umms.core.coordinatesystem.GenomicSpace Member List

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

containsDataFor(String chromosome)	umms.core.coordinatesystem.GenomicSpace
GenomicSpace(Map< String, Integer > chromosomeSizes)	umms.core.coordinatesystem.GenomicSpace
GenomicSpace(String chromosomeSizes)	umms.core.coordinatesystem.GenomicSpace
GenomicSpace(String chromosomeSizes, String maskedRegionFile)	umms.core.coordinatesystem.GenomicSpace
GenomicSpace(Map< String, Integer > chromosomeSizes, String maskedRegionFile)	umms.core.coordinatesystem.GenomicSpace
GenomicSpace(String chromosomeSizes, String maskedRegionFile, double pctMaskedAllowed)	umms.core.coordinatesystem.GenomicSpace
getChromosomeNames()	umms.core.coordinatesystem.GenomicSpace
getEntireChromosome(String chrName)	umms.core.coordinatesystem.GenomicSpace
getFragment(String chr, int start, int end)	umms.core.coordinatesystem.GenomicSpace
getFragment(Annotation annotation)	umms.core.coordinatesystem.GenomicSpace
getLength()	umms.core.coordinatesystem.GenomicSpace
getLength(String chr)	umms.core.coordinatesystem.GenomicSpace
getOverlappingRegion(String chr, int start, int end)	umms.core.coordinatesystem.GenomicSpace
getReferenceAnnotation(String name)	umms.core.coordinatesystem.GenomicSpace
getReferenceAnnotations()	umms.core.coordinatesystem.GenomicSpace
getReferenceNames()	umms.core.coordinatesystem.GenomicSpace
getSize(Annotation region)	umms.core.coordinatesystem.GenomicSpace
getUnmaskedLength(String chr)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(int windowSize, String chr, int start, int end, int overlap)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(int windowSize, String chr, int start, int end, int overlap, boolean backward)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(Annotation window, int windowSize, int overlap)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(Annotation window, int windowSize, int overlap, boolean considerStrand)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(String chr, int windowSize, int overlap)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(int windowSize, int overlap)	umms.core.coordinatesystem.GenomicSpace
getWindowIterator(Collection< Gene > baseGenes, int windowSize, int overlap)	umms.core.coordinatesystem.GenomicSpace
hasChromosome(String chr)	umms.core.coordinatesystem.GenomicSpace
isValidWindow(Annotation window)	umms.core.coordinatesystem.GenomicSpace
PERMUTATION_ATTEMPTS	umms.core.coordinatesystem.GenomicSpace	static
permuteAnnotation(Annotation a)	umms.core.coordinatesystem.GenomicSpace
permuteAnnotation(Annotation a, Annotation bounds)	umms.core.coordinatesystem.GenomicSpace
setPercentMaskedAllowed(double pct)	umms.core.coordinatesystem.GenomicSpace
setSeed(long seed)	umms.core.coordinatesystem.GenomicSpace	static