broad.core.multiplealignment.MAFAlignment Class Reference

Inheritance diagram for broad.core.multiplealignment.MAFAlignment:

Collaboration diagram for broad.core.multiplealignment.MAFAlignment:

Classes
class	MAFHeader
class	MAFMultipleAlignmentBlock

Public Member Functions
	MAFAlignment ()
	MAFAlignment (String indexFile) throws IOException, ParseException
MAFHeader	getHeader ()
void	encode ()
void	encodeAsMatrix ()
void	reverse ()
int	length ()
Map< String, Short >	getColumn (int i)
Map< String, Matrix >	getColumnsAsVector (int start, int number)
void	addShortEncodedColumn (Map< String, Short > col)
void	addShortEncodedRegion (Map< String, short[]> region)
void	addSequence (AlignedSequence seq)
void	addSequences (List< AlignedSequence > sequences)
boolean	isEmpty ()
void	write (BufferedWriter bw) throws IOException
MAFAlignment	getSubAlignment (int refStart, int refEnd, boolean reverse)
AlignedSequence	getAlignedSequence (String sequenceId, boolean fillInGapsBetweenBlocks)
AlignedSequence	getAlignedSequence (String sequenceId)
List< AlignedSequence >	getAlignedSequences (boolean fillGapsBetweenBlocks)
List< AlignedSequence >	getAlignedSequences ()
boolean	overlaps (LightweightGenomicAnnotation annotation)
boolean	contains (LightweightGenomicAnnotation annotation)
List< String >	getAlignedSequenceIds ()
int	getReferenceStart ()
int	getReferenceEnd ()
void	compress ()
MultipleAlignment	toMultipleAlignment (boolean fillGapsBetweenBlocks)
MultipleAlignment	toMultipleAlignment ()
MultipleAlignment	sampleColumns (int colNum, int numConsecutiveCols)
void	load (String fileName) throws IOException, ParseException
void	load (RandomAccessFile handle, List< String > sequencesToLoad) throws IOException, ParseException
void	load (RandomAccessFile handle, int referenceStart, int referenceEnd) throws IOException, ParseException
void	load (RandomAccessFile handle, int referenceStart, int referenceEnd, List< String > sequencesToLoad) throws IOException, ParseException
void	load (String fileName, int referenceStart, int referenceEnd) throws IOException, ParseException
IntervalTree< Long >	getIndex ()
void	writeIndex (String indexFileName) throws IOException
void	createIndex (String alignmentFile) throws IOException
void	setBlocks (List< MAFMultipleAlignmentBlock > blocks)
void	addBlock (MAFMultipleAlignmentBlock block) throws IllegalArgumentException
void	addBlocks (List< MAFMultipleAlignmentBlock > blocks) throws IllegalArgumentException
void	addBlocks (Iterator< MAFMultipleAlignmentBlock > blockIt) throws IllegalArgumentException
void	append (MAFAlignment mafAln) throws IllegalArgumentException
void	clear ()
Iterator < MAFMultipleAlignmentBlock >	getBlockIterator ()
void	loadIndex (String idxFile) throws IOException
Public Member Functions inherited from broad.core.multiplealignment.MultipleAlignment
	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 Member Functions
static void	main (String[] args) throws IOException, ParseException

Static Public Attributes
static String	USAGE
Static Public Attributes inherited from broad.core.multiplealignment.MultipleAlignment
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
void	setAlignedSequences (List< String > seqIds)
Protected Member Functions inherited from broad.core.multiplealignment.MultipleAlignment
MultipleAlignmentIO	getIOHelper ()
Iterator< AlignedSequence >	getAlignedSequences (String refId, int refStart, int refEnd, boolean reverse)

Additional Inherited Members
Static Protected Attributes inherited from broad.core.multiplealignment.MultipleAlignment
static int	UNGAPPED_ALPHABET_SIZE = 4

Constructor & Destructor Documentation

broad.core.multiplealignment.MAFAlignment.MAFAlignment

(

)

Here is the caller graph for this function:

broad.core.multiplealignment.MAFAlignment.MAFAlignment

(

String

indexFile

)

throws IOException, ParseException

Here is the call graph for this function:

Member Function Documentation

void broad.core.multiplealignment.MAFAlignment.addBlock

(

MAFMultipleAlignmentBlock

block

)

throws IllegalArgumentException

Here is the caller graph for this function:

void broad.core.multiplealignment.MAFAlignment.addBlocks

(

List< MAFMultipleAlignmentBlock >

blocks

)

throws IllegalArgumentException

Here is the caller graph for this function:

void broad.core.multiplealignment.MAFAlignment.addBlocks

(

Iterator< MAFMultipleAlignmentBlock >

blockIt

)

throws IllegalArgumentException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.addSequence

(

AlignedSequence

seq

)

void broad.core.multiplealignment.MAFAlignment.addSequences

(

List< AlignedSequence >

sequences

)

void broad.core.multiplealignment.MAFAlignment.addShortEncodedColumn

(

Map< String, Short >

col

)

void broad.core.multiplealignment.MAFAlignment.addShortEncodedRegion

(

Map< String, short[]>

region

)

void broad.core.multiplealignment.MAFAlignment.append

(

MAFAlignment

mafAln

)

throws IllegalArgumentException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.clear

(

)

void broad.core.multiplealignment.MAFAlignment.compress

(

)

Here is the caller graph for this function:

boolean broad.core.multiplealignment.MAFAlignment.contains

(

LightweightGenomicAnnotation

annotation

)

