Inheritance diagram for umms.core.alignment.AbstractPairedEndAlignment:

Collaboration diagram for umms.core.alignment.AbstractPairedEndAlignment:

Classes
enum	TranscriptionRead

Public Member Functions
	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 ()

Static Protected Member Functions
static BasicAnnotation	asAnnotation (SingleEndAlignment firstMate, SingleEndAlignment secondMate, boolean fullFragment)

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

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

Detailed Description

Author: prussell

Constructor & Destructor Documentation

umms.core.alignment.AbstractPairedEndAlignment.AbstractPairedEndAlignment ( BasicAnnotation b )

Parameters

b

Member Function Documentation

static BasicAnnotation umms.core.alignment.AbstractPairedEndAlignment.asAnnotation	(	SingleEndAlignment	firstMate,
		SingleEndAlignment	secondMate,
		boolean	fullFragment
	)

staticprotected

Get the alignment as an Annotation object

Parameters

firstMate	First mate
secondMate	Second mate
fullFragment	Whether to get full fragment as one block or separate reads as blocks

Returns: An annotation consisting of the aligned coordinates

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int umms.core.alignment.AbstractPairedEndAlignment.getAlignmentEnd ( )

Returns the end position of the alignment

Returns

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.AbstractPairedEndAlignment.getAlignmentStart ( )

Returns the start position of the alignment

Returns

Implements umms.core.alignment.Alignment.

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String umms.core.alignment.AbstractPairedEndAlignment.getAttribute ( String attribute )

Returns the value of the specified attribute

Implements umms.core.alignment.Alignment.

String umms.core.alignment.AbstractPairedEndAlignment.getChr ( )

Get chromosome

Returns

Implements umms.core.alignment.Alignment.

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String umms.core.alignment.AbstractPairedEndAlignment.getChromosome ( )

Returns the chromosome for this alignment

Returns: Reference name

int umms.core.alignment.AbstractPairedEndAlignment.getEnd ( )

Get end of the fragment

Returns

Implements umms.core.alignment.Alignment.

int umms.core.alignment.AbstractPairedEndAlignment.getFirstFragmentPositionStranded ( )

Get the beginning position of the fragment considering strand

Returns: Highest position if negative strand, lowest position otherwise

Implements umms.core.alignment.Alignment.

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Alignment umms.core.alignment.AbstractPairedEndAlignment.getFirstMate ( )

Get the first read

Returns: The first read in pair

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Collection<? extends Window> umms.core.alignment.AbstractPairedEndAlignment.getFragment ( CoordinateSpace C )

Returns an object for the fragment between the read pair in the specified coordinate space

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.AbstractPairedEndAlignment.getFragmentEnd ( )

Returns the end of the fragment

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.AbstractPairedEndAlignment.getFragmentMidpoint ( Annotation annot )

Get midpoint of fragment with respect to coordinate space

Parameters

annot Parent annotation

Returns: Fragment midpoint in coordinate space

Implements umms.core.alignment.Alignment.

Collection<Integer> umms.core.alignment.AbstractPairedEndAlignment.getFragmentSize ( CoordinateSpace C )

Returns the size of the fragment

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.AbstractPairedEndAlignment.getFragmentStart ( )

Returns the start of the fragment

Implements umms.core.alignment.Alignment.

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Strand umms.core.alignment.AbstractPairedEndAlignment.getFragmentStrand ( )

Returns the strand for the fragment, depending on the transcription read

Implements umms.core.alignment.Alignment.

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SAMFileHeader umms.core.alignment.AbstractPairedEndAlignment.getHeader ( )

Returns the SAM file header for this alignment

Returns

Implements umms.core.alignment.Alignment.

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int [] umms.core.alignment.AbstractPairedEndAlignment.getIntervalBetweenReads ( )

Get the coordinates of the first and last position of the interval between the reads

Returns: The coordinates of the space between the reads or null if single read or reads overlap

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.AbstractPairedEndAlignment.getLastFragmentPositionStranded ( )

Get the ending position of the fragment considering strand

Returns: Lowest position if negative strand, highest position otherwise

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.AbstractPairedEndAlignment.getMappingQuality ( )

Returns the sum of the mapping qualities of both mates

Implements umms.core.alignment.Alignment.

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Strand umms.core.alignment.AbstractPairedEndAlignment.getOrientation ( )

Returns: orientation or strand

Implements umms.core.annotation.Annotation.

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Annotation umms.core.alignment.AbstractPairedEndAlignment.getReadAlignmentBlocks ( CoordinateSpace C )

This method returns the alignment blocks that the read actually aligns to.

Parameters

C

Returns

Implements umms.core.alignment.Alignment.

