Inheritance diagram for broad.pda.datastructures.Alignments:

Collaboration diagram for broad.pda.datastructures.Alignments:

Public Member Functions
	Alignments (String ucsc)

	Alignments (String chr, int start, int end)

	Alignments (String chr, int start, int end, Strand strand)

	Alignments (String chr, int start, int end, String strand)

	Alignments (String chr, int start, int end, Strand strand, String name)

	Alignments (String chr, String start, String end)

	Alignments (Annotation a)

	Alignments (String fileName, boolean fromFileName)

	Alignments (LightweightGenomicAnnotation a)

	Alignments (Alignment record)

	Alignments (nextgen.core.alignment.Alignment record)

double	getCountScore ()

List< Double >	getScores ()

String	getSequence (Sequence chr, boolean repeatMask) throws Exception

String	getSequence (String genomeDir) throws Exception

void	setCountScore (double score)

void	setLine (String line)

void	setScores (List< Double > values)

void	addScore (double score)

double	getScore ()

String	toString ()

String	toFileName ()

String	toUCSC ()

String	toStringNum ()

boolean	overlapsCollection (Collection< Alignments > c)

boolean	overlapsAtAll (Alignments align)

boolean	overlapsAtAll (Set< Alignments > set)

boolean	within (Alignments bigger)

int	length ()

boolean	containedWithin (Alignments align)

boolean	containedWithin (Alignments interval, Alignments gene)

Alignments	merge (Alignments a1, Alignments a2)

Alignments	merge (Alignments a1)

int	getMidPoint ()

String	toStringWithScores ()

Public Member Functions inherited from broad.core.annotation.BasicGenomicAnnotation
	BasicGenomicAnnotation (String name)

	BasicGenomicAnnotation (String name, String chr, int start, int end)

	BasicGenomicAnnotation (String name, String chr, int start, int end, Strand strand)

	BasicGenomicAnnotation (LightweightGenomicAnnotation ga)

	BasicGenomicAnnotation (Annotation ga)

	BasicGenomicAnnotation (GenomicAnnotation ga)

	BasicGenomicAnnotation (String[] info)

int	getLength ()

String	toString ()

String	getId ()

void	setId (String id)

void	reduceToDifference (GenomicAnnotation other)

List< Annotation >	disect (Annotation a)

List< Annotation >	disect (List<?extends Annotation > disectors)

boolean	isFlankedBy (TwoSubjectAnnotation twoSubjectAnnotation, int buffer)

int	lastIdxWhereListSearchBroke ()

Sequence	getSequence ()

void	setSequence (Sequence sequence)

void	setOrientation (boolean orientation)

void	setThreePrimeBuffer (int bufferSize)

void	setFivePrimeBuffer (int bufferSize)

int	getFivePrimeBases ()

int	getThreePrimeBases ()

int	compareTo (GenomicAnnotation arg0)

int	getOrientedEnd ()

int	getOrientedStart ()

void	addBlock (String name, int start, int end)

boolean	mayHaveBlocks ()

Public Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
	BasicLightweightAnnotation ()

	BasicLightweightAnnotation (String chr, int start, int end)

	BasicLightweightAnnotation (String chr, int start, int end, String orientation)

	BasicLightweightAnnotation (String chr, int start, int end, Strand orientation, String name)

	BasicLightweightAnnotation (String chr, int start, int end, String orientation, double Scr)

	BasicLightweightAnnotation (String chr, String start, String end)

	BasicLightweightAnnotation (LightweightGenomicAnnotation annotation)

	BasicLightweightAnnotation (Annotation annotation)

String	getChromosomeString ()

int	getDistanceTo (LightweightGenomicAnnotation other)

double	getExtraScore (int i)

List< Double >	getExtraScores ()

String	getLocationString ()

long	getMiddle ()

int	getOverlap (LightweightGenomicAnnotation other)

double	getScore ()

void	setReversedOrientation (boolean isInReversedOrientation)

void	setScore (double score)

boolean	almostEqual (LightweightGenomicAnnotation other, int fudge)

boolean	contains (LightweightGenomicAnnotation other)

boolean	inReversedOrientation ()

boolean	overlaps (Collection<?extends Annotation > others, int buffer)

boolean	overlaps (Collection<?extends Annotation > others)

void	addExtraScore (double score)

void	removeExtraScores ()

void	setBoundariesFromAnnoations (List<?extends GenomicAnnotation > annotations)

void	stitchTo (LightweightGenomicAnnotation other)

void	takeIntersection (LightweightGenomicAnnotation other)

void	takeUnion (LightweightGenomicAnnotation other)

