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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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