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P

parent_idref - Variable in class pid.LabelValue
 
parseInteractions(Model) - Method in class manipulator.Converter
Parse the interactions
parseMolecules(Model) - Method in class manipulator.Converter
Parse the molecule bit.
parseOntology() - Method in class manipulator.Converter
Parse the "Ontology" section.
parsePathways(Model) - Method in class manipulator.Converter
Parse the pathway section
part_molecule_idref - Variable in class pid.MoleculePart
 
parts - Variable in class pid.Molecule
 
Pathway - Class in pid
A pathway from PID
Pathway() - Constructor for class pid.Pathway
Only constructor, initialise the arrays.
pathway_idref - Variable in class pid.Abstraction
 
pathway_name - Variable in class pid.Abstraction
 
PathwayComponent - Class in pid
A step in a pathway, pointing to an interaction.
PathwayComponent() - Constructor for class pid.PathwayComponent
 
pathwayComponents - Variable in class pid.Pathway
 
pathways - Variable in class pid.Model
 
PathwaysTest - Class in test
 
PathwaysTest() - Constructor for class test.PathwaysTest
 
pid - package pid
 
pid - Variable in class manipulator.Converter
 
PID - Class in pid
An Object mimicking the XML coming from PID
PID(String) - Constructor for class pid.PID
 
PID() - Constructor for class pid.PID
Default constructor.
pid - Variable in class test.InteractionsTest
 
pid - Variable in class test.MoleculesTest
 
pid - Variable in class test.OntologyTest
 
pid - Variable in class test.PathwaysTest
 
position - Variable in class pid.PTMTerm
 
PositiveCondition - Class in pid
A positive condition influencing an interaction
PositiveCondition() - Constructor for class pid.PositiveCondition
 
PreferredSymbolName - Class in pid
Set of symbols corresponding to the most used by the community.
PreferredSymbolName() - Constructor for class pid.PreferredSymbolName
 
Protein - Class in pid
Type of molecule, mostly used within PID
Protein() - Constructor for class pid.Protein
 
protein - Variable in class pid.PTMTerm
 
ptmExpression - Variable in class pid.ComplexComponent
 
ptmExpression - Variable in class pid.FamilyMember
 
ptmExpression - Variable in class pid.InteractionComponent
 
PTMExpression - Class in pid
A Post-Translational Modification (http://en.wikipedia.org/wiki/Posttranslational_modification) expression: A set of PTMs for this molecule.
PTMExpression() - Constructor for class pid.PTMExpression
Only constructor, initialise the array.
PTMTerm - Class in pid
A PTM for the current molecule.
PTMTerm() - Constructor for class pid.PTMTerm
 
ptmTerms - Variable in class pid.PTMExpression
 

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