LightweightGenomicAnnotation	intersect (LightweightGenomicAnnotation other)

Collection<?extends Annotation >	intersect (Collection<?extends Annotation > annotations)

int	hashCode ()

int	length ()

String	toUCSC ()

String	toString ()

int	compareTo (LightweightGenomicAnnotation b)

void	setOrientation (String orientation)

String	getChromosome ()

void	setChromosome (String chr)

Public Member Functions inherited from broad.core.annotation.LightweightGenomicAnnotation
int	getStart ()

int	getEnd ()

String	getName ()

void	setName (String name)

void	setStart (int start)

void	setEnd (int end)

Public Member Functions inherited from umms.core.annotation.Annotation
int	getSAMStart ()

int	getSAMEnd ()

String	getReferenceName ()

String	getChr ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

int	numBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

int	getSize ()

int	size ()

int	getLengthOnReference ()

boolean	isUnoriented ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate)

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

void	setOrientation (char orientation)

void	setOrientation (Strand orientation)

void	setOrientedStart (int orientedStart)

void	setOrientedEnd (int orientedEnd)

void	setReferenceName (String refName)

boolean	equals (Annotation other)

void	expand (int deltaStart, int deltaEnd)

Annotation	trim (int deltaStart, int deltaEnd)

void	shift (int delta)

void	moveToCoordinate (int coordinateInReference)

Annotation	copy ()

Annotation	minus (Annotation other)

Annotation	minus (Collection<?extends Annotation > others)

int	getDistanceTo (Annotation other)

String	toBED ()

String	toBED (int r, int g, int b)

String	toShortBED ()

String	toBEDGraph ()

String	getFullInfoString ()

boolean	overlaps (Annotation other, int buffer)

boolean	overlaps (Annotation other)

boolean	overlaps (Annotation other, int buffer, boolean considerOrientation)

boolean	overlaps (Annotation other, boolean considerOrientation)

boolean	overlapsStranded (Annotation other)

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

List< Annotation >	intersect (List<?extends Annotation > annotations)

int	compareToAnnotation (Annotation b)

void	stitchTo (Annotation next)

String	toCigar ()

boolean	fullyContains (Annotation annotation)

Annotation	complement ()

boolean	equals (Annotation other, boolean useOrientation)

Collection<?extends Annotation >	getSpliceConnections ()

int	getMidpoint ()

Public Member Functions inherited from broad.core.annotation.GenomicAnnotation
void	setReversedOrientation (boolean isInReversedOrientation)

void	setOrientation (String orientationString)

Strand	getOrientation ()

String	getLocationString ()

List<?extends Annotation >	getBlocks ()

Public Member Functions inherited from broad.core.annotation.Feature
String	getName ()

Static Public Member Functions
static int	distanceBetween (Alignments align1, Alignments align2)

static void	write (String save, Collection< Alignments > alignments) throws IOException

static void	write (String save, Collection< Alignments > alignments, boolean sort) throws IOException

static void	write (String save, Collection< Alignments > alignments, final int sortOnScore) throws IOException

static void	write (BufferedWriter writer, Collection< Alignments > alignments) throws IOException

static void	write (BufferedWriter writer, Collection< Alignments > alignments, boolean sort) throws IOException

Static Public Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
static Collection < BasicLightweightAnnotation >	mergeAllOverlappers (TreeSet< BasicLightweightAnnotation > regions)

static LightweightGenomicAnnotation	createFromUCSC (String ucsc)

static List< Annotation >	stitchList (Collection<?extends Annotation > sortedList, int maxDistanceToStitch)

Additional Inherited Members
Protected Member Functions inherited from broad.core.annotation.BasicGenomicAnnotation
	BasicGenomicAnnotation ()

Protected Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
void	setStart (String data)

Constructor & Destructor Documentation

broad.pda.datastructures.Alignments.Alignments ( String ucsc )

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broad.pda.datastructures.Alignments.Alignments	(	String	chr,
		int	start,
		int	end
	)

broad.pda.datastructures.Alignments.Alignments	(	String	chr,
		int	start,
		int	end,
		Strand	strand
	)

broad.pda.datastructures.Alignments.Alignments	(	String	chr,
		int	start,
		int	end,
		String	strand
	)

broad.pda.datastructures.Alignments.Alignments	(	String	chr,
		int	start,
		int	end,
		Strand	strand,
		String	name
	)

broad.pda.datastructures.Alignments.Alignments	(	String	chr,
		String	start,
		String	end
	)

broad.pda.datastructures.Alignments.Alignments ( Annotation a )

broad.pda.datastructures.Alignments.Alignments	(	String	fileName,
		boolean	fromFileName
	)

broad.pda.datastructures.Alignments.Alignments ( LightweightGenomicAnnotation a )

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broad.pda.datastructures.Alignments.Alignments ( Alignment record )

broad.pda.datastructures.Alignments.Alignments ( nextgen.core.alignment.Alignment record )

Member Function Documentation

void broad.pda.datastructures.Alignments.addScore ( double score )

boolean broad.pda.datastructures.Alignments.containedWithin ( Alignments align )

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boolean broad.pda.datastructures.Alignments.containedWithin	(	Alignments	interval,
		Alignments	gene
	)

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static int broad.pda.datastructures.Alignments.distanceBetween	(	Alignments	align1,
		Alignments	align2
	)

static

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double broad.pda.datastructures.Alignments.getCountScore ( )

int broad.pda.datastructures.Alignments.getMidPoint ( )

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double broad.pda.datastructures.Alignments.getScore ( )

Implements broad.core.annotation.Feature.

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List<Double> broad.pda.datastructures.Alignments.getScores ( )

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String broad.pda.datastructures.Alignments.getSequence	(	Sequence	chr,
		boolean	repeatMask
	)		throws Exception

String broad.pda.datastructures.Alignments.getSequence ( String genomeDir ) throws Exception

int broad.pda.datastructures.Alignments.length ( )

Returns: length of the Annotation; if it has blocks, the gaps between blocks are not included

Implements broad.core.annotation.LightweightGenomicAnnotation.

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Alignments broad.pda.datastructures.Alignments.merge	(	Alignments	a1,
		Alignments	a2
	)

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Alignments broad.pda.datastructures.Alignments.merge ( Alignments a1 )

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boolean broad.pda.datastructures.Alignments.overlapsAtAll ( Alignments align )

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boolean broad.pda.datastructures.Alignments.overlapsAtAll ( Set< Alignments > set )

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boolean broad.pda.datastructures.Alignments.overlapsCollection ( Collection< Alignments > c )

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void broad.pda.datastructures.Alignments.setCountScore ( double score )

void broad.pda.datastructures.Alignments.setLine ( String line )

void broad.pda.datastructures.Alignments.setScores ( List< Double > values )

String broad.pda.datastructures.Alignments.toFileName ( )

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String broad.pda.datastructures.Alignments.toString ( )

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String broad.pda.datastructures.Alignments.toStringNum ( )

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String broad.pda.datastructures.Alignments.toStringWithScores ( )

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String broad.pda.datastructures.Alignments.toUCSC ( )

Similar to getLocationString()

See also: getLocationString and provided only for backwards compatibility.

Implements broad.core.annotation.LightweightGenomicAnnotation.

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boolean broad.pda.datastructures.Alignments.within ( Alignments bigger )

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static void broad.pda.datastructures.Alignments.write	(	String	save,
		Collection< Alignments >	alignments
	)		throws IOException

static

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static void broad.pda.datastructures.Alignments.write	(	String	save,
		Collection< Alignments >	alignments,
		boolean	sort
	)		throws IOException

static

Write alignments

Parameters

save
alignments
sort	sort by genomic position

Exceptions

IOException

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static void broad.pda.datastructures.Alignments.write	(	String	save,
		Collection< Alignments >	alignments,
		final int	sortOnScore
	)		throws IOException

static

Write alignments sorted by score i

Parameters

args

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static void broad.pda.datastructures.Alignments.write	(	BufferedWriter	writer,
		Collection< Alignments >	alignments
	)		throws IOException

static

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static void broad.pda.datastructures.Alignments.write	(	BufferedWriter	writer,
		Collection< Alignments >	alignments,
		boolean	sort
	)		throws IOException

static

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

java/broad/pda/datastructures/Alignments.java

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation