public class parseBioPAX 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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parseBioPAX() |
Modifier and Type | Method and Description |
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static void |
main(java.lang.String[] args) |
java.lang.String |
reactionString(SbmlDocument.Sbml sbml,
java.lang.String _id,
boolean realNames,
boolean cutAmpersand) |
addControl, addConversionReaction, addIncludedParticipant, addInteractionReaction, addModifierToReaction, findIndependentSpecies, getAllCompartments, getTypeForParticipant, makeComment, makeLists, populateSbml