broad.pda.seq.graph.ChromosomeWithBubblesJGraphT Class Reference

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

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

Classes
class	BubbleEdge
enum	EdgeSourceType
class	ForwardAndBackIterator
class	MinReadFilter
class	RegionReadFilter
class	ReverseWindowIterator
class	WindowIterator

Public Member Functions
	ChromosomeWithBubblesJGraphT (String name)
	ChromosomeWithBubblesJGraphT (String name, int start, int end)
	ChromosomeWithBubblesJGraphT (String name, Collection<?extends Annotation > vertices, Collection<?extends Annotation > edges, Map<?extends Annotation, Double > edgeCounts, Map<?extends Annotation, Double > nodeCounts, double lambda, double numMarkers, double numReads, int minSplices) throws IllegalArgumentException
	ChromosomeWithBubblesJGraphT (String name, Collection<?extends Annotation > vertices, Collection<?extends Annotation > edges) throws IllegalArgumentException
	ChromosomeWithBubblesJGraphT (String name, Map<?extends Annotation, Double > nodes, Map< BubbleEdge, Double > edges, double lambda, double numMarkers, double numReads, double minEdgeSupport)
	ChromosomeWithBubblesJGraphT (String name, Collection<?extends Annotation > nodes, Collection<?extends Annotation > edges, double lambda, double numMarkers, double numReads, int minSplices) throws IllegalArgumentException
boolean	addEdge (Annotation v1, Annotation v2, BubbleEdge e)
boolean	addNewEdge (BubbleEdge e, Annotation v1, Annotation v2)
boolean	addVertex (Annotation v)
Collection< Gene >	getGenePaths (double alpha)
Collection< Gene >	getGenePaths (double alpha, double minSpliceFrequency)
Collection< Path >	getAllPaths ()
Collection< Path >	getAllPaths (double minSpliceFrequency)
Collection< Gene >	getOrphanNodes ()
Collection< Gene >	getOrphanNodes (Alignments region)
Collection< Path >	getOrphanPaths ()
Collection< Path >	getPaths (double alpha)
Collection< Path >	getPaths (double alpha, double minSpliceFrequency)
Set< BubbleEdge >	getEdges (Collection< Annotation > vertices)
Collection< Annotation >	findReachableTargetVertices (Annotation source, Collection< Annotation > alreadyTraversed, Collection< Annotation > sinkVertices, Collection< Annotation > reachableSinks, int counter, DirectedGraph< Annotation, BubbleEdge > g)
List< Path >	getPaths (Annotation startNode, Annotation endNode, double alpha, double minSpliceFreq, DirectedGraph< Annotation, BubbleEdge > g)
List< Path >	getPaths (Annotation startNode, Annotation endNode, double alpha, Collection< EdgeSourceType > validEdgeTypes, double minSpliceFreq, DirectedGraph< Annotation, BubbleEdge > g)
boolean	checkOrientation (Collection< BubbleEdge > edges)
Annotation	getOppositeVertex (Annotation v, BubbleEdge e)
Collection< Gene >	getPaths (int start, int end)
Collection< Gene >	getPaths (int start, int end, boolean forward)
Collection< Gene >	getPaths (int start, int end, double alpha, boolean forward)
Collection< Gene >	getPaths (int start, int end, double alpha, Collection< EdgeSourceType > validTypes)
Collection< Gene >	getBackwardPaths (int start, int end, double alpha, Collection< EdgeSourceType > validTypes)
Collection< BubbleEdge >	getBackwardEdges (Annotation vertex, double alpha, Collection< EdgeSourceType > validTypes)
void	setSpliceWeight (double spliceWeight)
Collection< BubbleEdge >	getIncidentEdges (Annotation vertex)
Collection< Annotation >	getSourceVertices (Collection< EdgeSourceType > validTypes, DirectedGraph< Annotation, BubbleEdge > g)
Collection< Annotation >	getSinkVertices (Collection< EdgeSourceType > validTypes, DirectedGraph< Annotation, BubbleEdge > g)
Collection< BubbleEdge >	getForwardEdges (Annotation vertex, double alpha, Collection< EdgeSourceType > validTypes)
Collection< BubbleEdge >	getValidOutgoingEdges (Annotation vertex, double alpha, Collection< EdgeSourceType > validTypes, DirectedGraph< Annotation, BubbleEdge > g)
int	inOrientedDegree (Annotation v, Collection< EdgeSourceType > validTypes, DirectedGraph< Annotation, BubbleEdge > g)
int	outOrientedDegree (Annotation v, Collection< EdgeSourceType > validTypes, DirectedGraph< Annotation, BubbleEdge > g)
boolean	isSpanningGap (int start, int end)
boolean	isGap (int start, int end)
boolean	isInAllGaps (int start, int end)
void	removeSpanningGapNodes ()
boolean	removeVertex (Annotation vertex)
boolean	removeEdge (BubbleEdge e)
Collection< BubbleEdge >	getOutOrUnorientedEdges (Annotation v)
Collection< BubbleEdge >	getInOrUnorientedEdges (Annotation v)
void	addEdgeAddingMissingVertices (Annotation intron, float count)
Annotation	findEdge (int start, int end)
List< Annotation >	getOverlappingVertices (int start, int end)
BubbleEdge	createEdge (Alignments connection, Annotation v1, Annotation v2, Integer count, EdgeSourceType type)
VertexPair< Annotation >	getNodePair (BubbleEdge edge)
WindowIterator	iterator (int windowSize, int start, int overlap)
WindowIterator	iterator (int windowSize, int start, int overlap, boolean skipGapSpanningWindows)
WindowIterator	iterator (int windowSize, int start)
double	getLocalRate (Annotation exon)
double	getLambda ()
int	getRelativeGenomeLength ()
double	getNumberOfMarkers ()
double	getNumberOfReads ()
String	getName ()
double	getRPKMConstant ()
Map< Annotation, Double >	getLocalRate ()
int	getEnd ()
int	getStart ()
void	setStart (int start)
void	setEnd (int end)
double	getSpliceWeight ()
int	getChromosomeLength ()
void	setLocalRate (Collection< Path > paths)
void	setLocalRate (Map< Annotation, Double > localRateMap)
void	setRPKMConstant (double num)
void	setExonScores (Annotation node, Double score)
void	setChromosomeLength (int chromosomeLength)
void	writeGraph (String save, boolean setUpShortExonLabels) throws IOException
void	writeGraph (String save) throws IOException
void	writeGraph (String save, Alignments region) throws IOException
void	writeGraph (String save, Alignments region, boolean setUpShortExonLabels) throws IOException
void	writeGraph (String save, Alignments region, boolean setUpShortExonLabels, String graphName) throws IOException

