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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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