umms.core.alignment.Alignment Interface Reference

Inheritance diagram for umms.core.alignment.Alignment:

Collaboration diagram for umms.core.alignment.Alignment:

Public Member Functions
String	getReadName ()
int	getFragmentStart ()
int	getFragmentEnd ()
Collection< Integer >	getFragmentSize (CoordinateSpace C)
int	getMappingQuality ()
boolean	isPaired ()
boolean	isNegativeStrand ()
boolean	isChimera ()
boolean	isDuplicate ()
void	setDuplicateFlag (boolean duplicateFlag)
Strand	getFragmentStrand ()
int	getLastFragmentPositionStranded ()
int	getFirstFragmentPositionStranded ()
int	getFragmentMidpoint (Annotation annot)
Collection<?extends Window >	getFragment (CoordinateSpace C)
Annotation	getReadAlignmentBlocks (CoordinateSpace C)
int	getStart ()
int	getEnd ()
String	getChr ()
int	getAlignmentStart ()
int	getAlignmentEnd ()
boolean	isMapped ()
Object	getAttribute (String string)
String	getReadSequence ()
double	getWeight ()
boolean	isProperPair ()
void	setProperPairFlag (boolean properPairFlag)
SAMRecord	toSAMRecord ()
Collection< Annotation >	getReadAlignments (CoordinateSpace space)
Collection< Alignment >	getReadMates ()
Collection<?extends Annotation >	getSpliceConnections ()
boolean	hasIndel ()
void	setFragmentStrand (TranscriptionRead strand)
int[]	getIntervalBetweenReads ()
void	setHeader (SAMFileHeader header)
SAMFileHeader	getHeader ()
Public Member Functions inherited from umms.core.annotation.Annotation
int	getSAMStart ()
int	getSAMEnd ()
String	getReferenceName ()
String	getName ()
Strand	getOrientation ()
Strand	getStrand ()
boolean	hasOrientation ()
int	numBlocks ()
List<?extends Annotation >	getBlocks ()
List<?extends Annotation >	getBlocks (boolean oriented)
int	length ()
int	getSize ()
int	size ()
int	getLengthOnReference ()
int	getOrientedStart ()
int	getOrientedEnd ()
double	getScore ()
boolean	isUnoriented ()
int	getReferenceCoordinateAtPosition (int positionInAnnotation)
int	getPositionAtReferenceCoordinate (int referenceCoordinate)
int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)
int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)
void	setStart (int start)
void	setEnd (int end)
void	setOrientation (char orientation)
void	setOrientation (Strand orientation)
void	setOrientedStart (int orientedStart)
void	setOrientedEnd (int orientedEnd)
void	setReferenceName (String refName)
void	setName (String name)
void	setScore (double score)
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 ()
List< Annotation >	disect (Annotation a)
List< Annotation >	disect (List<?extends Annotation > disectors)
Annotation	minus (Annotation other)
Annotation	minus (Collection<?extends Annotation > others)
int	getDistanceTo (Annotation other)
String	toUCSC ()
String	toBED ()
String	toBED (int r, int g, int b)
String	toShortBED ()
String	toBEDGraph ()
String	getFullInfoString ()
boolean	overlaps (Annotation other, int buffer)
boolean	overlaps (Collection<?extends Annotation > others, int buffer)
boolean	overlaps (Annotation other)
boolean	overlaps (Collection<?extends Annotation > others)
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)
int	getMidpoint ()

Detailed Description

Based on the Alignment interface in IGV. This interface represents any read or pair of reads aligned to the genome

Author

skadri

Member Function Documentation

int umms.core.alignment.Alignment.getAlignmentEnd

(

)

Returns the end position of the alignment

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

int umms.core.alignment.Alignment.getAlignmentStart

(

)

Returns the start position of the alignment

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

Object umms.core.alignment.Alignment.getAttribute

(

String

string

)

Returns the value for the specified attribute

Parameters

string

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

String umms.core.alignment.Alignment.getChr

(

)

Get chromosome

Returns

Implements umms.core.annotation.Annotation.

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

int umms.core.alignment.Alignment.getEnd

(

)

Get end of the fragment

Returns

Implements umms.core.annotation.Annotation.

Implemented in umms.core.alignment.AbstractPairedEndAlignment.

