diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index 6215374c9d25eda9f77427651d89d826e9254b74..b4e503a8b33abb0476ea9ff5b0c19e681c148201 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -312,7 +312,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private void assignChargeToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
if (element.getCharge() != null) {
- assignValueToFeature(element, multiExtension, speciesType, element.getCharge().toString(), BioEntityFeature.CHARGE);
+ assignValueToFeature(element, multiExtension, speciesType, element.getCharge().toString(),
+ BioEntityFeature.CHARGE);
}
}
@@ -399,6 +400,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
Collections.sort(modifications);
multiDistinguisher += "\n" + StringUtils.join(modifications, ",");
}
+ multiDistinguisher += "\n" + element.getPositionToCompartment();
}
String result = element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n"
+ complexName
@@ -472,7 +474,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private void createModificationGlyph(ModificationResidue mr, AbstractReferenceGlyph speciesGlyph) {
org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
-
+
MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
SpeciesFeature feature = null;
String featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr);
diff --git a/converter-sbml/testFiles/cd_for_multi/position_to_compartment_in_aliases.xml b/converter-sbml/testFiles/cd_for_multi/position_to_compartment_in_aliases.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0b2a4d4298eb1358c5ce3c1ff91cf2d50167adf9
--- /dev/null
+++ b/converter-sbml/testFiles/cd_for_multi/position_to_compartment_in_aliases.xml
@@ -0,0 +1,132 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="132.0" y="88.0" w="263.0" h="142.0"/>
+<celldesigner:namePoint x="142.0" y="98.0"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s3" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="85.0" y="133.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="-47.0" y="45.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa3" species="s1" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="232.0" y="130.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="100.0" y="42.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s1" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>