From e6778b9c822915d5464e6663e8478b09a6a3db51 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Sun, 18 Nov 2018 18:57:02 +0100
Subject: [PATCH] common code for render information
---
.../model/sbml/SbmlBioEntityExporter.java | 29 ++++++++++---------
.../compartment/SbmlCompartmentExporter.java | 2 +-
.../sbml/reaction/SbmlReactionExporter.java | 7 ++---
3 files changed, 20 insertions(+), 18 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 58f4824698..190a2bb028 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
@@ -150,16 +150,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
protected ColorDefinition getColorDefinition(Color color) {
RenderLayoutPlugin renderPlugin = getRenderPlugin();
- LocalRenderInformation renderInformation = null;
- for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
- if (lri.getId().equals("minerva_definitions")) {
- renderInformation = lri;
- }
- }
- if (renderInformation == null) {
- renderInformation = new LocalRenderInformation("minerva_definitions");
- renderPlugin.addLocalRenderInformation(renderInformation);
- }
+ LocalRenderInformation renderInformation = getRenderInformation(renderPlugin);
for (ColorDefinition cd : renderInformation.getListOfColorDefinitions()) {
if (cd.getValue().equals(color)) {
@@ -168,11 +159,24 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
ColorDefinition colorDefinition = new ColorDefinition("color_" + colorToString(color), color);
-
renderInformation.addColorDefinition(colorDefinition);
return colorDefinition;
}
+ protected LocalRenderInformation getRenderInformation(RenderLayoutPlugin renderPlugin) {
+ LocalRenderInformation renderInformation = null;
+ for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+ if (lri.getId().equals("minerva_definitions")) {
+ renderInformation = lri;
+ }
+ }
+ if (renderInformation == null) {
+ renderInformation = new LocalRenderInformation("minerva_definitions");
+ renderPlugin.addLocalRenderInformation(renderInformation);
+ }
+ return renderInformation;
+ }
+
protected void assignStyleToGlyph(AbstractReferenceGlyph speciesGlyph, LocalStyle style) {
RenderGraphicalObjectPlugin rgop = new RenderGraphicalObjectPlugin(speciesGlyph);
rgop.setObjectRole(style.getRoleList().get(0));
@@ -181,12 +185,11 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
protected LocalStyle createStyle(T element) {
- LocalRenderInformation renderInformation = new LocalRenderInformation();
+ LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
LocalStyle style = new LocalStyle();
style.getRoleList().add("style_" + element.getElementId());
style.setGroup(new RenderGroup());
renderInformation.addLocalStyle(style);
- getRenderPlugin().addLocalRenderInformation(renderInformation);
return style;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
index 03eaf4aa30..d47b472dc0 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -31,7 +31,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
result = getSbmlModel().createCompartment("comp_" + (getNextId()));
}
//for now we don't have this information - needed for validation
- result.setConstant(true);
+ result.setConstant(false);
return result;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index 7132465eac..441ee02e45 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -77,13 +77,13 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
- speciesReference.setConstant(true);
+ speciesReference.setConstant(false);
speciesReferenceByReactionNode.put(product, speciesReference);
}
for (Reactant reactant : reaction.getReactants()) {
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(reactant.getElement().getElementId());
SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
- speciesReference.setConstant(true);
+ speciesReference.setConstant(false);
speciesReferenceByReactionNode.put(reactant, speciesReference);
}
for (Modifier modifier : reaction.getModifiers()) {
@@ -263,13 +263,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
private LocalStyle createStyleForModifier(Modifier modifier) {
- LocalRenderInformation renderInformation = new LocalRenderInformation();
+ LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
LocalStyle style = new LocalStyle();
style.getRoleList()
.add("style_" + modifier.getReaction().getElementId() + "_modifier_" + modifier.getElement().getElementId());
style.setGroup(new RenderGroup());
renderInformation.addLocalStyle(style);
- getRenderPlugin().addLocalRenderInformation(renderInformation);
style.getGroup().setStroke(modifier.getLine().getType().name());
return style;
}
--
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