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P
- p - Variable in class org.pathvisio.libgpml.model.TestAlias
- p - Variable in class org.pathvisio.libgpml.model.TestAnchor
- p - Variable in class org.pathvisio.libgpml.model.TestAnnotation
- p - Variable in class org.pathvisio.libgpml.model.TestCitation
- p - Variable in class org.pathvisio.libgpml.model.TestCopy
- p - Variable in class org.pathvisio.libgpml.model.TestElementId
- p - Variable in class org.pathvisio.libgpml.model.TestEvidence
- p - Variable in class org.pathvisio.libgpml.model.TestGraph
- p - Variable in class org.pathvisio.libgpml.model.TestGraphLink
- p - Variable in class org.pathvisio.libgpml.model.TestGroup
- p - Variable in class org.pathvisio.libgpml.model.TestGroupNested
- p - Variable in class org.pathvisio.libgpml.model.TestLinePoint
- p - Variable in class org.pathvisio.libgpml.model.TestReferenceable
- p - Variable in class org.pathvisio.libgpml.model.TestState
- PARALOG - Static variable in class org.pathvisio.libgpml.model.type.GroupType
- parent - Variable in class org.pathvisio.libgpml.debug.DebugList.DebugIterator
- PARENT - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
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String values for
DataNode.StatephosphositePathwayElement.Commentinformation in GPML2013a. - PARENTID - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- PARENTID_DB - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- PARENTSYMBOL - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- PARENTSYMBOL_DB - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- parse(File) - Static method in class org.pathvisio.libgpml.util.RootElementFinder
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Handles root element.
- pathway - Variable in class org.pathvisio.libgpml.model.PathwayModel
- Pathway - Class in org.pathvisio.libgpml.model
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The Pathway class stores information or metadata for a Pathway Model.
- Pathway() - Constructor for class org.pathvisio.libgpml.model.Pathway
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Instantiates a pathway with default values.
- PATHWAY - org.pathvisio.libgpml.model.type.ObjectType
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The pathway description, one per pathway.
- PATHWAY - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
- PATHWAY - Static variable in class org.pathvisio.libgpml.model.type.GroupType
- PATHWAY_AUTHOR - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
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Some GPML2013a properties are removed from GPML2021 and therefore cannot be mapped to the Java model.
- PATHWAY_EMAIL - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- PATHWAY_LASTMODIFIED - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- PATHWAY_MAINTAINER - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- Pathway.Author - Class in org.pathvisio.libgpml.model
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This class stores information for an Author.
- PathwayElement - Class in org.pathvisio.libgpml.model
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Abstract class of pathway elements which are part of a pathway, have an elementId, have Comment, Children: DataNode, State, Interaction, GraphicalLine, Label, Shape, Group.
- PathwayElement() - Constructor for class org.pathvisio.libgpml.model.PathwayElement
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Instantiates a pathway element with meta data information.
- PathwayElement.AnnotationRef - Class in org.pathvisio.libgpml.model
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This class stores information for an AnnotationRef with source
Annotation, targetReferenceable.Annotatable, and a list ofPathwayElement.CitationRefand/orPathwayElement.EvidenceRef. - PathwayElement.CitationRef - Class in org.pathvisio.libgpml.model
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This class stores information for a CitationRef with source
Citation, targetReferenceable.Citable, and a list ofPathwayElement.AnnotationRef. - PathwayElement.Comment - Class in org.pathvisio.libgpml.model
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This class stores all information relevant to a Comment.
- PathwayElement.EvidenceRef - Class in org.pathvisio.libgpml.model
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This class stores information for a EvidenceRef which references an
Evidence. - PathwayElement.InfoRef - Class in org.pathvisio.libgpml.model
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Abstract class of
PathwayElement.AnnotationRef,PathwayElement.CitationRef, andPathwayElement.EvidenceRef. - pathwayElements - Variable in class org.pathvisio.libgpml.model.Group
- pathwayModel - Variable in class org.pathvisio.libgpml.model.PathwayObject
- PathwayModel - Class in org.pathvisio.libgpml.model
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This class stores information for a Pathway model.
- PathwayModel() - Constructor for class org.pathvisio.libgpml.model.PathwayModel
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Initializes a pathway model object with default
Pathway. - PathwayModel.StatusFlagEvent - Class in org.pathvisio.libgpml.model
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Event for a change in the "changed" status of this Pathway
- PathwayModel.StatusFlagListener - Interface in org.pathvisio.libgpml.model
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Implement this interface if you want to be notified when the "changed" status changes.
- PathwayModelEvent - Class in org.pathvisio.libgpml.model
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Used to notify listeners of changes to the model, i.e a Pathway or PathwayElement.
- PathwayModelEvent(PathwayObject, int) - Constructor for class org.pathvisio.libgpml.model.PathwayModelEvent
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Instantiates a pathway model event.
- PathwayModelExporter - Interface in org.pathvisio.libgpml.io
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Interface for an exporter that writes a pathway to a file.
- PathwayModelImporter - Interface in org.pathvisio.libgpml.io
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Implemented by classes that can import a pathway from various different types.
- PathwayModelIO - Interface in org.pathvisio.libgpml.io
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Common methods for
PathwayModelImporters andPathwayModelExporters - PathwayModelListener - Interface in org.pathvisio.libgpml.model
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Implement this if you want to be notified of changes to a PathwayModel.
- pathwayModified(PathwayModelEvent) - Method in interface org.pathvisio.libgpml.model.PathwayModelListener
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Notifies of pathway model modified.
- pathwayModified(PathwayModelEvent) - Method in class org.pathvisio.libgpml.model.Test
- PathwayObject - Class in org.pathvisio.libgpml.model
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Abstract class of pathway elements which are part of a pathway and have an elementId.
- PathwayObject() - Constructor for class org.pathvisio.libgpml.model.PathwayObject
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Instantiates a pathway element.
- PathwayObjectEvent - Class in org.pathvisio.libgpml.model
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This event is used to notify
PathwayObjectListeners of changes to properties of a PathwayElement. - PathwayObjectEvent(PathwayObject, Object, boolean) - Constructor for class org.pathvisio.libgpml.model.PathwayObjectEvent
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Constructor.
- PathwayObjectListener - Interface in org.pathvisio.libgpml.model
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Implement this if you want to be notified of changes to properties of a PathwayElement.
- PENTAGON - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
- PHENOTYPE - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
- Point(double, double) - Constructor for class org.pathvisio.libgpml.util.LinAlg.Point
- Point(Point2D) - Constructor for class org.pathvisio.libgpml.util.LinAlg.Point
- position - Variable in class org.pathvisio.libgpml.model.LineElement.Anchor
- POSITION - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- pow(double, double) - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape
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Function for the base to the exponent power.
- previous() - Method in class org.pathvisio.libgpml.debug.DebugList.DebugIterator
- previousIndex() - Method in class org.pathvisio.libgpml.debug.DebugList.DebugIterator
- printx(PrintStream, String, Object) - Static method in class org.pathvisio.libgpml.util.Utils
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Helper function to print the contents of maps or collections, or maps of maps, collections of maps, collections of collections etc.
- project(LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg
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Projection of p1 on p2: p1.p2 ----- .
- project(LinAlg.Point, LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg
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Projection of point q on a line through p with direction vector v If p is 0,0, it's the same as the two-argument function with the same name.
- PROPERTIES - Static variable in class org.pathvisio.libgpml.prop.PropertyManager
- property - Variable in class org.pathvisio.libgpml.model.PathwayObjectEvent
- Property - Interface in org.pathvisio.libgpml.prop
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This interface defines a typed property.
- PROPERTY_TYPES - Static variable in class org.pathvisio.libgpml.prop.PropertyManager
- PropertyManager - Class in org.pathvisio.libgpml.prop
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This PropertyManager handles the registration/lookups of everything related to TypedProperties.
- PropertyManager() - Constructor for class org.pathvisio.libgpml.prop.PropertyManager
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Private constructor - not meant to be instantiated.
- PropertyType - Interface in org.pathvisio.libgpml.prop
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This interface represents a type (the Type in Property).
- PROTEIN - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
- PROTEIN_MODIFICATION - Static variable in class org.pathvisio.libgpml.model.type.StateType
- pt3 - Variable in class org.pathvisio.libgpml.model.TestLinePoint
- pt4 - Variable in class org.pathvisio.libgpml.model.TestLinePoint
- PTM - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
- PublicationXref(Element, String) - Constructor for class org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref
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Instantiates a PublicationXref object.
- pwElement - Variable in class org.pathvisio.libgpml.model.PathwayObjectEvent
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