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 58f48246984a8e5b344111cf8c5a1468fee8dde8..190a2bb028a68693626e4e0b417a5ce4fbd42246 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 03eaf4aa30da20ac4d1ac03b22cd141e87cd0d9d..d47b472dc0d2920154d1d807a1cd8aa43a5ec53f 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 7132465eac8eb9cf4413af7b581afa2377c060bc..441ee02e450c67864debaa1f489399fd54f78157 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; }