umms.core.coordinatesystem.TranscriptomeSpace Member List

This is the complete list of members for umms.core.coordinatesystem.TranscriptomeSpace, including all inherited members.

getChromosomeNames()	umms.core.coordinatesystem.TranscriptomeSpace
getEntireChromosome(String chrName)	umms.core.coordinatesystem.TranscriptomeSpace
getFragment(String chr, int start, int end)	umms.core.coordinatesystem.TranscriptomeSpace
getFragment(Annotation annotation)	umms.core.coordinatesystem.TranscriptomeSpace
getLength()	umms.core.coordinatesystem.TranscriptomeSpace
getLength(String chr)	umms.core.coordinatesystem.TranscriptomeSpace
getOverlappingRegion(String chr, int start, int end)	umms.core.coordinatesystem.TranscriptomeSpace
getPositionCountMap(Gene region, AlignmentModel data)	umms.core.coordinatesystem.TranscriptomeSpace
getReferenceAnnotation(String name)	umms.core.coordinatesystem.TranscriptomeSpace
getReferenceAnnotations()	umms.core.coordinatesystem.TranscriptomeSpace
getReferenceNames()	umms.core.coordinatesystem.TranscriptomeSpace
getSize(Annotation region)	umms.core.coordinatesystem.TranscriptomeSpace
getTranscriptomeSpace(String bedFile)	umms.core.coordinatesystem.TranscriptomeSpace	static
getWindowIterator(Collection< Gene > baseGenes, int windowSize, int overlap)	umms.core.coordinatesystem.TranscriptomeSpace
getWindowIterator(int windowSize, String chr, int start, int end, int overlap)	umms.core.coordinatesystem.TranscriptomeSpace
getWindowIterator(Annotation window, int windowSize, int overlap)	umms.core.coordinatesystem.TranscriptomeSpace
getWindowIterator(String chr, int windowSize, int overlap)	umms.core.coordinatesystem.TranscriptomeSpace
getWindowIterator(int windowSize, int overlap)	umms.core.coordinatesystem.TranscriptomeSpace
hasChromosome(String chr)	umms.core.coordinatesystem.TranscriptomeSpace
isValidWindow(Annotation a)	umms.core.coordinatesystem.TranscriptomeSpace
moveAnnotation(Annotation read, int relativeStart, Annotation gene)	umms.core.coordinatesystem.TranscriptomeSpace
PERMUTATION_ATTEMPTS	umms.core.coordinatesystem.TranscriptomeSpace	static
permuteAnnotation(Annotation a)	umms.core.coordinatesystem.TranscriptomeSpace
permuteAnnotation(Annotation a, Annotation bounds)	umms.core.coordinatesystem.TranscriptomeSpace
TranscriptomeSpace(Map< String, Collection< Gene >> chrToGenesMap)	umms.core.coordinatesystem.TranscriptomeSpace
TranscriptomeSpace(File bamFile, String genomeSeq)	umms.core.coordinatesystem.TranscriptomeSpace
TranscriptomeSpace(File bamFile, Map< String, Collection< Gene >> chrToGenesMap, String genomeSeq)	umms.core.coordinatesystem.TranscriptomeSpace