| containsDataFor(String chromosome) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getChromosomeNames() | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getEntireChromosome(String chrName) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getFragment(String chr, int start, int end) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getFragment(Annotation annotation) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getLength() | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getLength(String chr) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getOverlappingRegion(String chr, int start, int end) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getReferenceAnnotation(String name) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getReferenceAnnotations() | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getReferenceNames() | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getSize(Annotation region) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getUnmaskedLength(String chr) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(int windowSize, String chr, int start, int end, int overlap) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(int windowSize, String chr, int start, int end, int overlap, boolean backward) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(Annotation window, int windowSize, int overlap) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(Annotation window, int windowSize, int overlap, boolean considerStrand) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(String chr, int windowSize, int overlap) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(int windowSize, int overlap) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| getWindowIterator(Collection< Gene > baseGenes, int windowSize, int overlap) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| hasChromosome(String chr) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| isValidWindow(Annotation window) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| PERMUTATION_ATTEMPTS | umms.core.coordinatesystem.TranscriptInGenomicSpace | static |
| permuteAnnotation(Annotation a) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| permuteAnnotation(Annotation a, Annotation bounds) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| setPercentMaskedAllowed(double pct) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| setSeed(long seed) | umms.core.coordinatesystem.TranscriptInGenomicSpace | static |
| TranscriptInGenomicSpace(Map< String, Integer > chromosomeSizes) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| TranscriptInGenomicSpace(String chromosomeSizes) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| TranscriptInGenomicSpace(String chromosomeSizes, String maskedRegionFile) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| TranscriptInGenomicSpace(Map< String, Integer > chromosomeSizes, String maskedRegionFile) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
| TranscriptInGenomicSpace(String chromosomeSizes, String maskedRegionFile, double pctMaskedAllowed) | umms.core.coordinatesystem.TranscriptInGenomicSpace | |
1.8.7
