| A_CODE | broad.core.multiplealignment.MultipleAlignment | static |
| addBlock(MAFMultipleAlignmentBlock block) | broad.core.multiplealignment.MAFAlignment | |
| addBlocks(List< MAFMultipleAlignmentBlock > blocks) | broad.core.multiplealignment.MAFAlignment | |
| addBlocks(Iterator< MAFMultipleAlignmentBlock > blockIt) | broad.core.multiplealignment.MAFAlignment | |
| addSequence(AlignedSequence seq) | broad.core.multiplealignment.MAFAlignment | |
| addSequences(List< AlignedSequence > sequences) | broad.core.multiplealignment.MAFAlignment | |
| addShortEncodedColumn(Map< String, Short > col) | broad.core.multiplealignment.MAFAlignment | |
| addShortEncodedColumnMatrix(Map< String, Matrix > col) | broad.core.multiplealignment.MultipleAlignment | |
| addShortEncodedRegion(Map< String, short[]> region) | broad.core.multiplealignment.MAFAlignment | |
| append(MAFAlignment mafAln) | broad.core.multiplealignment.MAFAlignment | |
| broad::core::multiplealignment::MultipleAlignment.append(MultipleAlignment other) | broad.core.multiplealignment.MultipleAlignment | |
| C_CODE | broad.core.multiplealignment.MultipleAlignment | static |
| clear() | broad.core.multiplealignment.MAFAlignment | |
| compress() | broad.core.multiplealignment.MAFAlignment | |
| contains(LightweightGenomicAnnotation annotation) | broad.core.multiplealignment.MAFAlignment | |
| createIndex(String alignmentFile) | broad.core.multiplealignment.MAFAlignment | |
| decodeShort(Short nucleotide) | broad.core.multiplealignment.MultipleAlignment | |
| encode() | broad.core.multiplealignment.MAFAlignment | |
| broad::core::multiplealignment::MultipleAlignment.encode(boolean distinguishMissingSequence) | broad.core.multiplealignment.MultipleAlignment | |
| encodeAsMatrix() | broad.core.multiplealignment.MAFAlignment | |
| G_CODE | broad.core.multiplealignment.MultipleAlignment | static |
| GAP_CODE | broad.core.multiplealignment.MultipleAlignment | static |
| getAlignedSequence(String sequenceId, boolean fillInGapsBetweenBlocks) | broad.core.multiplealignment.MAFAlignment | |
| getAlignedSequence(String sequenceId) | broad.core.multiplealignment.MAFAlignment | |
| getAlignedSequenceIds() | broad.core.multiplealignment.MAFAlignment | |
| getAlignedSequences(boolean fillGapsBetweenBlocks) | broad.core.multiplealignment.MAFAlignment | |
| getAlignedSequences() | broad.core.multiplealignment.MAFAlignment | |
| broad::core::multiplealignment::MultipleAlignment.getAlignedSequences(String refId, int refStart, int refEnd, boolean reverse) | broad.core.multiplealignment.MultipleAlignment | protected |
| getAsMatrix() | broad.core.multiplealignment.MultipleAlignment | |
| getBlockIterator() | broad.core.multiplealignment.MAFAlignment | |
| getColumn(int i) | broad.core.multiplealignment.MAFAlignment | |
| getColumnsAsVector(int start, int number) | broad.core.multiplealignment.MAFAlignment | |
| getConcatenatedSubAlignment(String refId, List<?extends GenomicAnnotation > annotations) | broad.core.multiplealignment.MultipleAlignment | |
| getHeader() | broad.core.multiplealignment.MAFAlignment | |
| getIndex() | broad.core.multiplealignment.MAFAlignment | |
| getIOHelper() | broad.core.multiplealignment.MultipleAlignment | protected |
| getNumberOfAligningSequences() | broad.core.multiplealignment.MultipleAlignment | |
| getReference() | broad.core.multiplealignment.MultipleAlignment | |
| getReferenceEnd() | broad.core.multiplealignment.MAFAlignment | |
| getReferenceId() | broad.core.multiplealignment.MultipleAlignment | |
| getReferenceStart() | broad.core.multiplealignment.MAFAlignment | |
| getScore() | broad.core.multiplealignment.MultipleAlignment | |
