umms.core.scripture.OrientedChromosomeTranscriptGraph Class Reference

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Classes
class	TranscriptGraphEdge
class	TranscriptGraphEdgeFactory

Public Member Functions
	OrientedChromosomeTranscriptGraph (String name, String orientation)
TranscriptGraphEdge	addEdge (Annotation v1, Annotation v2)
boolean	addAnnotationToGraph (Annotation a)
boolean	addVertex (Annotation v)
int	connectVertexToGraph (Annotation v)
TranscriptGraphEdge	addEdge (Annotation v1, Annotation v2, boolean augmentCount)
List< GraphPath< Annotation, TranscriptGraphEdge > >	getPaths ()
Collection< Annotation >	getSourceVertices ()
Collection< Annotation >	getSinkVertices ()
Collection< Annotation >	getOrphanVertices ()
void	writeGraph (String save, Alignments region, boolean setUpShortExonLabels, String graphName) throws IOException
VertexPair< Annotation >	getNodePair (TranscriptGraphEdge edge)
Collection< GraphPath < Annotation, TranscriptGraphEdge > >	getOrphanPaths ()

Static Public Member Functions
static Gene	pathToGene (GraphPath< Annotation, TranscriptGraphEdge > gp)

Protected Member Functions
	OrientedChromosomeTranscriptGraph (EdgeFactory< Annotation, TranscriptGraphEdge > edgeFactory)

Constructor & Destructor Documentation

umms.core.scripture.OrientedChromosomeTranscriptGraph.OrientedChromosomeTranscriptGraph ( EdgeFactory< Annotation, TranscriptGraphEdge >  edgeFactory )

protected

umms.core.scripture.OrientedChromosomeTranscriptGraph.OrientedChromosomeTranscriptGraph	(	String	name,
		String	orientation
	)

Member Function Documentation

boolean umms.core.scripture.OrientedChromosomeTranscriptGraph.addAnnotationToGraph

(

Annotation

a

)

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TranscriptGraphEdge umms.core.scripture.OrientedChromosomeTranscriptGraph.addEdge	(	Annotation	v1,
		Annotation	v2
	)

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TranscriptGraphEdge umms.core.scripture.OrientedChromosomeTranscriptGraph.addEdge	(	Annotation	v1,
		Annotation	v2,
		boolean	augmentCount
	)

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boolean umms.core.scripture.OrientedChromosomeTranscriptGraph.addVertex

(

Annotation

v

)

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int umms.core.scripture.OrientedChromosomeTranscriptGraph.connectVertexToGraph

(

Annotation

v

)

Adds an exon to a graph

Parameters

v

Returns

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VertexPair<Annotation> umms.core.scripture.OrientedChromosomeTranscriptGraph.getNodePair

(

TranscriptGraphEdge

edge

)

Returns the pair of vertices for a specified edge

Parameters

edge

Returns

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Collection<GraphPath<Annotation, TranscriptGraphEdge> > umms.core.scripture.OrientedChromosomeTranscriptGraph.getOrphanPaths

(

)

Returns all orphan paths in graph (self edges for orphan vertices)

Returns

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Collection<Annotation> umms.core.scripture.OrientedChromosomeTranscriptGraph.getOrphanVertices

(

)

Returns a collection of all orphan vertices.

Returns

All vertices having allowed edge types.

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List<GraphPath<Annotation, TranscriptGraphEdge> > umms.core.scripture.OrientedChromosomeTranscriptGraph.getPaths

(

)

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Collection<Annotation> umms.core.scripture.OrientedChromosomeTranscriptGraph.getSinkVertices

(

)

Returns a collection of all the possible target/end vertices for this graph.

Returns

All vertices having allowed edge types.

Collection<Annotation> umms.core.scripture.OrientedChromosomeTranscriptGraph.getSourceVertices

(

)

Returns a collection of all the possible source/start vertices for the specified graph.

Returns

All vertices having allowed edge types.

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static Gene umms.core.scripture.OrientedChromosomeTranscriptGraph.pathToGene ( GraphPath< Annotation, TranscriptGraphEdge >  gp )

static

void umms.core.scripture.OrientedChromosomeTranscriptGraph.writeGraph	(	String	save,
		Alignments	region,
		boolean	setUpShortExonLabels,
		String	graphName
	)		throws IOException

Writes the graph to a file

Parameters

save
region
setUpShortExonLabels
graphName

Exceptions

IOException

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The documentation for this class was generated from the following file:

• java/umms/core/scripture/OrientedChromosomeTranscriptGraph.java