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hierarchichalalignmentformatapi
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- g -
get() :
hal::CLParser
,
hal::MetaData
getAlignment() :
hal::Genome
getArgument() :
hal::CLParser
getArrayIndex() :
hal::Sequence
,
hal::ColumnIterator
,
hal::DNAIterator
,
hal::Segment
getAtomic() :
hal::GappedSegmentIterator
getBottomParseIndex() :
hal::TopSegment
getBottomParseOffset() :
hal::TopSegment
getBottomSegment() :
hal::BottomSegmentIterator
getBottomSegmentArrayIndex() :
hal::Sequence
getBottomSegmentEndIterator() :
hal::SegmentedSequence
getBottomSegmentIterator() :
hal::SegmentedSequence
getBranchLength() :
hal::Alignment
getChar() :
hal::DNAIterator
getChild() :
hal::Genome
getChildIndex() :
hal::BottomSegment
,
hal::GappedSegmentIterator
,
hal::Genome
getChildIndexG() :
hal::BottomSegment
getChildNames() :
hal::Alignment
getChildReversed() :
hal::BottomSegment
,
hal::GappedBottomSegmentIterator
getColumnIterator() :
hal::SegmentedSequence
getColumnMap() :
hal::ColumnIterator
getDeletedRange() :
hal::Rearrangement
getDNAEndIterator() :
hal::SegmentedSequence
getDNAIterator() :
hal::SegmentedSequence
getDuplicatedRange() :
hal::Rearrangement
getEndOffset() :
hal::SlicedSegment
getEndPosition() :
hal::Segment
,
hal::Sequence
getFlag() :
hal::CLParser
getFullName() :
hal::Sequence
getGapLengthThreshold() :
hal::Rearrangement
getGappedBottomSegmentIterator() :
hal::SegmentedSequence
getGappedTopSegmentIterator() :
hal::SegmentedSequence
getGapThreshold() :
hal::GappedSegmentIterator
getGenome() :
hal::DNAIterator
,
hal::Segment
,
hal::Sequence
getID() :
hal::Rearrangement
getInsertedRange() :
hal::Rearrangement
getLeafNamesBelow() :
hal::Alignment
getLeft() :
hal::GappedBottomSegmentIterator
,
hal::GappedTopSegmentIterator
getLeftArrayIndex() :
hal::GappedSegmentIterator
getLeftBreakpoint() :
hal::Rearrangement
getLeftChildIndex() :
hal::BottomSegment
getLeftParentIndex() :
hal::TopSegment
getLength() :
hal::Rearrangement
,
hal::Segment
getMap() :
hal::MetaData
getMappedSegments() :
hal::Segment
getMetaData() :
hal::Alignment
,
hal::Genome
getName() :
hal::Genome
,
hal::Sequence
getNewickTree() :
hal::Alignment
getNextParalogyIndex() :
hal::TopSegment
getNumBottomSegments() :
hal::SegmentedSequence
getNumChildren() :
hal::BottomSegment
,
hal::Genome
getNumContainedGapBases() :
hal::Rearrangement
getNumContainedGaps() :
hal::Rearrangement
getNumGapBases() :
hal::GappedSegmentIterator
getNumGaps() :
hal::GappedSegmentIterator
getNumGenomes() :
hal::Alignment
getNumSegments() :
hal::GappedSegmentIterator
getNumSequences() :
hal::Genome
getNumTopSegments() :
hal::SegmentedSequence
getOption() :
hal::CLParser
getParent() :
hal::Genome
getParentIndex() :
hal::TopSegment
getParentName() :
hal::Alignment
getParentReversed() :
hal::GappedTopSegmentIterator
,
hal::TopSegment
getRearrangement() :
hal::SegmentedSequence
getReferenceGenome() :
hal::ColumnIterator
getReferenceSequence() :
hal::ColumnIterator
getReferenceSequencePosition() :
hal::ColumnIterator
getReversed() :
hal::DNAIterator
,
hal::SlicedSegment
getRight() :
hal::GappedBottomSegmentIterator
,
hal::GappedTopSegmentIterator
getRightArrayIndex() :
hal::GappedSegmentIterator
getRightBreakpoint() :
hal::Rearrangement
getRightChildIndex() :
hal::BottomSegment
getRightParentIndex() :
hal::TopSegment
getRootName() :
hal::Alignment
getSequence() :
hal::Genome
,
hal::DNAIterator
,
hal::Segment
,
hal::DNAIterator
,
hal::SequenceIterator
,
hal::Segment
,
hal::Genome
getSequenceBySite() :
hal::Genome
getSequenceEndIterator() :
hal::Genome
getSequenceIterator() :
hal::Genome
getSequenceLength() :
hal::SegmentedSequence
getSource() :
hal::MappedSegment
getStartOffset() :
hal::SlicedSegment
getStartPosition() :
hal::Sequence
,
hal::Segment
getString() :
hal::Segment
,
hal::SegmentedSequence
getSubString() :
hal::SegmentedSequence
getTopParseIndex() :
hal::BottomSegment
getTopParseOffset() :
hal::BottomSegment
getTopSegment() :
hal::TopSegmentIterator
getTopSegmentArrayIndex() :
hal::Sequence
getTopSegmentEndIterator() :
hal::SegmentedSequence
getTopSegmentIterator() :
hal::SegmentedSequence
getVersion() :
hal::Alignment
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