halapi
hierarchichalalignmentformatapi
hal::HDF5Sequence Member List
This is the complete list of members for hal::HDF5Sequence, including all inherited members.
_array (defined in hal::HDF5Sequence)hal::HDF5Sequence [mutable, protected]
_genome (defined in hal::HDF5Sequence)hal::HDF5Sequence [mutable, protected]
_index (defined in hal::HDF5Sequence)hal::HDF5Sequence [mutable, protected]
dataType(hal_size_t maxNameLength) (defined in hal::HDF5Sequence)hal::HDF5Sequence [static]
getArrayIndex() const hal::HDF5Sequence [virtual]
getBottomSegmentIterator(hal_index_t position)hal::HDF5Sequence [virtual]
getBottomSegmentIterator(hal_index_t position) const hal::HDF5Sequence [virtual]
getGenome() const hal::HDF5Sequence [virtual]
getGenome()hal::HDF5Sequence [virtual]
getName() const (defined in hal::HDF5Sequence)hal::HDF5Sequence
getNumBottomSegments() const hal::HDF5Sequence [virtual]
getNumTopSegments() const hal::HDF5Sequence [virtual]
getSequenceLength() const hal::HDF5Sequence [virtual]
getStartPosition() const hal::HDF5Sequence [virtual]
getString(std::string &outString) const hal::HDF5Sequence [virtual]
getSubString(std::string &outString, hal_size_t start, hal_size_t length) const hal::HDF5Sequence [virtual]
getTopSegmentIterator(hal_index_t position)hal::HDF5Sequence [virtual]
getTopSegmentIterator(hal_index_t position) const hal::HDF5Sequence [virtual]
HDF5Sequence(HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index)hal::HDF5Sequence
HDF5SequenceIterator (defined in hal::HDF5Sequence)hal::HDF5Sequence [friend]
lengthOffset (defined in hal::HDF5Sequence)hal::HDF5Sequence [protected, static]
nameOffset (defined in hal::HDF5Sequence)hal::HDF5Sequence [protected, static]
numBottomSegmentsOffset (defined in hal::HDF5Sequence)hal::HDF5Sequence [protected, static]
numTopSegmentsOffset (defined in hal::HDF5Sequence)hal::HDF5Sequence [protected, static]
set(hal_size_t startPosition, const Sequence::Info &sequenceInfo) (defined in hal::HDF5Sequence)hal::HDF5Sequence
setString(const std::string &inString)hal::HDF5Sequence [virtual]
setSubString(const std::string &intString, hal_size_t start, hal_size_t length)hal::HDF5Sequence [virtual]
startOffset (defined in hal::HDF5Sequence)hal::HDF5Sequence [protected, static]
~HDF5Sequence()hal::HDF5Sequence
~SegmentedSequence()=0hal::SegmentedSequence [inline, protected, pure virtual]
~Sequence()=0hal::Sequence [inline, protected, pure virtual]
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