broad.core.sequence.Sequence Class Reference

Inheritance diagram for broad.core.sequence.Sequence:

Collaboration diagram for broad.core.sequence.Sequence:

Classes
class	KmerInfo

Public Member Functions
	Sequence (String id)
	Sequence (String id, boolean isLarge)
	Sequence (String id, int expectedSize)
String	getId ()
void	setForwardStrand (boolean isForwardStrand)
void	setId (String id)
void	unloadSequence ()
void	unloadEncodedSequence ()
void	unloadAllSequences ()
int	getLength ()
void	setCharAt (int position, char newCharacter) throws IllegalAccessException
String	getSequenceBases ()
void	setSequenceBases (String sequence)
void	append (String partialSequence)
Sequence	shuffle ()
void	append (char c)
boolean	isGap (int position)
List< GenomicAnnotation >	getSoftmaskedRegions ()
int	countSoftMaskedBases ()
void	maskSoftmaskedRegions ()
short[]	getEncodedSequence ()
Matrix	getVectorEncodedSequence ()
Matrix	encodeSequenceAsVector ()
short[]	encodeSequence ()
short[]	encodeSequenceIgnoreCase ()
short[]	encodeSequenceIgnoreCase (boolean distinguishMissingSequence)
List< Short >	compute454Flow (char[] flowOrder)
List< Short >	compute454Flow (char[] flowOrder, int start, int end)
float	gcContent ()
boolean	contains (String motif)
void	reverse ()
void	uppercase ()
void	mask (Annotation region, boolean softmask)
SequenceRegion	getRegion (int start, int end)
void	getRegion (SequenceRegion region)
void	getRegion (SequenceRegion region, boolean softmask)
void	getRegion (SequenceRegion region, boolean softmask, Map< String, IntervalTree< Alignments >> okRepeats)
void	getRegions (List<?extends SequenceRegion > regions)
SequenceRegion	extractRegionBasedOnGC (float targetGC, int size, int buffer)
boolean	isForwardStrand ()
StringBuilder	getSequenceBuilder ()
int	getGapsSize ()
WindowSlider	getSlider (int windowSize, int overlap)
List< SequenceRegion >	chunk (int chunkSize, int chunkOverlap)
int	getEnd ()
List< int[]>	findUngappedSequenceChunks ()
Collection< Annotation >	getMatches (String s, int windowStart, int windowEnd, boolean includeRC)
Sequence	getSubSequence (SequenceRegion region, int extension)
Sequence	getSubSequence (String name, int start, int end, int extension)
Sequence	getSubSequence (String name, int start, int end)
Sequence	getSubsequence (Gene annot)
Sequence	getSubsequence (Annotation annot)
void	setCapacity (int size)
Sequence	scramble ()
Sequence	getAntisense ()
String	getRefseqGeneName ()
String	getRefseqSpeciesName ()
String	getRefseqRnaClassName ()
Map< String, KmerInfo >	buildKmerMap (int kmer)

Static Public Member Functions
static short[]	encodeSequence (StringBuilder bases)
static short[]	encodeSequenceIgnoreCase (StringBuilder sequence)
static short[]	encodeSequenceIgnoreCase (StringBuilder sequence, boolean distinguishMissingSequence)
static float	computeGCContent (String dnaString)
static float[]	computeSequenceComposition (String dnaString)
static Sequence	reverseSequence (Sequence seq)
static String	reverseSequence (String seq)
static String	decode (short[] shortEncodedSequence)
static String	generateRandomSequence (int oligoSize)
static String	get3Prime (String seq, int numBases)
static Collection< String >	generateAll5Mers ()
static Collection< String >	generateAllKmers (int k)
static String	complement (String seq)

Static Public Attributes
static final char[]	SHORT_READ_FLOW = {'T','A','C','G'}
static final char[]	LONG_READ_FLOW = {'G','A','T','C'}
static final short	SHORT_ENCODED_A = 0
static final short	SHORT_ENCODED_C = 1
static final short	SHORT_ENCODED_G = 2
static final short	SHORT_ENCODED_T = 3
static final short	SHORT_ENCODED_GAP = 4
static final short	SHORT_ENCODED_a = 5
static final short	SHORT_ENCODED_c = 6
static final short	SHORT_ENCODED_g = 7
static final short	SHORT_ENCODED_t = 8
static final short	SHORT_ENCODED_N = 9

Constructor & Destructor Documentation

broad.core.sequence.Sequence.Sequence

(

String

id

)

