umms.core.coordinatesystem.MaskedGenomicSpace Member List

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

getChromosomeNames()	umms.core.coordinatesystem.MaskedGenomicSpace
getEntireChromosome(String chrName)	umms.core.coordinatesystem.MaskedGenomicSpace
getFragment(String chr, int start, int end)	umms.core.coordinatesystem.MaskedGenomicSpace
getFragment(Annotation annotation)	umms.core.coordinatesystem.MaskedGenomicSpace
getLength()	umms.core.coordinatesystem.MaskedGenomicSpace
getLength(String chr)	umms.core.coordinatesystem.MaskedGenomicSpace
getOverlappingRegion(String chr, int start, int end)	umms.core.coordinatesystem.MaskedGenomicSpace
getReferenceAnnotation(String name)	umms.core.coordinatesystem.MaskedGenomicSpace
getReferenceAnnotations()	umms.core.coordinatesystem.MaskedGenomicSpace
getReferenceNames()	umms.core.coordinatesystem.MaskedGenomicSpace
getSize(Annotation region)	umms.core.coordinatesystem.MaskedGenomicSpace
getWindowIterator(int windowSize, String chr, int start, int end, int overlap)	umms.core.coordinatesystem.MaskedGenomicSpace
getWindowIterator(String chr, int windowSize, int overlap)	umms.core.coordinatesystem.MaskedGenomicSpace
getWindowIterator(int windowSize, int overlap)	umms.core.coordinatesystem.MaskedGenomicSpace
getWindowIterator(Annotation window, int windowSize, int overlap)	umms.core.coordinatesystem.MaskedGenomicSpace
getWindowIterator(Collection< Gene > baseGenes, int windowSize, int overlap)	umms.core.coordinatesystem.MaskedGenomicSpace
hasChromosome(String chr)	umms.core.coordinatesystem.MaskedGenomicSpace
isValidWindow(Annotation window)	umms.core.coordinatesystem.MaskedGenomicSpace
MaskedGenomicSpace(Map< String, Integer > chrSizes, Map< String, Collection< Annotation >> maskedRegions, int distance)	umms.core.coordinatesystem.MaskedGenomicSpace
MaskedGenomicSpace(Map< String, Integer > chrSizes, Map< String, Collection< Annotation >> maskedRegions, int distance, boolean constantWidth)	umms.core.coordinatesystem.MaskedGenomicSpace
permuteAnnotation(Annotation a)	umms.core.coordinatesystem.MaskedGenomicSpace
permuteAnnotation(Annotation a, Annotation bounds)	umms.core.coordinatesystem.MaskedGenomicSpace