Detailed Description

Implements jung.Graph for Dijkstra (FOR NOW ONLY)

Constructor & Destructor Documentation

broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.ChromosomeWithBubblesJGraphT

(

String

name

)

CONSTRUCTORS TODO: A constructor that instantiates the class with a graph. Application: subgraph

broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.ChromosomeWithBubblesJGraphT	(	String	name,
		int	start,
		int	end
	)

broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.ChromosomeWithBubblesJGraphT	(	String	name,
		Collection<?extends Annotation >	vertices,
		Collection<?extends Annotation >	edges,
		Map<?extends Annotation, Double >	edgeCounts,
		Map<?extends Annotation, Double >	nodeCounts,
		double	lambda,
		double	numMarkers,
		double	numReads,
		int	minSplices
	)		throws IllegalArgumentException

Constructs a chromosome with bubbles with a given set of nodes and connections between them. The graph will keep track of how many times a given edge has been added. Nodes in this case are though as exons of putative transcripts.

Parameters

name	- Name of the chromosome.
vertices	Collection of nodes, note than duplicate nodes will be ignored
edges	Collection of edges connecting nodes. We assume a close-open( [start, end) ) specification of the annotation, thus edge connects two nodes if the start of the edge is node1.getEnd() and the end of the edge is node2.getStart() - 1. Edges must be sorted.
edgeCounts	Map of edges to their counts
nodeCounts	Map of vertices to their counts
lambda
numMarkers
numReads
minSplices

Exceptions

IllegalArgumentException

if a node or and edge are on a different chromsome than the chromosomeWithBubbles instance.

