broad.core.motif.SequenceMotifCluster Class Reference

Inheritance diagram for broad.core.motif.SequenceMotifCluster:

Collaboration diagram for broad.core.motif.SequenceMotifCluster:

Public Member Functions
	SequenceMotifCluster (String corePattern, int minsuccessiveCores, int maxPatternDistance) throws SearchException
List< SequenceRegion >	match (Sequence seq)
List< SequenceRegion >	match (Sequence seq, boolean includeRegionSequence)
Public Member Functions inherited from broad.core.motif.SequenceMotif
	SequenceMotif (Pattern motif)
	SequenceMotif (String corePattern, String identifier) throws SearchException
	SequenceMotif (String corePattern) throws SearchException
	SequenceMotif (String corePattern, int minsuccessive) throws SearchException
	SequenceMotif (String corePattern, int minsuccessive, String identifier) throws SearchException
String	getId ()
String	getConsensusSequence ()
int	getNumPossibleKmers ()
Pattern	getMotif ()
List< SequenceRegion >	match (Sequence seq)
boolean	equals (Object o)
String	toString ()
int	hashCode ()
List< SequenceRegion >	match (Sequence geneSeq, List< SequenceRegion > list, int length)

Static Public Member Functions
static void	main (String[] args) throws NumberFormatException, SearchException, IOException
Static Public Member Functions inherited from broad.core.motif.SequenceMotif
static int	numPossibleKmers (String consensusSequence)
static void	main (String[] args) throws NumberFormatException, SearchException, IOException

Static Public Attributes
static String	USAGE
Static Public Attributes inherited from broad.core.motif.SequenceMotif
static String	USAGE

Additional Inherited Members
Protected Member Functions inherited from broad.core.motif.SequenceMotif
void	setMotif (Pattern motif)
Pattern[]	getCoreMotifs ()

Constructor & Destructor Documentation

broad.core.motif.SequenceMotifCluster.SequenceMotifCluster	(	String	corePattern,
		int	minsuccessiveCores,
		int	maxPatternDistance
	)		throws SearchException

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Member Function Documentation

static void broad.core.motif.SequenceMotifCluster.main ( String[]  args ) throws NumberFormatException, SearchException, IOException

static

Parameters

args

Exceptions

SearchException
NumberFormatException
IOException

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List<SequenceRegion> broad.core.motif.SequenceMotifCluster.match

(

Sequence

seq

)

List<SequenceRegion> broad.core.motif.SequenceMotifCluster.match	(	Sequence	seq,
		boolean	includeRegionSequence
	)

Member Data Documentation

String broad.core.motif.SequenceMotifCluster.USAGE

static

Initial value:

= "Usage: SequenceMotifCluster TASK=<task_num> <task_args>\n" +
    "\tTasks:\n" +
    "\t\t1. Get list of motif matches: IN=<fasta sequence> MOTIF=<Core Motif e.g. YRNRY> SUSCCESSIVE=<number of consecutive core motifs> MINLENGTH=<minimum total length to report> MAXSPACING=<max spacing between motifs>\n"

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

• java/broad/core/motif/SequenceMotifCluster.java