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broad.core.sequence.Sequence.Sequence	(	String	id,
		boolean	isLarge
	)

broad.core.sequence.Sequence.Sequence	(	String	id,
		int	expectedSize
	)

Member Function Documentation

void broad.core.sequence.Sequence.append

(

String

partialSequence

)

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void broad.core.sequence.Sequence.append

(

char

c

)

Map<String, KmerInfo> broad.core.sequence.Sequence.buildKmerMap

(

int

kmer

)

Gvien a kmer size, it builds a map of all kmers found

Parameters

kmer

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List<SequenceRegion> broad.core.sequence.Sequence.chunk	(	int	chunkSize,
		int	chunkOverlap
	)

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static String broad.core.sequence.Sequence.complement ( String  seq )

static

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List<Short> broad.core.sequence.Sequence.compute454Flow

(

char[]

flowOrder

)

List<Short> broad.core.sequence.Sequence.compute454Flow	(	char[]	flowOrder,
		int	start,
		int	end
	)

static float broad.core.sequence.Sequence.computeGCContent ( String  dnaString )

static

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static float [] broad.core.sequence.Sequence.computeSequenceComposition ( String  dnaString )

static

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boolean broad.core.sequence.Sequence.contains

(

String

motif

)

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int broad.core.sequence.Sequence.countSoftMaskedBases

(

)

static String broad.core.sequence.Sequence.decode ( short[]  shortEncodedSequence )

static

short [] broad.core.sequence.Sequence.encodeSequence

(

)

static short [] broad.core.sequence.Sequence.encodeSequence ( StringBuilder  bases )

static

Matrix broad.core.sequence.Sequence.encodeSequenceAsVector

(

)

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short [] broad.core.sequence.Sequence.encodeSequenceIgnoreCase

(

)

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short [] broad.core.sequence.Sequence.encodeSequenceIgnoreCase

(

boolean

distinguishMissingSequence

)

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static short [] broad.core.sequence.Sequence.encodeSequenceIgnoreCase ( StringBuilder  sequence )

static

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static short [] broad.core.sequence.Sequence.encodeSequenceIgnoreCase ( StringBuilder  sequence, boolean  distinguishMissingSequence  )

static

SequenceRegion broad.core.sequence.Sequence.extractRegionBasedOnGC	(	float	targetGC,
		int	size,
		int	buffer
	)

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List<int []> broad.core.sequence.Sequence.findUngappedSequenceChunks

(

)

Finds the list of ungapped regions in the sequence.

Returns

A list of two sized integer arrays with the start and end of the ungapped regions. The convention here is semi closed intervals, each list items is of the form [start, end).

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float broad.core.sequence.Sequence.gcContent

(

)

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static Collection<String> broad.core.sequence.Sequence.generateAll5Mers ( )

static

static Collection<String> broad.core.sequence.Sequence.generateAllKmers ( int  k )

static

Get all kmers composed of the bases A, C, G, T

Parameters

k

K

Returns

All 4^k kmers

static String broad.core.sequence.Sequence.generateRandomSequence ( int  oligoSize )

static

static String broad.core.sequence.Sequence.get3Prime ( String  seq, int  numBases  )

static

Sequence broad.core.sequence.Sequence.getAntisense

(

)

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short [] broad.core.sequence.Sequence.getEncodedSequence

(

)

int broad.core.sequence.Sequence.getEnd

(

)

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int broad.core.sequence.Sequence.getGapsSize

(

)

String broad.core.sequence.Sequence.getId

(

)

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int broad.core.sequence.Sequence.getLength

(

)

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Collection<Annotation> broad.core.sequence.Sequence.getMatches	(	String	s,
		int	windowStart,
		int	windowEnd,
		boolean	includeRC
	)

Get all matches for a string as annotations with respect to this sequence Search a window Case is ignored

Parameters

s	The string
windowStart	Start position of window to search
windowEnd	End of window to search
includeRC	Also search for reverse complement of string

Returns

Collection of annotations representing string matches

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String broad.core.sequence.Sequence.getRefseqGeneName

(

)

Get the Refseq gene name which appears between the last pair of parentheses in fasta header

Returns

gene name

String broad.core.sequence.Sequence.getRefseqRnaClassName

(

)

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String broad.core.sequence.Sequence.getRefseqSpeciesName

(

)

Get the species name that appears right after the transcript ID or the PREDICTED tag

Returns

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SequenceRegion broad.core.sequence.Sequence.getRegion	(	int	start,
		int	end
	)

Parameters

start	- start of the region to extract the starting base will be included starting at 0
end	- the end of the region to extract, the base at position end will not be included.