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broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.ChromosomeWithBubblesJGraphT	(	String	name,
		Collection<?extends Annotation >	vertices,
		Collection<?extends Annotation >	edges
	)		throws IllegalArgumentException

Constructs a chromosome with bubbles with a given set of nodes and connections between them. The graph will keep track of how many times a given edge has been added. Nodes in this case are though as exons of putative transcripts.

Parameters

name	- Name of the chromosome.
vertices	Collection of nodes, note than duplicate nodes will be ignored
edges	Collection of edges connecting nodes. We assume a close-open( [start, end) ) specification of the annotation, thus edge connects two nodes if the start of the edge is node1.getEnd() and the end of the edge is node2.getStart() - 1. Edges must be sorted.

Exceptions

IllegalArgumentException

if a node or and edge are on a different chromsome than the chromosomeWithBubbles instance.

broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.ChromosomeWithBubblesJGraphT	(	String	name,
		Map<?extends Annotation, Double >	nodes,
		Map< BubbleEdge, Double >	edges,
		double	lambda,
		double	numMarkers,
		double	numReads,
		double	minEdgeSupport
	)

Constructs a chromosome with bubbles with a given set of nodes, edges.

Parameters

name	Name of the chromosome.
nodes	Collection of nodes, note than duplicate nodes will be ignored
edges	Collection of edges connecting nodes. We assume a close-open( [start, end) ) specification of the annotation, thus edge connects two nodes if the start of the edge is node1.getEnd() and the end of the edge is node2.getStart() - 1. Edges must be sorted.
lambda
numMarkers
numReads
minEdgeSupport

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broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.ChromosomeWithBubblesJGraphT	(	String	name,
		Collection<?extends Annotation >	nodes,
		Collection<?extends Annotation >	edges,
		double	lambda,
		double	numMarkers,
		double	numReads,
		int	minSplices
	)		throws IllegalArgumentException

//??? This constructor is not used. And does not return the correct paths

Parameters

name
nodes
edges
fromBE	//??? //NOT USED
lambda
numMarkers
numReads	??? This will always return a Null Pointer Exception
name
nodes
edges
lambda
numMarkers
numReads
minSplices

Exceptions

IllegalArgumentException

Member Function Documentation

boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.addEdge	(	Annotation	v1,
		Annotation	v2,
		BubbleEdge	e
	)

Adds an edge e between vertices v1 and v2

Parameters

e
v1
v2

Returns

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void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.addEdgeAddingMissingVertices	(	Annotation	intron,
		float	count
	)

Returns a collection of edges of the allowed edge types that originate at the specified vertex (if oriented) or have the specified vertex as an end point

Parameters

v	Specified vertex

Returns

collection of edges Creates bubbles that connect the splice junctions specified in the data model. Nodes in the graphs (bubbles) are single base pairs indicating the splice junction.

Parameters

model
minAligmentGap	Adds an edge to the graph, adding missing vertices to the graph.
intron
count

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.addNewEdge	(	BubbleEdge	e,
		Annotation	v1,
		Annotation	v2
	)

Adds a new edge between v1 and v2

Parameters

e
v1
v2

Returns

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.addVertex

(

Annotation

v

)

Adds vertex v to the graph

Parameters

v

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.checkOrientation

(

Collection< BubbleEdge >

edges

)

BubbleEdge broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.createEdge	(	Alignments	connection,
		Annotation	v1,
		Annotation	v2,
		Integer	count,
		EdgeSourceType	type
	)

Creates an edge of type between v1 and v2 for connection alignment with weight

Parameters

connection
v1
v2
count
type

Returns

Annotation broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.findEdge	(	int	start,
		int	end
	)

Returns edge between start and end

Parameters

start
end

Returns

Collection<Annotation> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.findReachableTargetVertices	(	Annotation	source,
		Collection< Annotation >	alreadyTraversed,
		Collection< Annotation >	sinkVertices,
		Collection< Annotation >	reachableSinks,
		int	counter,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

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Collection<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getAllPaths

(

)

Returns the collection of Paths through the graph. Will call getAllPaths with 0 minimum splicing frequency.

