halapi
hierarchichalalignmentformatapi
|
_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()=0 | hal::SegmentedSequence | [inline, protected, pure virtual] |
~Sequence()=0 | hal::Sequence | [inline, protected, pure virtual] |