Inheritance diagram for broad.pda.seq.graph.Path:

Collaboration diagram for broad.pda.seq.graph.Path:

Classes
class	StandardTransformer

Public Member Functions
	Path (Collection< BubbleEdge > edges, double spliceWeight)

	Path (Collection< BubbleEdge > edges, Transformer< BubbleEdge, Number > transformer, double spliceWeight)

	Path (double spliceWeight)

	Path ()

	Path (Gene gene, ChromosomeWithBubblesJGraphT graph)

boolean	addPairedEnd (Alignment align)

double	getScore ()

double	getWeight ()

int	getStart ()

int	getEnd ()

String	getChromosome ()

boolean	addEdge (BubbleEdge edge)

boolean	addEdges (Collection< BubbleEdge > edges)

Collection< BubbleEdge >	getEdges ()

List< BubbleEdge >	getEdgeList ()

boolean	removeEdge (BubbleEdge edge)

int	getNumberOfEdges ()

Gene	toGene ()

Gene	toGene (double[] extraFields)

String	getOrientation ()

int	compareTo (Path b)

boolean	equals (Object o)

int	hashCode ()

Alignments	getAlignment ()

Collection< Alignment >	getPairedEndEdges ()

void	addPairedEndEdges (Collection< Alignment > pairedEndEdges2)

String	toString ()

Collection< Annotation >	getSortedNodes ()

Annotation	getStartVertex ()

Annotation	getEndVertex ()

boolean	overlapsLeft (Alignment read)

Collection< Annotation >	getOverlappingNodes (Alignment read)

boolean	overlapsRight (Alignment read)

boolean	overlaps (Path leftPath)

double	getPercentConsistent (EmpiricalDistribution pairedInsertDistribution)

Path	copy ()

double	getCoverage ()

int	getSize ()

void	setLocalLambda (double localLambda)

double	getLocalLambda ()

Gene	toFilledInGene ()

double	getNodeCount (Annotation v1)

void	setSpliceWeight (double weight)

double	getSpliceWeight ()

void	setIsToComplex (boolean isToComplex)

boolean	isToComplex ()

Graph< Annotation, BubbleEdge >	getGraph ()

Constructor & Destructor Documentation

broad.pda.seq.graph.Path.Path	(	Collection< BubbleEdge >	edges,
		double	spliceWeight
	)

broad.pda.seq.graph.Path.Path	(	Collection< BubbleEdge >	edges,
		Transformer< BubbleEdge, Number >	transformer,
		double	spliceWeight
	)

broad.pda.seq.graph.Path.Path ( double spliceWeight )

broad.pda.seq.graph.Path.Path ( )

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broad.pda.seq.graph.Path.Path	(	Gene	gene,
		ChromosomeWithBubblesJGraphT	graph
	)

Member Function Documentation

boolean broad.pda.seq.graph.Path.addEdge ( BubbleEdge edge )

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boolean broad.pda.seq.graph.Path.addEdges ( Collection< BubbleEdge > edges )

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boolean broad.pda.seq.graph.Path.addPairedEnd ( Alignment align )

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void broad.pda.seq.graph.Path.addPairedEndEdges ( Collection< Alignment > pairedEndEdges2 )

int broad.pda.seq.graph.Path.compareTo ( Path b )

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Path broad.pda.seq.graph.Path.copy ( )

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boolean broad.pda.seq.graph.Path.equals ( Object o )

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Alignments broad.pda.seq.graph.Path.getAlignment ( )

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String broad.pda.seq.graph.Path.getChromosome ( )

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double broad.pda.seq.graph.Path.getCoverage ( )

List<BubbleEdge> broad.pda.seq.graph.Path.getEdgeList ( )

Returns the edges making up the path. The first edge in this path is incident to the start vertex. The last edge is incident to the end vertex. The vertices along the path can be obtained by traversing from the start vertex, finding its opposite across the first edge, and then doing the same successively across subsequent edges; Graphs#getPathVertexList provides a convenience method for this.

Whether or not the returned edge list is modifiable depends on the path implementation.

Returns: list of edges traversed by the path

Collection<BubbleEdge> broad.pda.seq.graph.Path.getEdges ( )

int broad.pda.seq.graph.Path.getEnd ( )

TODO: This may be to slow, maybe compute end on the fly as Path is being constructed

Returns: genomic end of the path.

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Annotation broad.pda.seq.graph.Path.getEndVertex ( )

Returns the end vertex in the path.

Returns: the end vertex

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Graph<Annotation, BubbleEdge> broad.pda.seq.graph.Path.getGraph ( )

Returns the graph over which this path is defined. The path may also be valid with respect to other graphs.

Returns: the containing graph

double broad.pda.seq.graph.Path.getLocalLambda ( )

double broad.pda.seq.graph.Path.getNodeCount ( Annotation v1 )

int broad.pda.seq.graph.Path.getNumberOfEdges ( )

String broad.pda.seq.graph.Path.getOrientation ( )

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Collection<Annotation> broad.pda.seq.graph.Path.getOverlappingNodes ( Alignment read )

Collection<Alignment> broad.pda.seq.graph.Path.getPairedEndEdges ( )

double broad.pda.seq.graph.Path.getPercentConsistent ( EmpiricalDistribution pairedInsertDistribution )

double broad.pda.seq.graph.Path.getScore ( )

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int broad.pda.seq.graph.Path.getSize ( )

Collection<Annotation> broad.pda.seq.graph.Path.getSortedNodes ( )

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double broad.pda.seq.graph.Path.getSpliceWeight ( )

int broad.pda.seq.graph.Path.getStart ( )

TODO: This may be to slow, maybe compute start on the fly as Path is being constructed

Returns: genomic start of the path.

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Annotation broad.pda.seq.graph.Path.getStartVertex ( )

Returns the start vertex in the path.

Returns: the start vertex

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double broad.pda.seq.graph.Path.getWeight ( )

Returns the weight assigned to the path. Typically, this will be the sum of the weights of the edge list entries (as defined by the containing graph), but some path implementations may use other definitions.