broad.core.motif.PositionWeightMatrixIO Class Reference

Collaboration diagram for broad.core.motif.PositionWeightMatrixIO:

Public Member Functions
	PositionWeightMatrixIO ()
void	load (InputStream is) throws IOException, ParseException
void	write (OutputStream os, NumberFormat formatter, List< PositionWeightMatrix > pwms) throws IOException
void	writeUNIPROBE (OutputStream os, NumberFormat formatter, List< PositionWeightMatrix > pwms) throws IOException
void	write (OutputStream os, NumberFormat formatter) throws IOException
List< PositionWeightMatrix >	getMatrices ()
void	addPseudoCounts ()

Static Public Member Functions
static void	main (String[] args) throws Exception

Static Public Attributes
static final String	USAGE

Constructor & Destructor Documentation

broad.core.motif.PositionWeightMatrixIO.PositionWeightMatrixIO

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)

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Member Function Documentation

void broad.core.motif.PositionWeightMatrixIO.addPseudoCounts

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)

List<PositionWeightMatrix> broad.core.motif.PositionWeightMatrixIO.getMatrices

(

)

void broad.core.motif.PositionWeightMatrixIO.load

(

InputStream

is

)

throws IOException, ParseException

static void broad.core.motif.PositionWeightMatrixIO.main ( String[]  args ) throws Exception

static

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void broad.core.motif.PositionWeightMatrixIO.write	(	OutputStream	os,
		NumberFormat	formatter,
		List< PositionWeightMatrix >	pwms
	)		throws IOException

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void broad.core.motif.PositionWeightMatrixIO.write	(	OutputStream	os,
		NumberFormat	formatter
	)		throws IOException

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void broad.core.motif.PositionWeightMatrixIO.writeUNIPROBE	(	OutputStream	os,
		NumberFormat	formatter,
		List< PositionWeightMatrix >	pwms
	)		throws IOException

Member Data Documentation

final String broad.core.motif.PositionWeightMatrixIO.USAGE

static

Initial value:

= "Usage: PositionWeightMatrixIO TASK=<task_num> <task_args> -pwm <PWM file in FASTA fromat>\n" +
    "\tTasks:" +
    "\n\t\t1. Report matches of a PWMs to a sequence -in <Sequence file or standard input in FASTA format> -pwm <File containing PWMs> -minScore <Minimum Score to report>" +
    "\n\t\t\t-start <start matching at this point on the corresponding sequence include as many starts as sequenceIds> -end <Stop matching at this point on the corresponding sequence include as many ends as sequenceIds> " +
    "\n\t\t\t[-seqId <Sequence Ids in the fasta file to search on specify as many as targets you want to search on, if non is specified all start/ends will be assume to relate to first sequence in file>] "+
    "\n\t\tic Compute information content of all motifs on the file -pwm <File containing PWMs>" +
    "\n"

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

• java/broad/core/motif/PositionWeightMatrixIO.java