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All Classes Namespaces Functions Pages
Here is a list of all documented class members with links to the class documentation for each member:

### - 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