From 17ba584eb55ab0ef8ec54274d6548c7d75bf577b Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Feb 2018 15:18:41 +0100
Subject: [PATCH] species parser extracted to separte package
---
.../model/sbml/SbmlBioEntityExporter.java | 35 ++++++++++++++++---
.../model/sbml/SbmlCompartmentExporter.java | 6 ++--
.../converter/model/sbml/SbmlExporter.java | 1 +
.../converter/model/sbml/SbmlParser.java | 1 +
.../model/sbml/SbmlReactionExporter.java | 17 +++++----
.../model/sbml/SbmlReactionParser.java | 1 +
.../{ => species}/SbmlSpeciesExporter.java | 10 +++---
.../sbml/{ => species}/SbmlSpeciesParser.java | 5 +--
8 files changed, 53 insertions(+), 23 deletions(-)
rename converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/{ => species}/SbmlSpeciesExporter.java (73%)
rename converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/{ => species}/SbmlSpeciesParser.java (94%)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index b864632fea..3367dd33ba 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -16,13 +16,14 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
-public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.sbml.jsbml.AbstractNamedSBase> extends XmlParser {
+public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.sbml.jsbml.AbstractNamedSBase>
+ extends XmlParser {
Logger logger = Logger.getLogger(SbmlBioEntityExporter.class);
- Layout layout;
+ private Layout layout;
- lcsb.mapviewer.model.map.model.Model minervaModel;
- Model sbmlModel;
+ private lcsb.mapviewer.model.map.model.Model minervaModel;
+ private Model sbmlModel;
Map<String, S> sbmlElementByElementId = new HashMap<>();
Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
@@ -57,7 +58,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
public abstract S createSbmlElement(T element) throws InconsistentModelException;
- protected S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
+ public S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
String mapKey = element.getClass().getSimpleName() + "\n" + element.getElementId() + "\n" + compartmentName;
if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
S sbmlElement = createSbmlElement(element);
@@ -88,4 +89,28 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
return (idCounter++) + "";
}
+ protected Model getSbmlModel() {
+ return sbmlModel;
+ }
+
+ protected void setSbmlModel(Model sbmlModel) {
+ this.sbmlModel = sbmlModel;
+ }
+
+ protected Layout getLayout() {
+ return layout;
+ }
+
+ protected void setLayout(Layout layout) {
+ this.layout = layout;
+ }
+
+ protected lcsb.mapviewer.model.map.model.Model getMinervaModel() {
+ return minervaModel;
+ }
+
+ protected void setMinervaModel(lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.minervaModel = minervaModel;
+ }
+
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
index 269927153d..5d6ed3439f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
@@ -18,17 +18,17 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
@Override
public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
- return sbmlModel.createCompartment("comp_" + (getNextId()));
+ return getSbmlModel().createCompartment("comp_" + (getNextId()));
}
@Override
protected List<Compartment> getElementList() {
- return minervaModel.getCompartments();
+ return getMinervaModel().getCompartments();
}
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
- return layout.createCompartmentGlyph(glyphId, sbmlCompartmentId);
+ return getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index d05941bef4..57d7dd8793 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -11,6 +11,7 @@ import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index ee244ef561..beed330498 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -28,6 +28,7 @@ import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
index 7f39759342..e769a96c8c 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
@@ -21,7 +21,6 @@ import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
-import org.sbml.jsbml.text.parser.ParseException;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
@@ -61,7 +60,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
if (result != null) {
return result;
}
- result = sbmlModel.createReaction(reactionId);
+ result = getSbmlModel().createReaction(reactionId);
result.setReversible(reaction.isReversible());
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
@@ -88,7 +87,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
SbmlKinetics kinetics = reaction.getKinetics();
KineticLaw result = new KineticLaw();
for (SbmlParameter minervaParameter : kinetics.getParameters()) {
- if (minervaModel.getParameterById(minervaParameter.getElementId()) == null) {
+ if (getMinervaModel().getParameterById(minervaParameter.getElementId()) == null) {
LocalParameter parameter = new LocalParameter();
parameter.setId(minervaParameter.getElementId());
parameter.setName(minervaParameter.getName());
@@ -102,11 +101,11 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
Node node = super.getXmlDocumentFromString(kinetics.getDefinition());
for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", node)) {
String id = super.getNodeValue(ciNode).trim();
- Element element = minervaModel.getElementByElementId(id);
+ Element element = getMinervaModel().getElementByElementId(id);
if (element != null) {
String sbmlId = null;
- Species species= speciesExporter.sbmlElementByElementId.get(id);
- if (species !=null) {
+ Species species = speciesExporter.sbmlElementByElementId.get(id);
+ if (species != null) {
sbmlId = species.getId();
} else {
sbmlId = compartmentExporter.sbmlElementByElementId.get(id).getId();
@@ -143,10 +142,10 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
try {
// handle case when input data cannot doesn't come from SBML parser and contains
// "__" that mess up identifier uniqueness
- reactionGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+ reactionGlyph = getLayout().createReactionGlyph(glyphId, sbmlElementId);
} catch (IllegalArgumentException e) {
glyphId += "_" + getNextId();
- reactionGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+ reactionGlyph = getLayout().createReactionGlyph(glyphId, sbmlElementId);
}
return reactionGlyph;
@@ -154,7 +153,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
@Override
protected Collection<Reaction> getElementList() {
- return minervaModel.getReactions();
+ return getMinervaModel().getReactions();
}
@Override
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index a623cd3695..6b6e41c57a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -29,6 +29,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
+import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.PolylineData;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
similarity index 73%
rename from converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesExporter.java
rename to converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index cbde58157f..17a1a9e100 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.species;
import java.util.List;
@@ -6,6 +6,8 @@ import org.apache.log4j.Logger;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
+import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
@@ -21,7 +23,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
@Override
public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
- org.sbml.jsbml.Species result = sbmlModel.createSpecies("species_" + (getNextId()));
+ org.sbml.jsbml.Species result = getSbmlModel().createSpecies("species_" + (getNextId()));
if (element.getCompartment() != null) {
result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment(), null));
}
@@ -30,13 +32,13 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
- AbstractReferenceGlyph speciesGlyph = layout.createSpeciesGlyph(glyphId, sbmlElementId);
+ AbstractReferenceGlyph speciesGlyph = getLayout().createSpeciesGlyph(glyphId, sbmlElementId);
return speciesGlyph;
}
@Override
protected List<Species> getElementList() {
- return minervaModel.getSpeciesList();
+ return getMinervaModel().getSpeciesList();
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
similarity index 94%
rename from converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
rename to converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index 1a9826c4e3..f93acacea8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.species;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
@@ -15,6 +15,7 @@ import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.SbmlElementParser;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
@@ -51,7 +52,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
@Override
- protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
+ public List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
List<Element> result = super.mergeLayout(elements, sbmlLayout, sbmlModel);
--
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