompartmentRef() != null) {
Glyph compartmentGlyph = (Glyph) g.getCompartmentRef();
Compartment compartmentAlias = model.getElementByElementId(compartmentGlyph.getId());
- newAlias.setCompartment(compartmentAlias);
- compartmentAlias.addElement(newAlias);
- } else if (newAlias.getComplex() == null) {
+ newSpecies.setCompartment(compartmentAlias);
+ compartmentAlias.addElement(newSpecies);
+ } else if (newSpecies.getComplex() == null) {
// If the alias is in any compartment, assign it to that compartment
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;
+ boolean dx1 = compartmentAlias.getX() + compartmentAlias.getWidth() - newSpecies.getX() >= 0;
+ boolean dx2 = compartmentAlias.getX() - (newSpecies.getX() + newSpecies.getWidth()) <= 0;
+ boolean dy1 = compartmentAlias.getY() + compartmentAlias.getHeight() - newSpecies.getY() >= 0;
+ boolean dy2 = compartmentAlias.getY() - (newSpecies.getY() + newSpecies.getHeight()) <= 0;
if (dx1 && dx2 && dy1 && dy2) {
- newAlias.setCompartment(compartmentAlias);
- compartmentAlias.addElement(newAlias);
+ newSpecies.setCompartment(compartmentAlias);
+ compartmentAlias.addElement(newSpecies);
}
}
}
@@ -665,11 +664,11 @@ public class SbgnmlXmlParser {
// Parse units of information
for (Glyph child : g.getGlyph()) {
if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.UNIT_OF_INFORMATION)) {
- parseUnitOfInformation(child, newAlias);
+ parseUnitOfInformation(child, newSpecies);
}
}
- model.addElement(newAlias);
+ model.addElement(newSpecies);
}
/**
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 60d826079576c3520910e84811d00bdfe0a86e90..4940e5d439bfb89945ccdecee6ba3fb5ad8f49df 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
@@ -58,6 +58,9 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
*/
private static Logger logger = Logger.getLogger(ProteinConverter.class.getName());
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
private ElementUtils eu = new ElementUtils();
/**
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 b63e8970efd216abb5a64b5debcd45a3f5fe26b6..83355856444bdb59b0bf7e60f3623c537831ca1c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -21,11 +21,11 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Phenotype;
@@ -364,7 +364,8 @@ 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.getElement().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");
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
index 6bd52eb98f8c5a4c0556cdfcb77ad7a1fa67d3d4..a21596815a7af72d5e5b80ac68eec6bee8461762 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.reactome.utils;
-import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -11,8 +10,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
@@ -51,10 +50,11 @@ public class DataFormatter {
* @param list
* Species to transform
* @return human readable String representation of the linput Species list
- * @throws IOException
* @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
*/
- private String speciesListToString(List<Element> list) throws IOException, AnnotatorException {
+ private String speciesListToString(List<Element> list) throws AnnotatorException {
String result = "";
for (Element species : list) {
if (!result.equals("")) {
@@ -108,10 +108,11 @@ public class DataFormatter {
* @param result
* MatchResult to process.
* @return human readable String representing invalid local inputs
- * @throws IOException
* @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
*/
- public String getInvalidLocalInputString(MatchResult result) throws IOException, AnnotatorException {
+ public String getInvalidLocalInputString(MatchResult result) throws AnnotatorException {
return speciesListToString(result.getInvalidLocalInput());
}
@@ -121,10 +122,11 @@ public class DataFormatter {
* @param result
* MatchResult to process.
* @return human readable String representing invalid local output
- * @throws IOException
* @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
*/
- public String getInvalidLocalOutputString(MatchResult result) throws IOException, AnnotatorException {
+ public String getInvalidLocalOutputString(MatchResult result) throws AnnotatorException {
return speciesListToString(result.getInvalidLocalOutput());
}
@@ -134,10 +136,11 @@ public class DataFormatter {
* @param result
* MatchResult to process.
* @return human readable String representing invalid local modifiers
- * @throws IOException
* @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
*/
- public String getInvalidLocalModifierString(MatchResult result) throws IOException, AnnotatorException {
+ public String getInvalidLocalModifierString(MatchResult result) throws AnnotatorException {
return speciesListToString(result.getInvalidLocalModifier());
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
index e0d388081f08d78c2f9c9fcbd28e9379df5534d1..f8bb0ad229124dd544d300037d99778d8c4263fe 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
@@ -26,6 +26,13 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class ElementUtil {
+ /**
+ * Returns human readable id of the element from paramter.
+ *
+ * @param element
+ * element to be identified
+ * @return human readable id of the element from paramter
+ */
public String getElementTag(AnnotatedObject element) {
return new ElementUtils().getElementTag(element);
}
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 c6e710375c882574489ef1f2b1e25ad9209611b0..2075c95384af374854e41020db3c5804fe326398 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
@@ -52,6 +52,9 @@ public class ReactionComparator {
* @return resul of reaction comparison. For more details see:
* {@link MatchResult}
* @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
+ *
*/
public MatchResult compareReactions(Reaction reaction, ReactomeReactionlikeEvent reactomeReaction) throws ComparatorException {
MatchResult result = new MatchResult();
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 2a7c77ff9065027a44c47b5b63ed3f3451b784ec..e73db35d17601f3e32b4b1cba9f838c53166f31d 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.reactome.utils;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -23,9 +24,9 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
@@ -84,6 +85,13 @@ public class ReactomeQueryUtil {
@Autowired
private ChebiAnnotator chebiBackend;
+ /**
+ * Provides human readable id of element.
+ *
+ * @param element
+ * element for which we want id string.
+ * @return human readable id of element
+ */
public String getElementTag(AnnotatedObject element) {
return new ElementUtils().getElementTag(element);
}
@@ -535,13 +543,13 @@ public class ReactomeQueryUtil {
* @param complex
* object for which identifiers are looked for
* @return set of known identifiers
- * @throws IOException
+ *
+ * @throws AnnotatorException
* thrown when there is a problem accessing external annotation
* service
- * @throws AnnotatorException
*/
- public Set<MiriamData> getIdsForComplex(Complex complex) throws IOException, AnnotatorException {
- Set<MiriamData> result = new HashSet<MiriamData>();
+ public Set<MiriamData> getIdsForComplex(Complex complex) throws AnnotatorException {
+ Set<MiriamData> result = new HashSet<>();
for (Species species : complex.getAllSimpleChildren()) {
result.addAll(getIdsForSpecies(species));
}
@@ -554,17 +562,16 @@ public class ReactomeQueryUtil {
* @param species
* object for which identifiers are looked for
* @return set of known identifiers
- * @throws IOException
+ * @throws AnnotatorException
* thrown when there is a problem accessing external annotation
* service
- * @throws AnnotatorException
*/
- public Set<MiriamData> getIdsForSpecies(Element species) throws IOException, AnnotatorException {
+ public Set<MiriamData> getIdsForSpecies(Element species) throws AnnotatorException {
Set<MiriamData> result = new HashSet<>();
if (species instanceof Protein) {
result.addAll(elementUtil.getMiriamByType(species, MiriamType.UNIPROT, true));
} else if (species instanceof Phenotype) {
- return null;
+ return Collections.emptySet();
} else if (species instanceof Chemical) {
result.addAll(elementUtil.getMiriamByType(species, MiriamType.CHEBI, true));
} else {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
index 6e8618289768bc3e6babd3916e9d55362f5b7982..a7bf80f52d8a5a4cae417dc6464164a3f0304eeb 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
@@ -35,32 +35,32 @@ public abstract class ANodeComparator<T extends Element, U extends ReactomeDatab
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ANodeComparator.class);
+ private static Logger logger = Logger.getLogger(ANodeComparator.class);
/**
* Service used for annotation of proteins (and finding annotation of
* proteins).
*/
@Autowired
- private HgncAnnotator hgncAnnotator;
+ private HgncAnnotator hgncAnnotator;
/**
* Util object used for processing elements.
*/
@Autowired
- private ElementUtil elementUtil;
+ private ElementUtil elementUtil;
/**
* Service accessing chebi database.
*/
@Autowired
- private ChebiAnnotator chebiBackend;
+ private ChebiAnnotator chebiBackend;
/**
* This object allows to query reactome database for missing elements.
*/
@Autowired
- private ReactomeQueryUtil rcu;
+ private ReactomeQueryUtil rcu;
/**
* Comparator that allows to compare everything with everything else.
@@ -71,13 +71,13 @@ public abstract class ANodeComparator<T extends Element, U extends ReactomeDatab
* Type of the object in internal representation for which the comparator is
* designed for.
*/
- private Class<T> speciesClass;
+ private Class<T> speciesClass;
/**
* Type of the object in reactome representation for which the comparator is
* designed for.
*/
- private Class<U> reactomeSpeciesClass;
+ private Class<U> reactomeSpeciesClass;
/**
* Default constructor.
@@ -232,6 +232,13 @@ public abstract class ANodeComparator<T extends Element, U extends ReactomeDatab
this.hgncAnnotator = hgncAnnotator;
}
+ /**
+ * Returns short string description identifing element.
+ *
+ * @param element
+ * element to be transformed into string id
+ * @return short string description identifing element
+ */
public String getElementTag(AnnotatedObject element) {
return new ElementUtils().getElementTag(element);
}