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S

save() - Method in class manipulator.Converter
Save the created objects in ".pid" file.
setAbbreviation(String) - Method in class pid.Name
 
setAbstraction(Abstraction) - Method in class pid.Interaction
 
setAminoAcid(String) - Method in class pid.PTMTerm
 
setBurger(XMLBurger) - Method in class manipulator.Converter
 
setComplexComponents(ArrayList<ComplexComponent>) - Method in class pid.Molecule
 
setComponents(ArrayList<InteractionComponent>) - Method in class pid.Interaction
 
setCondition_type(String) - Method in class pid.Condition
 
setConditions(ArrayList<Condition>) - Method in class pid.Interaction
 
setCreated(String) - Method in class pid.PID
 
setCurators(ArrayList<String>) - Method in class pid.Pathway
 
setEnd(int) - Method in class pid.MoleculePart
 
setEvidences(ArrayList<String>) - Method in class pid.Interaction
 
setExternal_pathway_id(String) - Method in class pid.Abstraction
 
setFullName(String) - Method in class pid.Name
 
setGo(String) - Method in class pid.LabelValue
 
setId(String) - Method in class pid.Interaction
 
setId(int) - Method in class pid.LabelType
 
setId(int) - Method in class pid.LabelValue
 
setId(int) - Method in class pid.Molecule
 
setId(int) - Method in class pid.Pathway
 
setInteraction_idref(String) - Method in class pid.PathwayComponent
 
setInteractions(ArrayList<Interaction>) - Method in class pid.Model
 
setInteractionType(String) - Method in class pid.Interaction
 
setLabels(ArrayList<Label>) - Method in class pid.ComplexComponent
 
setLabels(ArrayList<Label>) - Method in class pid.FamilyMember
 
setLabels(ArrayList<Label>) - Method in class pid.InteractionComponent
 
setLabelTypes(ArrayList<LabelType>) - Method in class pid.Ontology
 
setLabelValues(ArrayList<LabelValue>) - Method in class pid.LabelType
 
setLongName(String) - Method in class pid.Pathway
 
setMember_molecule_idref(int) - Method in class pid.FamilyMember
 
setMembers(ArrayList<FamilyMember>) - Method in class pid.Molecule
 
setModel(Model) - Method in class pid.PID
 
setModification(String) - Method in class pid.PTMTerm
 
setMolecule_idref(int) - Method in class pid.ComplexComponent
 
setMolecule_idref(int) - Method in class pid.InteractionComponent
 
setMolecules(ArrayList<Molecule>) - Method in class pid.Model
 
setName(String) - Method in class pid.LabelType
 
setName(String) - Method in class pid.LabelValue
 
setNames(ArrayList<Name>) - Method in class pid.Molecule
 
setOntology(Ontology) - Method in class pid.PID
 
setOrganism(String) - Method in class pid.Pathway
 
setOutputPath(String) - Method in class manipulator.Converter
 
setParent_idref(String) - Method in class pid.LabelValue
 
setPart_molecule_idref(int) - Method in class pid.MoleculePart
 
setParts(ArrayList<MoleculePart>) - Method in class pid.Molecule
 
setPathway_idref(int) - Method in class pid.Abstraction
 
setPathway_name(String) - Method in class pid.Abstraction
 
setPathwayComponents(ArrayList<PathwayComponent>) - Method in class pid.Pathway
 
setPathways(ArrayList<Pathway>) - Method in class pid.Model
 
setPid(PID) - Method in class manipulator.Converter
 
setPosition(int) - Method in class pid.PTMTerm
 
setProtein(String) - Method in class pid.PTMTerm
 
setPtmExpression(PTMExpression) - Method in class pid.ComplexComponent
 
setPtmExpression(PTMExpression) - Method in class pid.FamilyMember
 
setPtmExpression(PTMExpression) - Method in class pid.InteractionComponent
 
setPtmTerms(ArrayList<PTMTerm>) - Method in class pid.PTMExpression
 
setReferences(ArrayList<Integer>) - Method in class pid.Interaction
 
setReviewers(ArrayList<String>) - Method in class pid.Pathway
 
setShortName(String) - Method in class pid.Pathway
 
setSource(String) - Method in class pid.Interaction
 
setSource(String) - Method in class pid.Pathway
 
setStart(int) - Method in class pid.MoleculePart
 
setSubnet(boolean) - Method in class pid.Pathway
 
setValue(String) - Method in class pid.Label
 
setValue(String) - Method in class pid.Name
 
setWhole_molecule_idref(int) - Method in class pid.MoleculePart
 
shortName - Variable in class pid.Pathway
 
source - Variable in class pid.Interaction
 
source - Variable in class pid.Pathway
 
start() - Method in class manipulator.Converter
Start the parsing of the document
start - Variable in class pid.MoleculePart
 

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