Inheritance diagram for umms.core.feature.Window:

Collaboration diagram for umms.core.feature.Window:

Public Member Functions
void	addSourceAnnotation (Annotation annotation)

Collection<?extends Annotation >	getSourceAnnotations ()

Collection< Window >	getWindows (int windowSize, int stepSize)

Public Member Functions inherited from umms.core.annotation.Annotation
int	getStart ()

int	getSAMStart ()

int	getEnd ()

int	getSAMEnd ()

String	getReferenceName ()

String	getChr ()

String	getName ()

Strand	getOrientation ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

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)

Collection<?extends Annotation >	getSpliceConnections ()

int	getMidpoint ()