| addIsoform(GeneWithIsoforms iso, String set) | broad.pda.annotation.Locus | |
| distanceToOppositeStrand5primeNeighbor(BEDFileParser geneSet) | broad.pda.annotation.Locus | |
| getAllIsoforms(String excludeSet) | broad.pda.annotation.Locus | |
| getAllIsoforms() | broad.pda.annotation.Locus | |
| getAllMerged() | broad.pda.annotation.Locus | |
| getComaptibleBetweenAny2Sets(ArrayList< String > setLst, boolean isFully) | broad.pda.annotation.Locus | |
| getComaptibleIsoforms(Gene g, boolean isFully) | broad.pda.annotation.Locus | |
| getDistanceTo3primeNeighbor(BEDFileParser geneSet) | broad.pda.annotation.Locus | |
| getDistanceTo5primeNeighbor(BEDFileParser geneSet) | broad.pda.annotation.Locus | |
| getExonUnion() | broad.pda.annotation.Locus | |
| getIsComaptibleBetweenAny2Sets(ArrayList< String > setLst, boolean isFully) | broad.pda.annotation.Locus | |
| getIsComaptibleBetweenAny2Sets(ArrayList< String > set3Lst, BEDFileParser uniqIsoBed) | broad.pda.annotation.Locus | |
| getIsComaptibleBetweenSubsets(ArrayList< String > set1Lst, ArrayList< String > set2Lst, boolean isFully) | broad.pda.annotation.Locus | |
| getIsComaptibleBetweenSubsets(ArrayList< String > set1Lst, ArrayList< String > set2Lst, BEDFileParser uniqIsoBed) | broad.pda.annotation.Locus | |
| getIsComaptibleWithRefPerSet() | broad.pda.annotation.Locus | |
| getIsPartiallyComaptibleWithRefPerSet() | broad.pda.annotation.Locus | |
| getLongestIntornChainIso(String refSet) | broad.pda.annotation.Locus | |
| getMaxExonsCovered() | broad.pda.annotation.Locus | |
| getMaxPctCovered() | broad.pda.annotation.Locus | |
| getMaxPctGenomeCovered() | broad.pda.annotation.Locus | |
| getMaxScoreAcrossAllIso() | broad.pda.annotation.Locus | |
| getMaxScorePerSet() | broad.pda.annotation.Locus | |
| getMerged() | broad.pda.annotation.Locus | |
| getNumberOfIsoforms() | broad.pda.annotation.Locus | |
| getNumIsoformsPerSet() | broad.pda.annotation.Locus | |
| getReferenceTranscript() | broad.pda.annotation.Locus | |
| getSetIsoforms(String setName) | broad.pda.annotation.Locus | |
| getUnqComaptibleBetweenAny2Sets(ArrayList< String > setLst, Collection<?extends Gene > unqIsoSet, boolean isFully) | broad.pda.annotation.Locus | |
| getUnqComaptibleBetweenSubsets(ArrayList< String > set1Lst, ArrayList< String > set2Lst, Collection< Gene > unqIsoSet, boolean isFully) | broad.pda.annotation.Locus | |
| isFullyComaptible(Gene iso1, Gene iso2, boolean stringent) | broad.pda.annotation.Locus | static |
| isTerminiCoverageBias() | broad.pda.annotation.Locus | |
| Locus(GeneWithIsoforms g) | broad.pda.annotation.Locus | |
| numOfOverlapSets(ArrayList< String > setLst) | broad.pda.annotation.Locus | |
| pctOverlapWithRef() | broad.pda.annotation.Locus | |
| SelectLongestIntronChainCandidate(Collection< Gene > betweenSubsetsIsoSet) | broad.pda.annotation.Locus | static |
| selectRandIsoSubset(Integer maxIsoPerLoci) | broad.pda.annotation.Locus | |
| updateIsoformsNameWithLocusName() | broad.pda.annotation.Locus | |
1.8.7