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Collection<Annotation> umms.core.alignment.AbstractPairedEndAlignment.getReadAlignments ( CoordinateSpace space )

This will return the actual read alignments

Parameters

space Coordinate Space to return the blocks in

Implements umms.core.alignment.Alignment.

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Collection<Alignment> umms.core.alignment.AbstractPairedEndAlignment.getReadMates ( )

This will return the actual read alignment objects NOT BLOCKS

Implements umms.core.alignment.Alignment.

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String umms.core.alignment.AbstractPairedEndAlignment.getReadName ( )

Returns the name of this read pair.

Implements umms.core.alignment.Alignment.

String umms.core.alignment.AbstractPairedEndAlignment.getReadSequence ( )

Implements umms.core.alignment.Alignment.

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Alignment umms.core.alignment.AbstractPairedEndAlignment.getSecondMate ( )

Get the second read

Returns: The second read in pair

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int umms.core.alignment.AbstractPairedEndAlignment.getStart ( )

Get start of the fragment

Returns

Implements umms.core.alignment.Alignment.

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double umms.core.alignment.AbstractPairedEndAlignment.getWeight ( )

The weight to give this alignment in the scoring. For example, if you want to scale by number of hits, the weight would be 1/NH

Returns

Implements umms.core.alignment.Alignment.

boolean umms.core.alignment.AbstractPairedEndAlignment.hasIndel ( )

Returns whether the read contains an insertion or deletion

Returns

Implements umms.core.alignment.Alignment.

boolean umms.core.alignment.AbstractPairedEndAlignment.isChimera ( )

For single end, returns false. For paired end, returns true if reads successfully map to different chromosomes.

Returns

Implements umms.core.alignment.Alignment.

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boolean umms.core.alignment.AbstractPairedEndAlignment.isDuplicate ( )

Returns true is the alignment pair is a duplicate

Implements umms.core.alignment.Alignment.

boolean umms.core.alignment.AbstractPairedEndAlignment.isMapped ( )

Returns true if the alignment is mapped

Returns

Implements umms.core.alignment.Alignment.

boolean umms.core.alignment.AbstractPairedEndAlignment.isNegativeStrand ( )

For paired end, returns true if the read in direction of transcription is negative stranded

Returns: true if the read in direction of transcription is negative stranded

Implements umms.core.alignment.Alignment.

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boolean umms.core.alignment.AbstractPairedEndAlignment.isPaired ( )

Always returns true for objects of this class.

Implements umms.core.alignment.Alignment.

boolean umms.core.alignment.AbstractPairedEndAlignment.isProperPair ( )

Returns whether the alignment represented a proper pair defined by the aligner

Returns

Implements umms.core.alignment.Alignment.

void umms.core.alignment.AbstractPairedEndAlignment.moveToCoordinate ( int coordinateInReference )

Move an annotation, preserving the relationships between its blocks, to a new coordinate.

Parameters

coordinateInReference

Implements umms.core.annotation.Annotation.

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void umms.core.alignment.AbstractPairedEndAlignment.refreshAttributeMap ( )

Populate the attribute map with combined attribute values based on the two mates

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void umms.core.alignment.AbstractPairedEndAlignment.setAttribute	(	String	attribute,
		String	value
	)

Sets the specified attribute value

Parameters

attribute
value

void umms.core.alignment.AbstractPairedEndAlignment.setDuplicateFlag ( boolean duplicateFlag )

Sets the duplicate flag

Implements umms.core.alignment.Alignment.

void umms.core.alignment.AbstractPairedEndAlignment.setFragmentStrand ( TranscriptionRead transcriptionRead )

Sets the strand for the fragment to the strand of the transcription read

Parameters

transcriptionRead

Implements umms.core.alignment.Alignment.

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void umms.core.alignment.AbstractPairedEndAlignment.setHeader ( SAMFileHeader header )

Sets the SAM File header for this alignment

Parameters

header

Implements umms.core.alignment.Alignment.

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void umms.core.alignment.AbstractPairedEndAlignment.setProperPairFlag ( boolean properPairFlag )

Set whether the alignment represented a proper pair defined by the aligner

Returns

Implements umms.core.alignment.Alignment.

void umms.core.alignment.AbstractPairedEndAlignment.shift ( int delta )

Shift the positioning of the annotation by a given number of base pairs.

Parameters

delta

Positive or negative shift to apply to all blocks in the annotation.

delta=0

leaves the annotation unchanged.

Implements umms.core.annotation.Annotation.

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final SAMRecord umms.core.alignment.AbstractPairedEndAlignment.toSAMRecord ( )

Implements umms.core.alignment.Alignment.

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String umms.core.alignment.AbstractPairedEndAlignment.toString ( )

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

java/umms/core/alignment/AbstractPairedEndAlignment.java

Classes

Public Member Functions

Static Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation