broad.pda.feature.genome.DirectoryInstalledGenomeAssembly Member List

This is the complete list of members for broad.pda.feature.genome.DirectoryInstalledGenomeAssembly, including all inherited members.

areRepeatsInDeepDirHierarchy()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly	protected
delete(SequenceRegion region)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
DirectoryInstalledGenomeAssembly(File sequenceDirectory)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
doRepeatListNeedsCleanup()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly	protected
drawAutosome()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
drawChromosome()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
drawRandomAutosomeRegion(int size)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
drawRandomRegion(int size)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getAllChromosomes()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getAllNonRandomChromosomes()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getAnnotationDirectory()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getAutosomeGenomeSize()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getAutosomeNumber()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getAutosomes()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getChromosome(String chr)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getGenomeSize()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getNonRandomTotalSize()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getReducedRepresentation(int totalSize, List< GenomicAnnotation > toAvoid)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getRepeatFile(String chrSymbol)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getSequenceDir()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getUn()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
getX()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
insert(SequenceRegion region, GenomicAnnotation insertionPoint)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
invert(SequenceRegion region)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
sequenceDirectory	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly	protected
translocate(SequenceRegion region1, SequenceRegion region2)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
useMergedUn()	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly	protected
writeSizes(String outFile)	broad.pda.feature.genome.DirectoryInstalledGenomeAssembly