Returns

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void broad.core.sequence.Sequence.getRegion

(

SequenceRegion

region

)

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void broad.core.sequence.Sequence.getRegion	(	SequenceRegion	region,
		boolean	softmask
	)

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void broad.core.sequence.Sequence.getRegion	(	SequenceRegion	region,
		boolean	softmask,
		Map< String, IntervalTree< Alignments >>	okRepeats
	)

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void broad.core.sequence.Sequence.getRegions

(

List<?extends SequenceRegion >

regions

)

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String broad.core.sequence.Sequence.getSequenceBases

(

)

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StringBuilder broad.core.sequence.Sequence.getSequenceBuilder

(

)

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WindowSlider broad.core.sequence.Sequence.getSlider	(	int	windowSize,
		int	overlap
	)

List<GenomicAnnotation> broad.core.sequence.Sequence.getSoftmaskedRegions

(

)

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Sequence broad.core.sequence.Sequence.getSubSequence	(	SequenceRegion	region,
		int	extension
	)

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Sequence broad.core.sequence.Sequence.getSubSequence	(	String	name,
		int	start,
		int	end,
		int	extension
	)

Get subsequence with extension

Parameters

name	Name of new sequence to return
start	Start position of subsequence
end	Position after last position to include
extension	Extension

Returns

The subsequence

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Sequence broad.core.sequence.Sequence.getSubSequence	(	String	name,
		int	start,
		int	end
	)

Get subsequence

Parameters

name	Name of new sequence to return
start	Start position of subsequence
end	Position after last position to include

Returns

The subsequence

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Sequence broad.core.sequence.Sequence.getSubsequence

(

Gene

annot

)

Get the spliced transcribed sequence of an annotation Bases are reported in 5' to 3' direction

Parameters

annot

The annotation

Returns

Sequence with same name as annotation containing the transcribed sequence

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Sequence broad.core.sequence.Sequence.getSubsequence

(

Annotation

annot

)

Get the spliced transcribed sequence of an annotation Bases are reported in 5' to 3' direction

Parameters

annot

The annotation

Returns

Sequence with same name as annotation containing the transcribed sequence

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Matrix broad.core.sequence.Sequence.getVectorEncodedSequence

(

)

boolean broad.core.sequence.Sequence.isForwardStrand

(

)

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boolean broad.core.sequence.Sequence.isGap

(

int

position

)

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void broad.core.sequence.Sequence.mask	(	Annotation	region,
		boolean	softmask
	)

Mask part of sequence

Parameters

region	Region to mask. Masks blocks only.
softmask	If true, mask to lower case. If false, mask to Ns.

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void broad.core.sequence.Sequence.maskSoftmaskedRegions

(

)

void broad.core.sequence.Sequence.reverse

(

)

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static Sequence broad.core.sequence.Sequence.reverseSequence ( Sequence  seq )

static

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static String broad.core.sequence.Sequence.reverseSequence ( String  seq )

static

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Sequence broad.core.sequence.Sequence.scramble

(

)

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void broad.core.sequence.Sequence.setCapacity

(

int

size

)

void broad.core.sequence.Sequence.setCharAt	(	int	position,
		char	newCharacter
	)		throws IllegalAccessException

void broad.core.sequence.Sequence.setForwardStrand

(

boolean

isForwardStrand

)

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void broad.core.sequence.Sequence.setId

(

String

id

)

void broad.core.sequence.Sequence.setSequenceBases

(

String

sequence

)

Sequence broad.core.sequence.Sequence.shuffle

(

)

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void broad.core.sequence.Sequence.unloadAllSequences

(

)

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void broad.core.sequence.Sequence.unloadEncodedSequence

(

)

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void broad.core.sequence.Sequence.unloadSequence

(

)

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void broad.core.sequence.Sequence.uppercase

(

)

Member Data Documentation

final char [] broad.core.sequence.Sequence.LONG_READ_FLOW = {'G','A','T','C'}

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_A = 0

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_a = 5

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_C = 1

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_c = 6

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_G = 2

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_g = 7

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_GAP = 4

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_N = 9

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_T = 3

static

final short broad.core.sequence.Sequence.SHORT_ENCODED_t = 8

static

final char [] broad.core.sequence.Sequence.SHORT_READ_FLOW = {'T','A','C','G'}

static

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

• java/broad/core/sequence/Sequence.java