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 3af4e8ff053896a6f14ec4119d4956ee2d0a210b..5eeb0009a8db4fe800d06f8a23b223ab42c5e600 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 @@ -429,6 +429,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j multiDistinguisher += "\n" + StringUtils.join(complexChildIds, "\n"); } multiDistinguisher += "\n" + element.getActivity(); + multiDistinguisher += "\n" + element.getCharge(); + multiDistinguisher += "\n" + element.getHomodimer(); } String result = element.getClass().getSimpleName() + "\n" + annotationNames+"\n"+element.getName() + "\n" + compartmentName + "\n" + complexName diff --git a/converter-sbml/testFiles/cd_for_multi/species_with_different_dimer.xml b/converter-sbml/testFiles/cd_for_multi/species_with_different_dimer.xml new file mode 100644 index 0000000000000000000000000000000000000000..b6009c96bdc6eeb967d6f842339c6411b375258a --- /dev/null +++ b/converter-sbml/testFiles/cd_for_multi/species_with_different_dimer.xml @@ -0,0 +1,118 @@ +<?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:listOfComplexSpeciesAliases/> +<celldesigner:listOfSpeciesAliases> +<celldesigner:speciesAlias id="sa1" species="s2"> +<celldesigner:activity>inactive</celldesigner:activity> +<celldesigner:bounds x="127.0" y="100.0" w="80.0" h="40.0"/> +<celldesigner:font size="12"/> +<celldesigner:view state="usual"/> +<celldesigner:usualView> +<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="sa2" species="s1"> +<celldesigner:activity>inactive</celldesigner:activity> +<celldesigner:bounds x="233.0" y="101.0" w="86.0" h="46.0"/> +<celldesigner:font size="12"/> +<celldesigner:view state="usual"/> +<celldesigner:usualView> +<celldesigner:innerPosition x="0.0" y="0.0"/> +<celldesigner:boxSize width="86.0" height="46.0"/> +<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"/> +</listOfCompartments> +<listOfSpecies> +<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0"> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr1</celldesigner:proteinReference> +<celldesigner:state> +<celldesigner:homodimer>2</celldesigner:homodimer> +</celldesigner:state> +</celldesigner:speciesIdentity> +</celldesigner:extension> +</annotation> +</species> +<species metaid="s2" id="s2" name="s1" compartment="default" 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> +</listOfSpecies> +</model> +</sbml>