broad.core.motif.SequenceMotif Class Reference

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Public Member Functions
	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 int	numPossibleKmers (String consensusSequence)
static void	main (String[] args) throws NumberFormatException, SearchException, IOException

Static Public Attributes
static String	USAGE

Protected Member Functions
void	setMotif (Pattern motif)
Pattern[]	getCoreMotifs ()

Constructor & Destructor Documentation

broad.core.motif.SequenceMotif.SequenceMotif

(

Pattern

motif

)

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broad.core.motif.SequenceMotif.SequenceMotif	(	String	corePattern,
		String	identifier
	)		throws SearchException

broad.core.motif.SequenceMotif.SequenceMotif

(

String

corePattern

)

throws SearchException

broad.core.motif.SequenceMotif.SequenceMotif	(	String	corePattern,
		int	minsuccessive
	)		throws SearchException

broad.core.motif.SequenceMotif.SequenceMotif	(	String	corePattern,
		int	minsuccessive,
		String	identifier
	)		throws SearchException

Member Function Documentation

boolean broad.core.motif.SequenceMotif.equals

(

Object

o

)

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String broad.core.motif.SequenceMotif.getConsensusSequence

(

)

Pattern [] broad.core.motif.SequenceMotif.getCoreMotifs ( )

protected

String broad.core.motif.SequenceMotif.getId

(

)

Pattern broad.core.motif.SequenceMotif.getMotif

(

)

int broad.core.motif.SequenceMotif.getNumPossibleKmers

(

)

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int broad.core.motif.SequenceMotif.hashCode

(

)

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

static

Parameters

args

Exceptions

SearchException
NumberFormatException
IOException

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

(

Sequence

seq

)

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List<SequenceRegion> broad.core.motif.SequenceMotif.match	(	Sequence	geneSeq,
		List< SequenceRegion >	list,
		int	length
	)

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static int broad.core.motif.SequenceMotif.numPossibleKmers ( String  consensusSequence )

static

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void broad.core.motif.SequenceMotif.setMotif ( Pattern  motif )

protected

String broad.core.motif.SequenceMotif.toString

(

)

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Member Data Documentation

String broad.core.motif.SequenceMotif.USAGE

static

Initial value:

= "Usage: SequenceMotif 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>\n"

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

• java/broad/core/motif/SequenceMotif.java