| getSubAlignment(int refStart, int refEnd, boolean reverse) | broad.core.multiplealignment.MAFAlignment | |
| broad::core::multiplealignment::MultipleAlignment.getSubAlignment(String refId, int refStart, int refEnd, boolean reverse) | broad.core.multiplealignment.MultipleAlignment | |
| getUngappedReferenceIslands() | broad.core.multiplealignment.MultipleAlignment | |
| getUngappedSequenceReferenceIslands() | broad.core.multiplealignment.MultipleAlignment | |
| introduceGaps(boolean canGapReference, int maxNumberOfGaps) | broad.core.multiplealignment.MultipleAlignment | |
| isEmpty() | broad.core.multiplealignment.MAFAlignment | |
| isRefGapped() | broad.core.multiplealignment.MultipleAlignment | |
| length() | broad.core.multiplealignment.MAFAlignment | |
| load(String fileName) | broad.core.multiplealignment.MAFAlignment | |
| load(RandomAccessFile handle, List< String > sequencesToLoad) | broad.core.multiplealignment.MAFAlignment | |
| load(RandomAccessFile handle, int referenceStart, int referenceEnd) | broad.core.multiplealignment.MAFAlignment | |
| load(RandomAccessFile handle, int referenceStart, int referenceEnd, List< String > sequencesToLoad) | broad.core.multiplealignment.MAFAlignment | |
| load(String fileName, int referenceStart, int referenceEnd) | broad.core.multiplealignment.MAFAlignment | |
| loadIndex(String idxFile) | broad.core.multiplealignment.MAFAlignment | |
| MAFAlignment() | broad.core.multiplealignment.MAFAlignment | |
| MAFAlignment(String indexFile) | broad.core.multiplealignment.MAFAlignment | |
| main(String[] args) | broad.core.multiplealignment.MAFAlignment | static |
| MultipleAlignment() | broad.core.multiplealignment.MultipleAlignment | |
| MultipleAlignment(List<?extends MultipleAlignment > alnBlocks, String ref, String[] seqs) | broad.core.multiplealignment.MultipleAlignment | |
| overlaps(LightweightGenomicAnnotation annotation) | broad.core.multiplealignment.MAFAlignment | |
| broad::core::multiplealignment::MultipleAlignment.overlaps(SequenceRegion region) | broad.core.multiplealignment.MultipleAlignment | |
| permuteColumns() | broad.core.multiplealignment.MultipleAlignment | |
| remove(List< String > removeList) | broad.core.multiplealignment.MultipleAlignment | |
| reverse() | broad.core.multiplealignment.MAFAlignment | |
| sampleColumns(int colNum, int numConsecutiveCols) | broad.core.multiplealignment.MAFAlignment | |
| setAlignedSequences(List< String > seqIds) | broad.core.multiplealignment.MAFAlignment | protected |
| setBlocks(List< MAFMultipleAlignmentBlock > blocks) | broad.core.multiplealignment.MAFAlignment | |
| setIOHelper(MultipleAlignmentIO maio) | broad.core.multiplealignment.MultipleAlignment | |
| setReferenceId(String referenceId) | broad.core.multiplealignment.MultipleAlignment | |
| setRefGapped(boolean isRefGapped) | broad.core.multiplealignment.MultipleAlignment | |
| setScore(float score) | broad.core.multiplealignment.MultipleAlignment | |
| T_CODE | broad.core.multiplealignment.MultipleAlignment | static |
| toMultipleAlignment(boolean fillGapsBetweenBlocks) | broad.core.multiplealignment.MAFAlignment | |
| toMultipleAlignment() | broad.core.multiplealignment.MAFAlignment | |
| UNGAPPED_ALPHABET_SIZE | broad.core.multiplealignment.MultipleAlignment | protectedstatic |
| USAGE | broad.core.multiplealignment.MAFAlignment | static |
| write(BufferedWriter bw) | broad.core.multiplealignment.MAFAlignment | |
| broad::core::multiplealignment::MultipleAlignment.write(BufferedWriter bw, List< String > order) | broad.core.multiplealignment.MultipleAlignment | |
| writeIndex(String indexFileName) | broad.core.multiplealignment.MAFAlignment | |
1.8.7