Returns

collection of paths

Collection<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getAllPaths

(

double

minSpliceFrequency

)

Returns the collection of Paths through the graph with the minimum splice frequency

Parameters

minSpliceFrequency

minimum splice frequency for the edges

Returns

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Collection<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getBackwardEdges	(	Annotation	vertex,
		double	alpha,
		Collection< EdgeSourceType >	validTypes
	)

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getBackwardPaths	(	int	start,
		int	end,
		double	alpha,
		Collection< EdgeSourceType >	validTypes
	)

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int broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getChromosomeLength

(

)

Set<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getEdges

(

Collection< Annotation >

vertices

)

Returns all edges connecting the specified vertices

Parameters

vertices

Returns

int broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getEnd

(

)

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Collection<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getForwardEdges	(	Annotation	vertex,
		double	alpha,
		Collection< EdgeSourceType >	validTypes
	)

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getGenePaths

(

double

alpha

)

Returns a collection of paired end edges

Returns

Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getGenePaths	(	double	alpha,
		double	minSpliceFrequency
	)

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Collection<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getIncidentEdges

(

Annotation

vertex

)

Returns a collection of all incoming and outgoing edges of specified vertex

Parameters

vertex

Returns

collection of all edges for specified vertex

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Collection<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getInOrUnorientedEdges

(

Annotation

v

)

Returns a collection of edges that terminate at the specified vertex (if oriented) or have the specified vertex as an end point

Parameters

v	Specified vertex

Returns

collection of edges

double broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getLambda

(

)

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double broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getLocalRate

(

Annotation

exon

)

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Map<Annotation, Double> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getLocalRate

(

)

String broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getName

(

)

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VertexPair<Annotation> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getNodePair

(

BubbleEdge

edge

)

Returns the pair of vertices for a specified edge

Parameters

edge

Returns

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double broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getNumberOfMarkers

(

)

double broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getNumberOfReads

(

)

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Annotation broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getOppositeVertex	(	Annotation	v,
		BubbleEdge	e
	)

Returns the opposite vertex of the edge e from the vertex v

Parameters

v
e

Returns

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getOrphanNodes

(

)

Returns all orphan nodes in graph (Vertices without any edges orphan vertices)

Returns

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getOrphanNodes

(

Alignments

region

)

Returns all orphan nodes in region (Vertices without any edges orphan vertices)

Parameters

region

Returns

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Collection<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getOrphanPaths

(

)

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

Returns

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Collection<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getOutOrUnorientedEdges

(

Annotation

v

)

Returns a collection of edges that are of the allowed edge types.

Parameters

edgeList

Returns

filtered edges Returns a collection of edges that originate at the specified vertex (if oriented) or have the specified vertex as an end point

Parameters

v	Specified vertex

Returns

collection of edges

List<Annotation> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getOverlappingVertices	(	int	start,
		int	end
	)

Returns a list of all vertices overlapping region between start and end

Parameters

start
end

Returns

Collection<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths

(

double

alpha

)

Returns a collection of paths with alpha

Parameters

alpha

Returns

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Collection<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	double	alpha,
		double	minSpliceFrequency
	)

Returns a collection of paths with alpha and minimum spicing frequency

Parameters

alpha
minSpliceFrequency	minimum splicing frequency

Returns

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List<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	Annotation	startNode,
		Annotation	endNode,
		double	alpha,
		double	minSpliceFreq,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

Returns a collection of all paths starting from startNode with alpha and minimum splicing frequency

Parameters

startNode
alpha
minSpliceFreq	minimum splicing frequency

Returns

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List<Path> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	Annotation	startNode,
		Annotation	endNode,
		double	alpha,
		Collection< EdgeSourceType >	validEdgeTypes,
		double	minSpliceFreq,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

Returns a collection of all paths starting from startNode having the specified valid edge types

Parameters

startNode
alpha
validEdgeTypes
minSpliceFreq	minimum splicing frequency

Returns

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	int	start,
		int	end
	)

DO WE NEED THIS???? Returns collection of genes between start and end

Parameters

start
end

Returns

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	int	start,
		int	end,
		boolean	forward
	)

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	int	start,
		int	end,
		double	alpha,
		boolean	forward
	)

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Collection<Gene> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getPaths	(	int	start,
		int	end,
		double	alpha,
		Collection< EdgeSourceType >	validTypes
	)

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int broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getRelativeGenomeLength

(

)

double broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getRPKMConstant

(

)

Collection<Annotation> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getSinkVertices	(	Collection< EdgeSourceType >	validTypes,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

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

Parameters

validTypes

List of allowed edge types.

