Inheritance diagram for broad.core.sequence.FastaSequenceIO:

Collaboration diagram for broad.core.sequence.FastaSequenceIO:

Public Member Functions
	FastaSequenceIO (String fileName)

	FastaSequenceIO (File file)

	FastaSequenceIO ()

List< Sequence >	loadAll () throws IOException

List< Sequence >	loadAll (InputStream is) throws IOException

void	extractRecordsIntoSequenceList (List<?extends Sequence > sequenceList) throws Exception

void	mergeRecords (Sequence seq, String regEx) throws IOException

void	writeRecordsWithMinLength (int minimumLength, InputStream inIs, BufferedWriter bw) throws IOException

List< Sequence >	extractRecordsWithIDsMatching (List< String > regExs, boolean encode) throws IOException

List< Sequence >	extractRecordsWithIDsMatching (List< String > regExs, boolean encode, int expectedSize) throws IOException

List< Sequence >	extractRecordsWithIDLike (String regEx, boolean encode) throws IOException

List< Sequence >	extractRecordsWithIDLike (String regEx, boolean encode, int expectedSize) throws IOException

List< Sequence >	extractRecords (Collection< String > recordIdList, InputStream is) throws IOException

List< Sequence >	extractRecords (Collection< String > recordIdList, InputStream is, boolean largeSequences) throws IOException

List< Sequence >	extractRecords (Collection< String > recordIdList) throws IOException

void	extractRegion (SequenceRegion region) throws IOException

void	extractRegions (List<?extends SequenceRegion > regions) throws IOException

void	extractRegions (List<?extends SequenceRegion > regions, boolean useRegionOrientation) throws IOException

void	extractRegions (List<?extends SequenceRegion > regions, boolean useRegionOrientation, InputStream is) throws IOException

void	write (List<?extends Sequence > seqs, int lineLength) throws IOException

void	write (List<?extends Sequence > seqs) throws IOException

void	write (Sequence seq) throws IOException

void	write (Sequence seq, String fileName) throws IOException

void	append (List<?extends Sequence > records, String fileName) throws IOException

void	append (Sequence seq, String output) throws IOException

void	write (List<?extends Sequence > seqs, String fileName) throws IOException

void	write (List<?extends Sequence > seqs, String fileName, int lineLength) throws IOException

void	write (List<?extends Sequence > seqs, BufferedWriter bw, int lineLength) throws IOException

void	write (List<?extends Sequence > seqs, BufferedWriter bw) throws IOException

void	write (List<?extends Sequence > seqs, BufferedWriter bw, Map< String, String > names, String refID, String pos) throws IOException

void	write (Sequence seq, BufferedWriter bw, int lineLength) throws IOException

void	write (Sequence seq, BufferedWriter bw) throws IOException

void	unchunk (File[] inDirList, int chunkSize, String unchunkSeqName, String outputFile) throws IOException

void	setSource (File newSource)

void	breakUpMultifile (final int sizeToBreakup) throws IOException

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

static Collection< Sequence >	loadSequences (File fasta) throws IOException

static Map< String, Sequence >	loadSequencesByNameFromDirectory (File sequenceDirectory) throws Exception

static Map< String, Sequence >	loadSequencesByNameFromDirectory (File sequenceDirectory, boolean nonrandomOnly) throws Exception

static Collection< String >	getSequenceNames (String fasta) throws IOException

static Map< String, Sequence >	getChrSequencesFromFasta (String genomeFasta) throws IOException

static String	createSizeFile (String refFasta) throws IOException

Static Public Attributes
static final int	LINE_LENGTH = 60

Protected Member Functions
void	writeSequenceId (Sequence seq, BufferedWriter bw) throws IOException

Detailed Description

Suppose to be a very generic and smart Fasta manipulation Class. It is meant to handle both small and very large, multi and single fasta files.

As ussual its initial version will be soooo much less ambitious.

