| append(String partialSequence) | broad.core.sequence.Sequence | |
| append(char c) | broad.core.sequence.Sequence | |
| buildKmerMap(int kmer) | broad.core.sequence.Sequence | |
| chunk(int chunkSize, int chunkOverlap) | broad.core.sequence.Sequence | |
| complement(String seq) | broad.core.sequence.Sequence | static |
| compute454Flow(char[] flowOrder) | broad.core.sequence.Sequence | |
| compute454Flow(char[] flowOrder, int start, int end) | broad.core.sequence.Sequence | |
| computeGCContent(String dnaString) | broad.core.sequence.Sequence | static |
| computeSequenceComposition(String dnaString) | broad.core.sequence.Sequence | static |
| contains(String motif) | broad.core.sequence.Sequence | |
| countSoftMaskedBases() | broad.core.sequence.Sequence | |
| decode(short[] shortEncodedSequence) | broad.core.sequence.Sequence | static |
| encodeSequence() | broad.core.sequence.Sequence | |
| encodeSequence(StringBuilder bases) | broad.core.sequence.Sequence | static |
| encodeSequenceAsVector() | broad.core.sequence.Sequence | |
| encodeSequenceIgnoreCase() | broad.core.sequence.Sequence | |
| encodeSequenceIgnoreCase(boolean distinguishMissingSequence) | broad.core.sequence.Sequence | |
| encodeSequenceIgnoreCase(StringBuilder sequence) | broad.core.sequence.Sequence | static |
| encodeSequenceIgnoreCase(StringBuilder sequence, boolean distinguishMissingSequence) | broad.core.sequence.Sequence | static |
| extractRegionBasedOnGC(float targetGC, int size, int buffer) | broad.core.sequence.Sequence | |
| findUngappedSequenceChunks() | broad.core.sequence.Sequence | |
| gcContent() | broad.core.sequence.Sequence | |
| generateAll5Mers() | broad.core.sequence.Sequence | static |
| generateAllKmers(int k) | broad.core.sequence.Sequence | static |
| generateRandomSequence(int oligoSize) | broad.core.sequence.Sequence | static |
| get3Prime(String seq, int numBases) | broad.core.sequence.Sequence | static |
| getAntisense() | broad.core.sequence.Sequence | |
| getEncodedSequence() | broad.core.sequence.Sequence | |
| getEnd() | broad.core.sequence.Sequence | |
| getGapsSize() | broad.core.sequence.Sequence | |
| getId() | broad.core.sequence.Sequence | |
| getLength() | broad.core.sequence.Sequence | |
| getMatches(String s, int windowStart, int windowEnd, boolean includeRC) | broad.core.sequence.Sequence | |
| getRefseqGeneName() | broad.core.sequence.Sequence | |
| getRefseqRnaClassName() | broad.core.sequence.Sequence | |
| getRefseqSpeciesName() | broad.core.sequence.Sequence | |
| getRegion(int start, int end) | broad.core.sequence.Sequence | |
| getRegion(SequenceRegion region) | broad.core.sequence.Sequence | |
| getRegion(SequenceRegion region, boolean softmask) | broad.core.sequence.Sequence | |
| getRegion(SequenceRegion region, boolean softmask, Map< String, IntervalTree< Alignments >> okRepeats) | broad.core.sequence.Sequence | |
| getRegions(List<?extends SequenceRegion > regions) | broad.core.sequence.Sequence | |
| getSequenceBases() | broad.core.sequence.Sequence | |
| getSequenceBuilder() | broad.core.sequence.Sequence | |
| getSlider(int windowSize, int overlap) | broad.core.sequence.Sequence | |
| getSoftmaskedRegions() | broad.core.sequence.Sequence | |
| getSubSequence(SequenceRegion region, int extension) | broad.core.sequence.Sequence | |
| getSubSequence(String name, int start, int end, int extension) | broad.core.sequence.Sequence | |
| getSubSequence(String name, int start, int end) | broad.core.sequence.Sequence | |
| getSubsequence(Gene annot) | broad.core.sequence.Sequence | |
| getSubsequence(Annotation annot) | broad.core.sequence.Sequence | |
| getVectorEncodedSequence() | broad.core.sequence.Sequence | |
| isForwardStrand() | broad.core.sequence.Sequence | |
| isGap(int position) | broad.core.sequence.Sequence | |
| LONG_READ_FLOW | broad.core.sequence.Sequence | static |
| mask(Annotation region, boolean softmask) | broad.core.sequence.Sequence | |
| maskSoftmaskedRegions() | broad.core.sequence.Sequence | |
| reverse() | broad.core.sequence.Sequence | |
| reverseSequence(Sequence seq) | broad.core.sequence.Sequence | static |
| reverseSequence(String seq) | broad.core.sequence.Sequence | static |
| scramble() | broad.core.sequence.Sequence | |
| Sequence(String id) | broad.core.sequence.Sequence | |
| Sequence(String id, boolean isLarge) | broad.core.sequence.Sequence | |
| Sequence(String id, int expectedSize) | broad.core.sequence.Sequence | |
| setCapacity(int size) | broad.core.sequence.Sequence | |
| setCharAt(int position, char newCharacter) | broad.core.sequence.Sequence | |
| setForwardStrand(boolean isForwardStrand) | broad.core.sequence.Sequence | |
| setId(String id) | broad.core.sequence.Sequence | |
| setSequenceBases(String sequence) | broad.core.sequence.Sequence | |
| SHORT_ENCODED_a | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_A | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_C | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_c | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_g | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_G | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_GAP | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_N | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_t | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_T | broad.core.sequence.Sequence | static |
| SHORT_READ_FLOW | broad.core.sequence.Sequence | static |
| shuffle() | broad.core.sequence.Sequence | |
| unloadAllSequences() | broad.core.sequence.Sequence | |
| unloadEncodedSequence() | broad.core.sequence.Sequence | |
| unloadSequence() | broad.core.sequence.Sequence | |
| uppercase() | broad.core.sequence.Sequence | |
1.8.7