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int umms.core.alignment.Alignment.getFirstFragmentPositionStranded

(

)

Get the ending position of the read considering strand

Returns

Lowest position if negative strand, highest position otherwise

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

Collection<? extends Window> umms.core.alignment.Alignment.getFragment

(

CoordinateSpace

C

)

This method returns the fragment formed by the alignment in the coordinate space C, specified.

Parameters

C

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

int umms.core.alignment.Alignment.getFragmentEnd

(

)

Returns the end position of the alignment in genomic space.

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

int umms.core.alignment.Alignment.getFragmentMidpoint

(

Annotation

annot

)

Get midpoint of fragment with respect to coordinate space

Parameters

annot

Parent annotation

Returns

Fragment midpoint in coordinate space

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

Collection<Integer> umms.core.alignment.Alignment.getFragmentSize

(

CoordinateSpace

C

)

Returns the fragment size (insert+lengths of the reads)

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

int umms.core.alignment.Alignment.getFragmentStart

(

)

Returns the start position of the alignment in genomic space.

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

Strand umms.core.alignment.Alignment.getFragmentStrand

(

)

Returns the strand for the fragment

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

SAMFileHeader umms.core.alignment.Alignment.getHeader

(

)

Returns the SAM file header for this alignment

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

int [] umms.core.alignment.Alignment.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

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

int umms.core.alignment.Alignment.getLastFragmentPositionStranded

(

)

Get the ending position of the read considering strand

Returns

Lowest position if negative strand, highest position otherwise

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

int umms.core.alignment.Alignment.getMappingQuality

(

)

Returns the mapping quality

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

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Annotation umms.core.alignment.Alignment.getReadAlignmentBlocks

(

CoordinateSpace

C

)

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

Parameters

C

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

Collection<Annotation> umms.core.alignment.Alignment.getReadAlignments

(

CoordinateSpace

space

)

This will return the actual read alignments

Parameters

space

Coordinate Space to return the blocks in

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

Collection<Alignment> umms.core.alignment.Alignment.getReadMates

(

)

This will return the actual read alignment objects NOT BLOCKS

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

String umms.core.alignment.Alignment.getReadName

(

)

This method returns the name of the alignment

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

String umms.core.alignment.Alignment.getReadSequence

(

)

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

Collection<? extends Annotation> umms.core.alignment.Alignment.getSpliceConnections

(

)

Return the splice connections contained within this read

Returns

Implements umms.core.annotation.Annotation.

Implemented in umms.core.alignment.SingleEndAlignment.

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int umms.core.alignment.Alignment.getStart

(

)

Get start of the fragment

Returns

Implements umms.core.annotation.Annotation.

Implemented in umms.core.alignment.AbstractPairedEndAlignment.

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double umms.core.alignment.Alignment.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

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

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boolean umms.core.alignment.Alignment.hasIndel

(

)

Returns whether the read contains an insertion or deletion

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

boolean umms.core.alignment.Alignment.isChimera

(

)

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

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

boolean umms.core.alignment.Alignment.isDuplicate

(

)

Returns true if the alignment is flagged as a duplicate

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

boolean umms.core.alignment.Alignment.isMapped

(

)

Returns true if the alignment is mapped

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

boolean umms.core.alignment.Alignment.isNegativeStrand

(

)

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

Returns

Implements umms.core.annotation.Annotation.

Implemented in umms.core.alignment.AbstractPairedEndAlignment.

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boolean umms.core.alignment.Alignment.isPaired

(

)

Returns true if the alignment is true.

Returns

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

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boolean umms.core.alignment.Alignment.isProperPair

(

)

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

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

void umms.core.alignment.Alignment.setDuplicateFlag

(

boolean

duplicateFlag

)

Sets the isDuplicate Flag

Parameters

duplicateFlag

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

void umms.core.alignment.Alignment.setFragmentStrand

(

TranscriptionRead

strand

)

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.alignment.AbstractPairedEndAlignment.

void umms.core.alignment.Alignment.setHeader

(

SAMFileHeader

header

)

Sets the SAM File header for this alignment

Parameters

header

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

void umms.core.alignment.Alignment.setProperPairFlag

(

boolean

properPairFlag

)

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

Returns

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

SAMRecord umms.core.alignment.Alignment.toSAMRecord

(

)

Implemented in umms.core.alignment.AbstractPairedEndAlignment, and umms.core.alignment.SingleEndAlignment.

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

• java/umms/core/alignment/Alignment.java