Author: MGarber

Constructor & Destructor Documentation

broad.core.sequence.FastaSequenceIO.FastaSequenceIO ( String fileName )

broad.core.sequence.FastaSequenceIO.FastaSequenceIO ( File file )

broad.core.sequence.FastaSequenceIO.FastaSequenceIO ( )

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Member Function Documentation

void broad.core.sequence.FastaSequenceIO.append	(	List<?extends Sequence >	records,
		String	fileName
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.append	(	Sequence	seq,
		String	output
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.breakUpMultifile ( final int sizeToBreakup ) throws IOException

static String broad.core.sequence.FastaSequenceIO.createSizeFile ( String refFasta ) throws IOException

static

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List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecords	(	Collection< String >	recordIdList,
		InputStream	is
	)		throws IOException

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List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecords	(	Collection< String >	recordIdList,
		InputStream	is,
		boolean	largeSequences
	)		throws IOException

List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecords ( Collection< String > recordIdList ) throws IOException

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void broad.core.sequence.FastaSequenceIO.extractRecordsIntoSequenceList ( List<?extends Sequence > sequenceList ) throws Exception

List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecordsWithIDLike	(	String	regEx,
		boolean	encode
	)		throws IOException

List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecordsWithIDLike	(	String	regEx,
		boolean	encode,
		int	expectedSize
	)		throws IOException

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List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecordsWithIDsMatching	(	List< String >	regExs,
		boolean	encode
	)		throws IOException

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List<Sequence> broad.core.sequence.FastaSequenceIO.extractRecordsWithIDsMatching	(	List< String >	regExs,
		boolean	encode,
		int	expectedSize
	)		throws IOException

void broad.core.sequence.FastaSequenceIO.extractRegion ( SequenceRegion region ) throws IOException

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void broad.core.sequence.FastaSequenceIO.extractRegions ( List<?extends SequenceRegion > regions ) throws IOException

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void broad.core.sequence.FastaSequenceIO.extractRegions	(	List<?extends SequenceRegion >	regions,
		boolean	useRegionOrientation
	)		throws IOException

Extracts sequence regions from fasta file into

Parameters

regions
useRegionOrientation	if true it reverses the sequence extracted.

Exceptions

IOException

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void broad.core.sequence.FastaSequenceIO.extractRegions	(	List<?extends SequenceRegion >	regions,
		boolean	useRegionOrientation,
		InputStream	is
	)		throws IOException

Extracts sequence regions from fasta file into

Parameters

regions
useRegionOrientation	if true it reverses the sequence extracted.

Exceptions

IOException

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static Map<String, Sequence> broad.core.sequence.FastaSequenceIO.getChrSequencesFromFasta ( String genomeFasta ) throws IOException

static

Parameters

genomeFasta Fasta file of chromosomes

Returns: Map of chromosome name to sequence

Exceptions

IOException

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static Collection<String> broad.core.sequence.FastaSequenceIO.getSequenceNames ( String fasta ) throws IOException

static

List<Sequence> broad.core.sequence.FastaSequenceIO.loadAll ( ) throws IOException

List<Sequence> broad.core.sequence.FastaSequenceIO.loadAll ( InputStream is ) throws IOException

static Collection<Sequence> broad.core.sequence.FastaSequenceIO.loadSequences ( File fasta ) throws IOException

static

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static Map<String, Sequence> broad.core.sequence.FastaSequenceIO.loadSequencesByNameFromDirectory ( File sequenceDirectory ) throws Exception

static

static Map<String, Sequence> broad.core.sequence.FastaSequenceIO.loadSequencesByNameFromDirectory	(	File	sequenceDirectory,
		boolean	nonrandomOnly
	)		throws Exception

static

static void broad.core.sequence.FastaSequenceIO.main ( String[] args ) throws IOException

static

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void broad.core.sequence.FastaSequenceIO.mergeRecords	(	Sequence	seq,
		String	regEx
	)		throws IOException

void broad.core.sequence.FastaSequenceIO.setSource ( File newSource )

void broad.core.sequence.FastaSequenceIO.unchunk	(	File[]	inDirList,
		int	chunkSize,
		String	unchunkSeqName,
		String	outputFile
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	List<?extends Sequence >	seqs,
		int	lineLength
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write ( List<?extends Sequence > seqs ) throws IOException

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void broad.core.sequence.FastaSequenceIO.write ( Sequence seq ) throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	Sequence	seq,
		String	fileName
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	List<?extends Sequence >	seqs,
		String	fileName
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	List<?extends Sequence >	seqs,
		String	fileName,
		int	lineLength
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	List<?extends Sequence >	seqs,
		BufferedWriter	bw,
		int	lineLength
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	List<?extends Sequence >	seqs,
		BufferedWriter	bw
	)		throws IOException

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void broad.core.sequence.FastaSequenceIO.write	(	List<?extends Sequence >	seqs,
		BufferedWriter	bw,
		Map< String, String >	names,
		String	refID,
		String	pos
	)		throws IOException