Index

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U

UNDEFINED - Static variable in class org.pathvisio.libgpml.model.type.AnnotationType

UNDEFINED - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType

UNDEFINED - Static variable in class org.pathvisio.libgpml.model.type.StateType

UNDIRECTED - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType

UNDIRECTED_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract

In GPML2013a, we introduce a new Interaction Panel of ArrowHeadType.

unlink() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableFrom

Unlinks this linkableFrom (e.g.

unlink() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint

Unlinks this LinePoint from its LinkableTo elementRef.

unlinkAlias(Group, DataNode) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the link between given aliasRef and alias, and removes mapping from aliasRefToAliases of this pathway model.

unsetAliasRef() - Method in class org.pathvisio.libgpml.model.DataNode

Unsets the aliasRef, if any, from this data node.

unsetAllLinkableFroms() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor

Removes links from all GraphLink.LinkableFrom line points to this GraphLink.LinkableTo pathway element.

unsetAllLinkableFroms() - Method in class org.pathvisio.libgpml.model.ShapedElement

Removes links from all GraphLink.LinkableFrom line points to this GraphLink.LinkableTo pathway element.

unsetAnnotatable() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef

Unsets the annotatable, if any, from this annotationRef.

unsetAnnotation() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef

Unsets the annotation, if any, from this annotationRef.

unsetCitable() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef

Unsets the citable, if any, from this citationRef.

unsetCitation() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef

Unsets the citation, if any, from this citationRef.

unsetEvidence() - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef

Unsets the evidence, if any, from this evidenceRef.

unsetEvidenceable() - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef

Unsets the evidenceable, if any, from this evidenceRef.

unsetGroupRef() - Method in interface org.pathvisio.libgpml.model.Groupable

Unsets the parent group, if any, from this pathway element.

unsetGroupRef() - Method in class org.pathvisio.libgpml.model.LineElement

Unsets the parent group, if any, from this pathway element.

unsetGroupRef() - Method in class org.pathvisio.libgpml.model.ShapedElement

Unsets the parent group, if any, from this pathway element.

unsetPathwayModel() - Method in class org.pathvisio.libgpml.model.PathwayObject

Unsets the pathway model, if any, from this pathway element.

updateCoordinates() - Method in class org.pathvisio.libgpml.model.DataNode.State

Updates coordinates.

updateDimensions() - Method in class org.pathvisio.libgpml.model.Group

Updates Group centerX, centerY, width, and height.

updateGroups(PathwayModel) - Method in class org.pathvisio.libgpml.model.GPMLFormatAbstract

Removes group from pathwayModel if empty.

urlLink - Variable in class org.pathvisio.libgpml.model.Annotation

urlLink - Variable in class org.pathvisio.libgpml.model.Citation

urlLink - Variable in class org.pathvisio.libgpml.model.Evidence

use - Variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract.AttributeInfo

use of the attribute: can be "required" or "optional"

username - Variable in class org.pathvisio.libgpml.model.Pathway.Author

Utils - Class in org.pathvisio.libgpml.util

Various utility functions.

Utils() - Constructor for class org.pathvisio.libgpml.util.Utils

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