Returns

All vertices having allowed edge types.

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Collection<Annotation> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getSourceVertices	(	Collection< EdgeSourceType >	validTypes,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

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

Parameters

validTypes

List of allowed edge types.

Returns

All vertices having allowed edge types.

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double broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getSpliceWeight

(

)

int broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getStart

(

)

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Collection<BubbleEdge> broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.getValidOutgoingEdges	(	Annotation	vertex,
		double	alpha,
		Collection< EdgeSourceType >	validTypes,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

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int broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.inOrientedDegree	(	Annotation	v,
		Collection< EdgeSourceType >	validTypes,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

Returns the in degree of the given vertex for a list of allowed edge types

Parameters

v	specific vertex
validTypes	Collections of allowed edge types

Returns

in degree of given vertex

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.isGap	(	int	start,
		int	end
	)

Returns true if position starts in gap but goes past gap

Parameters

start
end

Returns

boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.isInAllGaps	(	int	start,
		int	end
	)

Returns true if the start and end positions are all found in gaps (introns??)

Parameters

start
end

Returns

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.isSpanningGap	(	int	start,
		int	end
	)

Returns true if this region spans an intron. Also, returns true if the position starts in gap but goes past gap.

Parameters

start
end

Returns

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WindowIterator broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.iterator	(	int	windowSize,
		int	start,
		int	overlap
	)

WindowIterator broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.iterator	(	int	windowSize,
		int	start,
		int	overlap,
		boolean	skipGapSpanningWindows
	)

WindowIterator broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.iterator	(	int	windowSize,
		int	start
	)

int broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.outOrientedDegree	(	Annotation	v,
		Collection< EdgeSourceType >	validTypes,
		DirectedGraph< Annotation, BubbleEdge >	g
	)

Returns the out degree of the given vertex for a list of allowed edge types

Parameters

v	specific vertex
validTypes	Collections of allowed edge types

Returns

out degree of given vertex

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.removeEdge

(

BubbleEdge

e

)

Removes edge from graph

Parameters

e

Returns

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void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.removeSpanningGapNodes

(

)

Removes all nodes that span a gap

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boolean broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.removeVertex

(

Annotation

vertex

)

Removes vertex from graph

Parameters

vertex

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void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setChromosomeLength

(

int

chromosomeLength

)

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setEnd

(

int

end

)

Sets the end of this graph

Parameters

end

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setExonScores	(	Annotation	node,
		Double	score
	)

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setLocalRate

(

Collection< Path >

paths

)

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setLocalRate

(

Map< Annotation, Double >

localRateMap

)

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setRPKMConstant

(

double

num

)

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setSpliceWeight

(

double

spliceWeight

)

Sets the splice weight for this graph

Parameters

spliceWeight

Value for splice weight

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.setStart

(

int

start

)

Sets the start of this graph

Parameters

start

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.writeGraph	(	String	save,
		boolean	setUpShortExonLabels
	)		throws IOException

Write the graph as a DOT format

Parameters

save
setUpShortExonLabels

Exceptions

IOException

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void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.writeGraph

(

String

save

)

throws IOException

Here is the call graph for this function:

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.writeGraph	(	String	save,
		Alignments	region
	)		throws IOException

Here is the call graph for this function:

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.writeGraph	(	String	save,
		Alignments	region,
		boolean	setUpShortExonLabels
	)		throws IOException

Here is the call graph for this function:

void broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.writeGraph	(	String	save,
		Alignments	region,
		boolean	setUpShortExonLabels,
		String	graphName
	)		throws IOException

Writes the graph to a file

Parameters

save
region
setUpShortExonLabels
graphName

Exceptions

IOException

Here is the call graph for this function:

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

• java/broad/pda/seq/graph/ChromosomeWithBubblesJGraphT.java