umms.core.annotation.AnnotationList< T extends Annotation > Member List

This is the complete list of members for umms.core.annotation.AnnotationList< T extends Annotation >, including all inherited members.

add(T annotation)	umms.core.annotation.AnnotationList< T extends Annotation >
addAll(Iterable<?extends T > annotations)	umms.core.annotation.AnnotationList< T extends Annotation >
addAll(AnnotationList<?extends T > otherSet)	umms.core.annotation.AnnotationList< T extends Annotation >
addFilter(Predicate< T > filter)	umms.core.annotation.AnnotationList< T extends Annotation >
addFilters(Collection< Predicate< T >> filters)	umms.core.annotation.AnnotationList< T extends Annotation >
AnnotationList()	umms.core.annotation.AnnotationList< T extends Annotation >
AnnotationList(CoordinateSpace cs)	umms.core.annotation.AnnotationList< T extends Annotation >
AnnotationList(CoordinateSpace cs, Collection<?extends T > annotations)	umms.core.annotation.AnnotationList< T extends Annotation >
AnnotationList(CoordinateSpace cs, T...annotations)	umms.core.annotation.AnnotationList< T extends Annotation >
annotations	umms.core.annotation.AnnotationList< T extends Annotation >	protected
collapse()	umms.core.annotation.AnnotationList< T extends Annotation >
coordinateSpace	umms.core.annotation.AnnotationList< T extends Annotation >	protected
ENFORCE_REFERENCE	umms.core.annotation.AnnotationList< T extends Annotation >	static
getBasesCovered(Annotation region, boolean fullyContained)	umms.core.annotation.AnnotationList< T extends Annotation >
getClosest(final Annotation query)	umms.core.annotation.AnnotationList< T extends Annotation >
getClosest(final Annotation query, boolean nonOverlapping)	umms.core.annotation.AnnotationList< T extends Annotation >
getClosestDownstream(final Annotation query)	umms.core.annotation.AnnotationList< T extends Annotation >
getClosestNonOverlapping(final Annotation query)	umms.core.annotation.AnnotationList< T extends Annotation >
getClosestUpstream(final Annotation query)	umms.core.annotation.AnnotationList< T extends Annotation >
getCoordinateSpace()	umms.core.annotation.AnnotationList< T extends Annotation >
getCount(Annotation region, boolean fullyContained)	umms.core.annotation.AnnotationList< T extends Annotation >
getCountExcludingRegion(Annotation region, Annotation excluded)	umms.core.annotation.AnnotationList< T extends Annotation >
getCountStrandedExcludingRegion(Annotation region, Annotation excluded)	umms.core.annotation.AnnotationList< T extends Annotation >
getDistanceToClosest(final Annotation query)	umms.core.annotation.AnnotationList< T extends Annotation >
getGlobalCount()	umms.core.annotation.AnnotationList< T extends Annotation >
getNumOverlappingAnnotations(Annotation region)	umms.core.annotation.AnnotationList< T extends Annotation >
getOverlappingAnnotationList(AnnotationList<?extends Annotation > other)	umms.core.annotation.AnnotationList< T extends Annotation >
getOverlappingAnnotationList(AnnotationList<?extends Annotation > other, boolean fullyContained)	umms.core.annotation.AnnotationList< T extends Annotation >
getOverlappingAnnotations(Annotation region, boolean fullyContained)	umms.core.annotation.AnnotationList< T extends Annotation >
getPermutedAnnotations(Annotation region)	umms.core.annotation.AnnotationList< T extends Annotation >
getRefSequenceLambda(String refname)	umms.core.annotation.AnnotationList< T extends Annotation >
hasAnnotationThatContains(Annotation region)	umms.core.annotation.AnnotationList< T extends Annotation >
hasAnnotationThatOverlaps(Annotation region)	umms.core.annotation.AnnotationList< T extends Annotation >
intersect(AnnotationList<?extends Annotation > other)	umms.core.annotation.AnnotationList< T extends Annotation >
iterator()	umms.core.annotation.AnnotationList< T extends Annotation >
minus(AnnotationList<?extends Annotation > other)	umms.core.annotation.AnnotationList< T extends Annotation >
removeAnnotation(T annotation)	umms.core.annotation.AnnotationList< T extends Annotation >
size()	umms.core.annotation.AnnotationList< T extends Annotation >
toList()	umms.core.annotation.AnnotationList< T extends Annotation >