broad.core.multiplealignment.MultipleAlignment Class Reference

Inheritance diagram for broad.core.multiplealignment.MultipleAlignment:

Classes
class	AlignedSequence

Public Member Functions
	MultipleAlignment ()
	MultipleAlignment (List<?extends MultipleAlignment > alnBlocks, String ref, String[] seqs)
void	encode ()
void	encode (boolean distinguishMissingSequence)
void	encodeAsMatrix ()
void	reverse ()
int	length ()
Map< String, Short >	getColumn (int i)
Map< String, Matrix >	getColumnsAsVector (int start, int number) throws ArrayIndexOutOfBoundsException
Map< String, Matrix >	getAsMatrix ()
void	addShortEncodedColumn (Map< String, Short > col)
void	addShortEncodedColumnMatrix (Map< String, Matrix > col)
void	addShortEncodedRegion (Map< String, short[]> region)
char	decodeShort (Short nucleotide)
void	addSequence (AlignedSequence seq)
void	addSequences (List< AlignedSequence > sequences)
boolean	isEmpty ()
void	setIOHelper (MultipleAlignmentIO maio)
void	write (BufferedWriter bw) throws IOException
void	write (BufferedWriter bw, List< String > order) throws IOException
MultipleAlignment	sampleColumns (int colNum, int numConsecutiveCols)
void	permuteColumns ()
float	getScore ()
void	setScore (float score)
AlignedSequence	getAlignedSequence (String containingSequenceId)
List< AlignedSequence >	getAlignedSequences ()
List< String >	getAlignedSequenceIds ()
boolean	overlaps (SequenceRegion region)
String	getReferenceId ()
void	setReferenceId (String referenceId)
int	getReferenceStart ()
AlignedSequence	getReference ()
int	getReferenceEnd ()
boolean	isRefGapped ()
void	setRefGapped (boolean isRefGapped)
MultipleAlignment	getConcatenatedSubAlignment (String refId, List<?extends GenomicAnnotation > annotations)
void	compress ()
void	remove (List< String > removeList)
MultipleAlignment	getSubAlignment (int refStart, int refEnd, boolean reverse)
int	getNumberOfAligningSequences ()
MultipleAlignment	getSubAlignment (String refId, int refStart, int refEnd, boolean reverse)
void	append (MultipleAlignment other)
List< int[]>	getUngappedReferenceIslands ()
List< int[]>	getUngappedSequenceReferenceIslands ()
void	introduceGaps (boolean canGapReference, int maxNumberOfGaps) throws IllegalAccessException

Static Public Attributes
static final short	A_CODE = Sequence.SHORT_ENCODED_A
static final short	C_CODE = Sequence.SHORT_ENCODED_C
static final short	G_CODE = Sequence.SHORT_ENCODED_G
static final short	T_CODE = Sequence.SHORT_ENCODED_T
static final short	GAP_CODE = Sequence.SHORT_ENCODED_GAP

Protected Member Functions
MultipleAlignmentIO	getIOHelper ()
Iterator< AlignedSequence >	getAlignedSequences (String refId, int refStart, int refEnd, boolean reverse)

Static Protected Attributes
static int	UNGAPPED_ALPHABET_SIZE = 4

Constructor & Destructor Documentation

broad.core.multiplealignment.MultipleAlignment.MultipleAlignment

(

)

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broad.core.multiplealignment.MultipleAlignment.MultipleAlignment	(	List<?extends MultipleAlignment >	alnBlocks,
		String	ref,
		String[]	seqs
	)

Constructs a multiple alignment object out of piecemeal multiple alignment blocks with, possible, different number of aligned sequences.

Parameters

exonAlnBlocks	The blocks to combined into a single multiple alignment block
string	reference sequence id
seqs	array of sequence ids, the end alignment will include all even in the cases where a sequence alignment is gap only.

Member Function Documentation

void broad.core.multiplealignment.MultipleAlignment.addSequence

(

AlignedSequence

seq

)

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void broad.core.multiplealignment.MultipleAlignment.addSequences

(

List< AlignedSequence >

sequences

)

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void broad.core.multiplealignment.MultipleAlignment.addShortEncodedColumn

(

Map< String, Short >

col

)

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void broad.core.multiplealignment.MultipleAlignment.addShortEncodedColumnMatrix

(

Map< String, Matrix >

col

)

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void broad.core.multiplealignment.MultipleAlignment.addShortEncodedRegion

(

Map< String, short[]>

region

)

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void broad.core.multiplealignment.MultipleAlignment.append

(

MultipleAlignment

other

)

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void broad.core.multiplealignment.MultipleAlignment.compress

(

)

Compresses alignment by removing columns containing reference gaps

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char broad.core.multiplealignment.MultipleAlignment.decodeShort

(

Short

nucleotide

)

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void broad.core.multiplealignment.MultipleAlignment.encode

(

)

void broad.core.multiplealignment.MultipleAlignment.encode

(

boolean

distinguishMissingSequence

)

void broad.core.multiplealignment.MultipleAlignment.encodeAsMatrix

(

)

AlignedSequence broad.core.multiplealignment.MultipleAlignment.getAlignedSequence

(

String

containingSequenceId

)

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List<String> broad.core.multiplealignment.MultipleAlignment.getAlignedSequenceIds

(

)

