Inheritance diagram for umms.core.alignment.SingleEndAlignment:

Collaboration diagram for umms.core.alignment.SingleEndAlignment:

Classes
class	WrapSamRecord

Public Member Functions
	SingleEndAlignment (SAMRecord read)

	SingleEndAlignment (org.broad.igv.sam.Alignment read)

	SingleEndAlignment (SAMRecord read, boolean isFirstMateFlag)

	SingleEndAlignment ()

void	setSplicedEdges (Collection< Annotation > se)

void	setHasIndel (boolean h)

String	toString ()

void	setIsFirstMate (boolean value)

boolean	getIsFirstMate ()

int	getReadLength ()

String	getReadName ()

String	getChromosome ()

int	getFragmentStart ()

int	getMappingQuality ()

boolean	isPaired ()

boolean	isChimera ()

int	getFragmentEnd ()

Collection< Integer >	getFragmentSize (CoordinateSpace C)

Collection<?extends Window >	getFragment (CoordinateSpace C)

Strand	getFragmentStrand ()

int	getLastFragmentPositionStranded ()

int	getFirstFragmentPositionStranded ()

boolean	isDuplicate ()

void	setDuplicateFlag (boolean duplicateFlag)

Annotation	getReadAlignmentBlocks (CoordinateSpace C)

String	getChr ()

int	getAlignmentStart ()

int	getAlignmentEnd ()

boolean	isMapped ()

Object	getAttribute (String string)

String	getReadSequence ()

double	getWeight ()

boolean	isProperPair ()

void	setProperPairFlag (boolean properPairFlag)

final SAMRecord	toSAMRecord ()

String	getCigarString ()

Collection< Annotation >	getReadAlignments (CoordinateSpace space)

Collection<?extends Annotation >	getSpliceConnections ()

boolean	equals (Annotation other)

Collection< Alignment >	getReadMates ()

void	setFragmentStrand (TranscriptionRead strand)

boolean	hasIndel ()

int[]	getIntervalBetweenReads ()

int	getFragmentMidpoint (Annotation annot)

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
boolean	isNegativeStrand ()

int	getStart ()

int	getEnd ()

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()

Constructor & Destructor Documentation

umms.core.alignment.SingleEndAlignment.SingleEndAlignment ( SAMRecord read )

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umms.core.alignment.SingleEndAlignment.SingleEndAlignment ( org.broad.igv.sam.Alignment read )

This is to populate our Alignment from the old legacy IGV alignments

Parameters

read

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umms.core.alignment.SingleEndAlignment.SingleEndAlignment	(	SAMRecord	read,
		boolean	isFirstMateFlag
	)

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umms.core.alignment.SingleEndAlignment.SingleEndAlignment ( )

Member Function Documentation

boolean umms.core.alignment.SingleEndAlignment.equals ( Annotation other )

Implements umms.core.annotation.Annotation.

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

Returns the end position of the alignment

Returns

Implements umms.core.alignment.Alignment.

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

Returns the start position of the alignment

Returns

Implements umms.core.alignment.Alignment.

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Object umms.core.alignment.SingleEndAlignment.getAttribute ( String string )

Returns the value for the specified attribute

Parameters

string

Returns

Implements umms.core.alignment.Alignment.

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

Get chromosome

Returns

Implements umms.core.alignment.Alignment.

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

Returns the chromosome for this alignment

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String umms.core.alignment.SingleEndAlignment.getCigarString ( )

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

Get the beginning position of the read considering strand

Returns: Highest position if negative strand, lowest position otherwise

Implements umms.core.alignment.Alignment.

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

Returns an object for the fragment from start to end of alignment in the specified coordinate space

Implements umms.core.alignment.Alignment.

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

Returns the end of the fragment

Implements umms.core.alignment.Alignment.

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int umms.core.alignment.SingleEndAlignment.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.SingleEndAlignment.getFragmentSize ( CoordinateSpace C )

Returns the size of the fragment

Implements umms.core.alignment.Alignment.

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

Returns the start of the fragment

Implements umms.core.alignment.Alignment.

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

Returns the strand for the fragment, which is same as read strand

Implements umms.core.alignment.Alignment.

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

Returns the SAM file header for this alignment

Returns

Implements umms.core.alignment.Alignment.

int [] umms.core.alignment.SingleEndAlignment.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.

boolean umms.core.alignment.SingleEndAlignment.getIsFirstMate ( )

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

Get the ending position of the read considering strand

Returns: Lowest position if negative strand, highest position otherwise

Implements umms.core.alignment.Alignment.

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

Returns the mapping quality of the alignment

Implements umms.core.alignment.Alignment.

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

Returns the alignment Blocks

Implements umms.core.alignment.Alignment.

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

This will return the actual read alignments

Parameters

space Coordinate Space to return the blocks in

Implements umms.core.alignment.Alignment.

int umms.core.alignment.SingleEndAlignment.getReadLength ( )

Returns the length of the read

Returns

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

Returns the alignment object

Returns

Implements umms.core.alignment.Alignment.

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

Returns the name of this read pair.

Implements umms.core.alignment.Alignment.

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

Implements umms.core.alignment.Alignment.

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Collection<? extends Annotation> umms.core.alignment.SingleEndAlignment.getSpliceConnections ( )

Return the splice connections contained within this read

Returns

Implements umms.core.alignment.Alignment.

double umms.core.alignment.SingleEndAlignment.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.SingleEndAlignment.hasIndel ( )

Returns whether the read contains an insertion or deletion

Returns

Implements umms.core.alignment.Alignment.

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

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

Returns

Implements umms.core.alignment.Alignment.

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

Returns true is the alignment pair is a duplicate

Implements umms.core.alignment.Alignment.

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

Returns true if the alignment is mapped

Returns

Implements umms.core.alignment.Alignment.

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

Always returns false for objects of this class.

Implements umms.core.alignment.Alignment.

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

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

Returns

Implements umms.core.alignment.Alignment.

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

Sets the duplicate flag

Implements umms.core.alignment.Alignment.

void umms.core.alignment.SingleEndAlignment.setFragmentStrand ( TranscriptionRead strand )

Sets the strand for the fragment to the strand passed as argument

Parameters

strand TODO: CHECK IF THIS IS CORRECT

Implements umms.core.alignment.Alignment.

void umms.core.alignment.SingleEndAlignment.setHasIndel ( boolean h )

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

Sets the SAM File header for this alignment

Parameters

header

Implements umms.core.alignment.Alignment.

void umms.core.alignment.SingleEndAlignment.setIsFirstMate ( boolean value )

Will set the value of the isFirstMate flag

Parameters

value true: this unpaired mate was the first mate false: this unpaired mate was second mate

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void umms.core.alignment.SingleEndAlignment.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.SingleEndAlignment.setSplicedEdges ( Collection< Annotation > se )

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

Implements umms.core.alignment.Alignment.

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

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

java/umms/core/alignment/SingleEndAlignment.java

Classes

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation