halapi
hierarchichalalignmentformatapi
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Public Member Functions | |
HDF5TopSegment (HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index) | |
~HDF5TopSegment () | |
hal_size_t | getLength () const |
void | setLength (hal_size_t length) |
const Genome * | getGenome () const |
Genome * | getGenome () |
hal_index_t | getStartPosition () const |
void | setStartPosition (hal_index_t startPos) |
hal_index_t | getNextParalogyIndex () const |
void | setNextParalogyIndex (hal_index_t parIdx) |
hal_index_t | getParentIndex () const |
void | setParentIndex (hal_index_t parIdx) |
hal_bool_t | getParentReversed () const |
void | setParentReversed (hal_bool_t isReversed) |
hal_index_t | getBottomParseIndex () const |
void | setBottomParseIndex (hal_index_t botParseIdx) |
hal_offset_t | getBottomParseOffset () const |
void | setBottomParseOffset (hal_offset_t botParseOffset) |
hal_index_t | getArrayIndex () const |
Static Public Member Functions | |
static H5::CompType | dataType () |
Protected Attributes | |
HDF5ExternalArray * | _array |
hal_index_t | _index |
HDF5Genome * | _genome |
Static Protected Attributes | |
static const size_t | genomeIndexOffset = 0 |
static const size_t | lengthOffset = sizeof(hal_index_t) |
static const size_t | bottomIndexOffset = lengthOffset + sizeof(hal_size_t) |
static const size_t | bottomOffsetOffset = bottomIndexOffset + sizeof(hal_index_t) |
static const size_t | parIndexOffset = bottomOffsetOffset + sizeof(hal_offset_t) |
static const size_t | parentIndexOffset = parIndexOffset + sizeof(hal_index_t) |
static const size_t | parentReversedOffset = parentIndexOffset + sizeof(hal_index_t) |
static const size_t | totalSize = parentReversedOffset + sizeof(hal_bool_t) |
Friends | |
class | HDF5TopSegmentIterator |
class | HDF5BottomSegmentIterator |
HDF5TopSegment::HDF5TopSegment | ( | HDF5Genome * | genome, |
HDF5ExternalArray * | array, | ||
hal_index_t | index | ||
) |
Constructor
genome | Smart pointer to genome to which segment belongs |
array | HDF5 array containg segment |
index | Index of segment in the array |
HDF5TopSegment::~HDF5TopSegment | ( | ) |
Destructor
hal_index_t hal::HDF5TopSegment::getArrayIndex | ( | ) | const [inline, virtual] |
Get the index of the segment in the segment array
Implements hal::Segment.
hal_index_t hal::HDF5TopSegment::getBottomParseIndex | ( | ) | const [inline, virtual] |
Get the index of the bottom segment in genome that contains the start coordinate of this top segment
Implements hal::TopSegment.
hal_offset_t hal::HDF5TopSegment::getBottomParseOffset | ( | ) | const [inline, virtual] |
Get the offset in the bottom parse segment that aligns with the start coordinate of this segment
Implements hal::TopSegment.
const Genome * hal::HDF5TopSegment::getGenome | ( | ) | const [inline, virtual] |
Get the containing (read-only) genome
Implements hal::Segment.
Genome * hal::HDF5TopSegment::getGenome | ( | ) | [inline, virtual] |
Get the containing genome
Implements hal::Segment.
hal_size_t hal::HDF5TopSegment::getLength | ( | ) | const [inline, virtual] |
Get the length of the segment (number of bases)
Implements hal::Segment.
hal_index_t hal::HDF5TopSegment::getNextParalogyIndex | ( | ) | const [inline, virtual] |
Get index of the next paralogous segment in the genome
Implements hal::Segment.
hal_index_t hal::HDF5TopSegment::getParentIndex | ( | ) | const [inline, virtual] |
Get index of the homologous segmenet in the ancestral genome
Implements hal::TopSegment.
hal_bool_t hal::HDF5TopSegment::getParentReversed | ( | ) | const [inline, virtual] |
Check whether segment is mapped to parent's reverse complement
Implements hal::TopSegment.
hal_index_t hal::HDF5TopSegment::getStartPosition | ( | ) | const [inline, virtual] |
Get the segment's start position in the genome
Implements hal::Segment.
void hal::HDF5TopSegment::setBottomParseIndex | ( | hal_index_t | botParseIdx | ) | [inline, virtual] |
Set the index of the bototm segment in the genome that contains the start coordinate of this top segment
botParseIndx | index to set |
Implements hal::TopSegment.
void hal::HDF5TopSegment::setBottomParseOffset | ( | hal_offset_t | botParseOffset | ) | [inline, virtual] |
Set the offset in the bottom parse segment that aligns with the start coordinate of this segment
botParseOffset | offset |
Implements hal::TopSegment.
void hal::HDF5TopSegment::setLength | ( | hal_size_t | length | ) | [inline, virtual] |
void hal::HDF5TopSegment::setNextParalogyIndex | ( | hal_index_t | parIdx | ) | [inline, virtual] |
Set index of the next paralogous segment in the genome
parIdx | of next segment in same genome that is homologous to this segment |
Implements hal::Segment.
void hal::HDF5TopSegment::setParentIndex | ( | hal_index_t | parIdx | ) | [inline, virtual] |
Set the index of the homologous segment in the ancestra genome
parIdx | parent index to set |
Implements hal::TopSegment.
void hal::HDF5TopSegment::setParentReversed | ( | hal_bool_t | isReversed | ) | [inline, virtual] |
Set whether segment is mapped to parent's reverse complement
isReversed | Flag |
Implements hal::TopSegment.
void hal::HDF5TopSegment::setStartPosition | ( | hal_index_t | startPos | ) | [inline, virtual] |
Set the segment's start position in the genome
startPos | Start position |
Implements hal::Segment.