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List<AlignedSequence> broad.core.multiplealignment.MultipleAlignment.getAlignedSequences

(

)

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Iterator<AlignedSequence> broad.core.multiplealignment.MultipleAlignment.getAlignedSequences ( String  refId, int  refStart, int  refEnd, boolean  reverse  )

protected

Map<String, Matrix> broad.core.multiplealignment.MultipleAlignment.getAsMatrix

(

)

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Map<String, Short> broad.core.multiplealignment.MultipleAlignment.getColumn

(

int

i

)

Assumes that encode has been called and each aligned sequence is encoded

Parameters

int	- alignment column

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Map<String, Matrix> broad.core.multiplealignment.MultipleAlignment.getColumnsAsVector	(	int	start,
		int	number
	)		throws ArrayIndexOutOfBoundsException

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MultipleAlignment broad.core.multiplealignment.MultipleAlignment.getConcatenatedSubAlignment	(	String	refId,
		List<?extends GenomicAnnotation >	annotations
	)

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MultipleAlignmentIO broad.core.multiplealignment.MultipleAlignment.getIOHelper ( )

protected

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int broad.core.multiplealignment.MultipleAlignment.getNumberOfAligningSequences

(

)

Computes the number of sequences that have aligning bases as opposed to being pure gap

Returns

Number of sequences that are not gap only.

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AlignedSequence broad.core.multiplealignment.MultipleAlignment.getReference

(

)

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int broad.core.multiplealignment.MultipleAlignment.getReferenceEnd

(

)

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String broad.core.multiplealignment.MultipleAlignment.getReferenceId

(

)

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int broad.core.multiplealignment.MultipleAlignment.getReferenceStart

(

)

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float broad.core.multiplealignment.MultipleAlignment.getScore

(

)

MultipleAlignment broad.core.multiplealignment.MultipleAlignment.getSubAlignment	(	int	refStart,
		int	refEnd,
		boolean	reverse
	)

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MultipleAlignment broad.core.multiplealignment.MultipleAlignment.getSubAlignment	(	String	refId,
		int	refStart,
		int	refEnd,
		boolean	reverse
	)

Parameters

refId	- The sequence id in which coordinates are given
refStart	- Start of region of interest in the refId sequence. Positions start in 1.
refEnd	- End of region of interest in the refId sequence. Positions start in 1.
reverse	- If true the multiple alignment will return all sequences in the opposite strand

Returns

The multiple alignment of the region of interest or an empty alignment if the coordinates do not overlap the refId aligned region.

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List<int[]> broad.core.multiplealignment.MultipleAlignment.getUngappedReferenceIslands

(

)

Finds the list of ungapped regions in the reference 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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List<int[]> broad.core.multiplealignment.MultipleAlignment.getUngappedSequenceReferenceIslands

(

)

Finds the list of ungapped sequence (as opposed to alignment gaps) regions in the reference 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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void broad.core.multiplealignment.MultipleAlignment.introduceGaps	(	boolean	canGapReference,
		int	maxNumberOfGaps
	)		throws IllegalAccessException

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boolean broad.core.multiplealignment.MultipleAlignment.isEmpty

(

)

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boolean broad.core.multiplealignment.MultipleAlignment.isRefGapped

(

)

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int broad.core.multiplealignment.MultipleAlignment.length

(

)

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boolean broad.core.multiplealignment.MultipleAlignment.overlaps

(

SequenceRegion

region

)

void broad.core.multiplealignment.MultipleAlignment.permuteColumns

(

)

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void broad.core.multiplealignment.MultipleAlignment.remove

(

List< String >

removeList

)

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void broad.core.multiplealignment.MultipleAlignment.reverse

(

)

MultipleAlignment broad.core.multiplealignment.MultipleAlignment.sampleColumns	(	int	colNum,
		int	numConsecutiveCols
	)

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void broad.core.multiplealignment.MultipleAlignment.setIOHelper

(

MultipleAlignmentIO

maio

)

void broad.core.multiplealignment.MultipleAlignment.setReferenceId

(

String

referenceId

)

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void broad.core.multiplealignment.MultipleAlignment.setRefGapped

(

boolean

isRefGapped

)

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void broad.core.multiplealignment.MultipleAlignment.setScore

(

float

score

)

void broad.core.multiplealignment.MultipleAlignment.write

(

BufferedWriter

bw

)

throws IOException

void broad.core.multiplealignment.MultipleAlignment.write	(	BufferedWriter	bw,
		List< String >	order
	)		throws IOException

Member Data Documentation

final short broad.core.multiplealignment.MultipleAlignment.A_CODE = Sequence.SHORT_ENCODED_A

static

final short broad.core.multiplealignment.MultipleAlignment.C_CODE = Sequence.SHORT_ENCODED_C

static

final short broad.core.multiplealignment.MultipleAlignment.G_CODE = Sequence.SHORT_ENCODED_G

static

final short broad.core.multiplealignment.MultipleAlignment.GAP_CODE = Sequence.SHORT_ENCODED_GAP

static

final short broad.core.multiplealignment.MultipleAlignment.T_CODE = Sequence.SHORT_ENCODED_T

static

int broad.core.multiplealignment.MultipleAlignment.UNGAPPED_ALPHABET_SIZE = 4

staticprotected

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

• java/broad/core/multiplealignment/MultipleAlignment.java