Inheritance diagram for umms.core.annotation.PSLRecord:

Collaboration diagram for umms.core.annotation.PSLRecord:

Classes
class	Factory

Public Member Functions
	PSLRecord (BasicAnnotation annotation)

void	setMatch (int m)

void	setMismatch (int m)

void	setRepMatch (int m)

void	setNcount (int c)

void	setQueryGap (int x)

void	setQueryGapBases (int x)

void	setTargetGap (int x)

void	setTargetGapBases (int x)

void	setQuerySize (int x)

void	setQueryStart (int x)

void	setQueryEnd (int x)

void	setTargetSize (int x)

int	getMatch ()

float	getPercentIdentity ()

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 ()

Protected Attributes
int	match

int[]	queryStarts

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

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

Detailed Description

Author: engreitz Class that I started writing but didn't finish to represent a PSL annotation file (output by BLAT) NOTE: Checking in because it might be helpful down the line, but it is not currently used anywhere

Constructor & Destructor Documentation

umms.core.annotation.PSLRecord.PSLRecord ( BasicAnnotation annotation )

Member Function Documentation

int umms.core.annotation.PSLRecord.getMatch ( )

float umms.core.annotation.PSLRecord.getPercentIdentity ( )

Get percent identity of match

Returns: Number of matched bases divided by total length of aligned segments

Here is the call graph for this function:

void umms.core.annotation.PSLRecord.setMatch ( int m )

void umms.core.annotation.PSLRecord.setMismatch ( int m )

void umms.core.annotation.PSLRecord.setNcount ( int c )

void umms.core.annotation.PSLRecord.setQueryEnd ( int x )

void umms.core.annotation.PSLRecord.setQueryGap ( int x )

void umms.core.annotation.PSLRecord.setQueryGapBases ( int x )

void umms.core.annotation.PSLRecord.setQuerySize ( int x )

void umms.core.annotation.PSLRecord.setQueryStart ( int x )

void umms.core.annotation.PSLRecord.setRepMatch ( int m )

void umms.core.annotation.PSLRecord.setTargetGap ( int x )

void umms.core.annotation.PSLRecord.setTargetGapBases ( int x )

void umms.core.annotation.PSLRecord.setTargetSize ( int x )

Member Data Documentation

int umms.core.annotation.PSLRecord.match

protected

int [] umms.core.annotation.PSLRecord.queryStarts

protected

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

java/umms/core/annotation/PSLRecord.java

Classes

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation