public class BioPAXToCellDesignerConverter extends BioPAXToSBMLConverter
BioPAXToSBMLConverter.BioPAXSpecies
alwaysMentionCompartment, biopax, bioPAXreactions, bpnm, compartments, complexList, considerCompartmentNameRatherThanId, controls, dnaList, dnaRegionList, includedSpecies, independentSpecies, independentSpeciesIds, proteinList, reactions, rnaList, rnaRegionList, sbmlDoc, smallMoleculeList, species, useBiopaxModelOntology
Constructor and Description |
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BioPAXToCellDesignerConverter() |
Modifier and Type | Method and Description |
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void |
changeClassesOfSpecies() |
void |
convertToCellDesigner() |
void |
createCompartments() |
void |
generateTags() |
static java.lang.String |
removeCompartmentSuffix(java.lang.String name) |
addControl, addConversionReaction, addIncludedParticipant, addInteractionReaction, addModifierToReaction, findIndependentSpecies, getAllCompartments, getTypeForParticipant, makeComment, makeLists, populateSbml
public void convertToCellDesigner() throws java.lang.Exception
java.lang.Exception
public void generateTags()
public void createCompartments()
public void changeClassesOfSpecies() throws java.lang.Exception
java.lang.Exception
public static java.lang.String removeCompartmentSuffix(java.lang.String name)