Uses of Class org.pathvisio.libgpml.model.PathwayElement

Packages that use PathwayElement
Package	Description
org.pathvisio.libgpml.model	Classes representing the pathway "model".

Uses of PathwayElement in org.pathvisio.libgpml.model

Subclasses of PathwayElement in org.pathvisio.libgpml.model
Modifier and Type	Class	Description
`class`	`DataNode`	This class stores information for a DataNode pathway element.
`class`	`DataNode.State`	This class stores all information relevant to a State pathway element.
`class`	`GraphicalLine`	This class stores information for GraphicalLine pathway element.
`class`	`Group`	This class stores all information relevant to a Group pathway element.
`class`	`Interaction`	This class stores information for an Interaction pathway element.
`class`	`Label`	This class stores all information relevant to a Label pathway element.
`class`	`LineElement`	This abstract class stores information for a Line pathway element, e.g.
`class`	`Pathway`	The Pathway class stores information or metadata for a Pathway Model.
`class`	`Shape`	This class stores all information relevant to a Shape pathway element.
`class`	`ShapedElement`	This class stores information for shaped pathway element `DataNode`, `DataNode.State`, `Label`, `Shape`, and `Group`.

Fields in org.pathvisio.libgpml.model declared as PathwayElement
Modifier and Type	Field	Description
`(package private) PathwayElement`	CopyElement.`newElement`
`(package private) PathwayElement`	CopyElement.`sourceElement`

Methods in org.pathvisio.libgpml.model that return PathwayElement
Modifier and Type	Method	Description
`PathwayElement`	CopyElement.`getNewElement()`	Returns the new pathway element.
`PathwayElement`	CopyElement.`getSourceElement()`	Returns source pathway element.
`PathwayElement`	PathwayElement.InfoRef.`getTopPathwayElement()`	Returns the top target pathway element `PathwayElement` for a `PathwayElement.AnnotationRef`, `PathwayElement.CitationRef`, or `PathwayElement.EvidenceRef`.

Methods in org.pathvisio.libgpml.model that return types with arguments of type PathwayElement
Modifier and Type	Method	Description
`java.util.List<PathwayElement>`	PathwayModel.`getPathwayElements()`	Returns all pathway elements for the pathway model (pathway, dataNodes, interactions, graphicalLines, labels, shapes, and groups).

Methods in org.pathvisio.libgpml.model with parameters of type PathwayElement
Modifier and Type	Method	Description
`void`	DataNode.`copyReferencesFrom(PathwayElement srcDataNode)`	Copies references from the given source data node, including state references.
`void`	PathwayElement.`copyReferencesFrom(PathwayElement srcElement)`	Copies references from the given source pathway element.
`void`	PathwayElement.`copyValuesFrom(PathwayElement src)`	Copies values from the given source pathway element.
`protected void`	GPML2013aReader.`readCommentGroup(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)`	Reads comment group (comment, biopaxref/citationRef, dynamic property) for pathway element from jdom element.
`protected void`	GPML2021Reader.`readCommentGroup(PathwayModel pathwayModel, PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)`	Reads comment group (comment, dynamic property, annotationRef, citationRef, evidenceRef) information for `PathwayElement` from jdom element.
`protected void`	GPML2013aReader.`readComments(PathwayElement pathwayElement, org.jdom2.Element e)`	Reads comment `PathwayElement.Comment` information for pathway element from jdom element.
`protected void`	GPML2021Reader.`readComments(PathwayElement pathwayElement, org.jdom2.Element e)`	Reads comment `PathwayElement.Comment` information for pathway element from jdom element.
`protected void`	GPML2013aReader.`readDynamicProperties(PathwayElement pathwayElement, org.jdom2.Element root)`	Reads gpml:Attribute or dynamic property information for `PathwayElement` from jdom element.
`protected void`	GPML2021Reader.`readDynamicProperties(PathwayElement pathwayElement, org.jdom2.Element e)`	Reads dynamic property `setDynamicProperty(java.lang.String, java.lang.String)` information for pathway element from jdom element.
`protected void`	GPML2013aReader.`readPublicationXrefs(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)`	Reads gpml:Biopax:bp:PublicationXref and BiopaxRef information for pathway element from jdom element.
`void`	CopyElement.`setNewElement(PathwayElement newElement)`	Sets the new pathway element.
`void`	CopyElement.`setSourceElement(PathwayElement sourceElement)`	Sets source pathway element.
`protected void`	GPML2013aWriter.`writeElementInfo(PathwayElement elementInfo, org.jdom2.Element e)`	Writes elementId, comment group {comment, dynamic property, annotationRef, citationRef) and evidenceRef `PathwayElement` information for datanodes, interactions, graphicalLines, labels, shapes, and group.
`protected void`	GPML2021Writer.`writeElementInfo(PathwayElement elementInfo, org.jdom2.Element e)`	Writes elementId, comment group {comment, dynamic property, annotationRef, citationRef) and evidenceRef `PathwayElement` information for

Constructors in org.pathvisio.libgpml.model with parameters of type PathwayElement
Constructor	Description
`CopyElement(PathwayElement newElement, PathwayElement sourceElement)`	Instantiates a CopyElement which holds references to a new pathway element and the original source element it was copied from.