From c94158a79f70fcaff8709b4b358c43751b14ba56 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 21 Dec 2017 16:22:16 +0100
Subject: [PATCH] export of elements use autogenerated ids
---
.../converter/model/sbml/SbmlBioEntityExporter.java | 6 ++++++
.../converter/model/sbml/SbmlCompartmentExporter.java | 2 +-
.../lcsb/mapviewer/converter/model/sbml/SbmlExporter.java | 3 ++-
.../converter/model/sbml/SbmlReactionExporter.java | 7 +++----
.../converter/model/sbml/SbmlSpeciesExporter.java | 3 +--
5 files changed, 13 insertions(+), 8 deletions(-)
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 1a18c6ef25..4e9d5a26ab 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
@@ -28,6 +28,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
private Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
+ private int idCounter = 0;
+
public SbmlBioEntityExporter(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
this.layout = sbmlLayout;
this.minervaModel = minervaModel;
@@ -81,4 +83,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
protected abstract AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId);
+ protected String getNextId() {
+ return (idCounter++) + "";
+ }
+
}
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 08b5be58ec..269927153d 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
@@ -18,7 +18,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
@Override
public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
- return sbmlModel.createCompartment("comp_" + element.getName());
+ return sbmlModel.createCompartment("comp_" + (getNextId()));
}
@Override
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 0a54f2fa59..df47256188 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
@@ -12,6 +12,7 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.species.Species;
public class SbmlExporter {
public String toXml(lcsb.mapviewer.model.map.model.Model model)
@@ -21,7 +22,7 @@ public class SbmlExporter {
Layout layout = createSbmlLayout(model, result);
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
- SbmlSpeciesExporter speciesExporter = new SbmlSpeciesExporter(layout, model, compartmentExporter);
+ SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model, compartmentExporter);
SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter);
compartmentExporter.exportElements(result);
speciesExporter.exportElements(result);
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 092a3b7679..e6be4a1c1e 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
@@ -15,18 +15,17 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sbml.jsbml.Reaction> {
Logger logger = Logger.getLogger(SbmlReactionExporter.class);
- private int idCounter = 0;
- private SbmlSpeciesExporter speciesExporter;
+ private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter;
public SbmlReactionExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel,
- SbmlSpeciesExporter speciesExporter) {
+ SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter) {
super(layout, minervaModel);
this.speciesExporter = speciesExporter;
}
@Override
public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
- org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (idCounter++));
+ org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
result.createProduct(sbmlSymbol);
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/SbmlSpeciesExporter.java
index 692095b88b..cbde58157f 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/SbmlSpeciesExporter.java
@@ -11,7 +11,6 @@ import lcsb.mapviewer.model.map.species.Species;
public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
Logger logger = Logger.getLogger(SbmlSpeciesExporter.class);
- private int idCounter = 0;
private SbmlCompartmentExporter compartmentExporter;
public SbmlSpeciesExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel,
@@ -22,7 +21,7 @@ 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_" + (idCounter++));
+ org.sbml.jsbml.Species result = sbmlModel.createSpecies("species_" + (getNextId()));
if (element.getCompartment() != null) {
result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment(), null));
}
--
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