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.createIndex

(

String

alignmentFile

)

throws IOException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.encode

(

)

void broad.core.multiplealignment.MAFAlignment.encodeAsMatrix

(

)

AlignedSequence broad.core.multiplealignment.MAFAlignment.getAlignedSequence	(	String	sequenceId,
		boolean	fillInGapsBetweenBlocks
	)

Here is the call graph for this function:

Here is the caller graph for this function:

AlignedSequence broad.core.multiplealignment.MAFAlignment.getAlignedSequence

(

String

sequenceId

)

Here is the call graph for this function:

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

(

)

Here is the caller graph for this function:

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

(

boolean

fillGapsBetweenBlocks

)

Here is the call graph for this function:

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

(

)

Here is the caller graph for this function:

Iterator<MAFMultipleAlignmentBlock> broad.core.multiplealignment.MAFAlignment.getBlockIterator

(

)

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

(

int

i

)

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

Parameters

int	- alignment column

Here is the caller graph for this function:

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

Here is the call graph for this function:

MAFHeader broad.core.multiplealignment.MAFAlignment.getHeader

(

)

IntervalTree<Long> broad.core.multiplealignment.MAFAlignment.getIndex

(

)

int broad.core.multiplealignment.MAFAlignment.getReferenceEnd

(

)

Here is the caller graph for this function:

int broad.core.multiplealignment.MAFAlignment.getReferenceStart

(

)

Here is the caller graph for this function:

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

Here is the call graph for this function:

boolean broad.core.multiplealignment.MAFAlignment.isEmpty

(

)

Here is the caller graph for this function:

int broad.core.multiplealignment.MAFAlignment.length

(

)

Here is the caller graph for this function:

void broad.core.multiplealignment.MAFAlignment.load

(

String

fileName

)

throws IOException, ParseException

Here is the caller graph for this function:

void broad.core.multiplealignment.MAFAlignment.load	(	RandomAccessFile	handle,
		List< String >	sequencesToLoad
	)		throws IOException, ParseException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.load	(	RandomAccessFile	handle,
		int	referenceStart,
		int	referenceEnd
	)		throws IOException, ParseException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.load	(	RandomAccessFile	handle,
		int	referenceStart,
		int	referenceEnd,
		List< String >	sequencesToLoad
	)		throws IOException, ParseException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.load	(	String	fileName,
		int	referenceStart,
		int	referenceEnd
	)		throws IOException, ParseException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.loadIndex

(

String

idxFile

)

throws IOException

Here is the caller graph for this function:

static void broad.core.multiplealignment.MAFAlignment.main ( String[]  args ) throws IOException, ParseException

static

Here is the call graph for this function:

boolean broad.core.multiplealignment.MAFAlignment.overlaps

(

LightweightGenomicAnnotation

annotation

)

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.reverse

(

)

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

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.setAlignedSequences ( List< String >  seqIds )

protected

void broad.core.multiplealignment.MAFAlignment.setBlocks

(

List< MAFMultipleAlignmentBlock >

blocks

)

Here is the call graph for this function:

MultipleAlignment broad.core.multiplealignment.MAFAlignment.toMultipleAlignment

(

boolean

fillGapsBetweenBlocks

)

Here is the call graph for this function:

MultipleAlignment broad.core.multiplealignment.MAFAlignment.toMultipleAlignment

(

)

void broad.core.multiplealignment.MAFAlignment.write

(

BufferedWriter

bw

)

throws IOException

Here is the call graph for this function:

void broad.core.multiplealignment.MAFAlignment.writeIndex

(

String

indexFileName

)

throws IOException

Member Data Documentation

String broad.core.multiplealignment.MAFAlignment.USAGE

static

Initial value:

= "Usage: MAFAlignment TASK=<task_num> <task_args>\n" +
    "\tTasks:" +
    "\n\t\t1. Extract alignments  -in <input file> -out <output file, default writes to standard out>  -start <chromosome start> -end <chromosome end> [-compress <if this flag is present, the alignment output will contain no reference alignment gaps> -outformat <Specify FASTA, PHYLIP or PHYLIPSEQ if a format other than MAF is decired for the output> -noPadding (include this flag if no padding betweein non contiguous MAF blocks is desired, not that any reference to alignment positions will be lost) ]\n" +
    "n\t\t2. Extract regions -in <alignment file in MAF format> -out <output file> -annotations <Anntation file (BED format by default)> [-format <[BED], SIMPLE,GFF>] -seqsToLoad <List of sequences to load or all if non specified> -compress <if the result should be devoid of reference gaps> -outformat <FASTA, PHYLIP, SEQPHYLIP, if none is specifed the default is MAF>]\n" +
    "n\t\t3. Create index file -in <alignment file in MAF format> -out <Index file name or standard output>\n"+
    "n\t\tExtractBed. Extract segements from a bed from different chrs : similar to extract region but will extract seq of each BED line and will generate an outfile for each  exon specified in the BED   -in <Directory of chr alignment file in MAF format ; dir/chrX.maf> -out <output prefix (will generate multiple out files, one for each record in the BED)> -annotations <Anntation file (BED format by default)> [-format <[BED], SIMPLE,GFF>] -seqsToLoad <List of sequences to load or all if non specified> -compress <if the result should be devoid of reference gaps> -outformat <FASTA, PHYLIP, SEQPHYLIP, if none is specifed the default is MAF>]  -fullBed <flag if you want each exon to be reported>\n"

---

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

• java/broad/core/multiplealignment/MAFAlignment.java