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