Inheritance diagram for umms.core.alignment.FragmentAlignment:

Collaboration diagram for umms.core.alignment.FragmentAlignment:

Public Member Functions
	FragmentAlignment (SingleEndAlignment read1, SingleEndAlignment read2)

	FragmentAlignment (SingleEndAlignment read1, SingleEndAlignment read2, TranscriptionRead transcriptionRead)

boolean	equals (Object o)

int	hashCode ()

Public Member Functions inherited from umms.core.alignment.AbstractPairedEndAlignment
	AbstractPairedEndAlignment (BasicAnnotation b)

void	refreshAttributeMap ()

String	getReadName ()

String	getChromosome ()

int	getMappingQuality ()

int[]	getIntervalBetweenReads ()

boolean	isPaired ()

boolean	isNegativeStrand ()

boolean	isDuplicate ()

void	setDuplicateFlag (boolean duplicateFlag)

Alignment	getFirstMate ()

Alignment	getSecondMate ()

int	getFragmentMidpoint (Annotation annot)

Collection<?extends Window >	getFragment (CoordinateSpace C)

Strand	getFragmentStrand ()

void	setFragmentStrand (TranscriptionRead transcriptionRead)

Collection< Integer >	getFragmentSize (CoordinateSpace C)

int	getFragmentStart ()

int	getFragmentEnd ()

void	setAttribute (String attribute, String value)

String	getAttribute (String attribute)

Annotation	getReadAlignmentBlocks (CoordinateSpace C)

Collection< Alignment >	getReadMates ()

String	toString ()

int	getStart ()

int	getEnd ()

String	getChr ()

int	getAlignmentStart ()

int	getAlignmentEnd ()

boolean	isMapped ()

boolean	isChimera ()

String	getReadSequence ()

double	getWeight ()

boolean	isProperPair ()

void	setProperPairFlag (boolean properPairFlag)

void	shift (int delta)

void	moveToCoordinate (int coord)

final SAMRecord	toSAMRecord ()

Strand	getOrientation ()

Collection< Annotation >	getReadAlignments (CoordinateSpace space)

boolean	hasIndel ()

int	getFirstFragmentPositionStranded ()

int	getLastFragmentPositionStranded ()

void	setHeader (SAMFileHeader header)

SAMFileHeader	getHeader ()

Public Member Functions inherited from umms.core.annotation.BasicAnnotation
	BasicAnnotation ()

	BasicAnnotation (SAMRecord samRecord)

	BasicAnnotation (String ucsc)

	BasicAnnotation (String referenceName, int start, int end, Strand orientation, String name)

	BasicAnnotation (String referenceName, Strand orientation, String name, Collection<?extends Annotation > blocks)

	BasicAnnotation (String referenceName, int start, int end)

	BasicAnnotation (String referenceName, int start, int end, Strand orientation)

	BasicAnnotation (String referenceName, int start, int end, String orientation)

	BasicAnnotation (BasicAnnotation other)

	BasicAnnotation (Annotation other)

	BasicAnnotation (Collection<?extends Annotation > blocks)

	BasicAnnotation (Collection<?extends Annotation > blocks, Strand orientation, String name)

	BasicAnnotation (Collection<?extends Annotation > blocks, String name)

	BasicAnnotation (String referenceName, CompoundInterval blocks, Strand orientation, String name)

	BasicAnnotation (String referenceName, CompoundInterval blocks, Strand orientation)

	BasicAnnotation (String referenceName, CompoundInterval blocks)

Annotation	copy ()

int	getStart ()

int	getEnd ()

int	getMidpoint ()

String	getReferenceName ()

String	getName ()

Strand	getOrientation ()

boolean	isUnoriented ()

List<?extends Annotation >	getBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

Annotation[]	getFlankingBlocks (Annotation spliceJunction)

int	numBlocks ()

int	length ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

double	getScore ()

String	toString ()

void	setStart (int start)

void	setEnd (int end)

void	setOrientation (Strand orientation)

void	setOrientedStart (int orientedStart)

void	setOrientedEnd (int orientedEnd)

void	setReferenceName (String refName)

void	setName (String n)

void	setScore (double s)

void	addBlocks (Annotation block)

void	addBlocks (Collection<?extends Annotation > blocks)

void	shift (int delta)

void	moveToCoordinate (int coordinateInReference)

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

boolean	overlaps (List<?extends Annotation > otherBlocks, int buffer)

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

List< Annotation >	disect (Annotation a)

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

Annotation	minus (Annotation other)

Annotation	minus (Collection<?extends Annotation > others)

void	stitchTo (Annotation next)

Annotation	complement ()

Collection<?extends Annotation >	getSpliceConnections ()

Public Member Functions inherited from umms.core.annotation.AbstractAnnotation
int	size ()

int	getSize ()

int	getMidpoint ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

String	getChr ()

int	getOrientedStart ()

int	getOrientedEnd ()

int	getLengthOnReference ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate)

void	setOrientation (char orientation)

void	expand (int deltaStart, int deltaEnd)

Annotation	trim (int deltaStart, int deltaEnd)

boolean	fullyContains (Annotation other)

boolean	overlaps (Annotation other)

boolean	overlaps (Annotation other, int buffer)

boolean	overlapsStranded (Annotation other)

boolean	overlaps (Annotation other, boolean considerOrientation)

boolean	overlaps (Collection<?extends Annotation > others)

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

String	toUCSC ()

String	toBED ()

final String	getFullInfoString ()

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

String	toShortBED ()

String	toBEDGraph ()

int	getDistanceTo (Annotation other)

String	toCigar ()

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

int	compareTo (Annotation other)

int	compareToAnnotation (Annotation b)

int	compareToAnnotation (Annotation b, boolean useOrientation)

boolean	equals (Annotation a)

boolean	equals (Annotation a, boolean useOrientation)

int	getSAMStart ()

int	getSAMEnd ()

Public Member Functions inherited from umms.core.alignment.Alignment
Collection<?extends Annotation >	getSpliceConnections ()

Additional Inherited Members
Static Public Member Functions inherited from umms.core.annotation.BasicAnnotation
static Annotation	createFromUCSC (String ucsc)

static BasicAnnotation	fromFullInfoString (String fullInfoString)

static void	main (String[] args) throws IOException

Static Public Member Functions inherited from umms.core.annotation.AbstractAnnotation
static Strand	getStrand (String orientation)

static Strand	getStrand (char orientation)

Static Public Attributes inherited from umms.core.annotation.AbstractAnnotation
static final int	MAX_DISTANCE = 1000000000

Static Protected Member Functions inherited from umms.core.alignment.AbstractPairedEndAlignment
static BasicAnnotation	asAnnotation (SingleEndAlignment firstMate, SingleEndAlignment secondMate, boolean fullFragment)

Protected Attributes inherited from umms.core.annotation.BasicAnnotation
CompoundInterval	blocks = new CompoundInterval()

Detailed Description

Author: prussell A full fragment alignment constructed from two paired reads

Constructor & Destructor Documentation

umms.core.alignment.FragmentAlignment.FragmentAlignment	(	SingleEndAlignment	read1,
		SingleEndAlignment	read2
	)

Constructs a paired end alignment object from two alignments.

Parameters

read1
read2

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umms.core.alignment.FragmentAlignment.FragmentAlignment	(	SingleEndAlignment	read1,
		SingleEndAlignment	read2,
		TranscriptionRead	transcriptionRead
	)

Constructs a paired end alignment object from two alignments and provides the read that is in the direction of transcription

Parameters

read1
read2
transcriptionRead

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Member Function Documentation

boolean umms.core.alignment.FragmentAlignment.equals ( Object o )

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int umms.core.alignment.FragmentAlignment.hashCode ( )

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

java/umms/core/alignment/FragmentAlignment.java

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation