halapi
hierarchichalalignmentformatapi
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Public Member Functions | |
HDF5BottomSegment (HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index) | |
~HDF5BottomSegment () | |
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_size_t | getNumChildren () const |
hal_index_t | getChildIndex (hal_size_t i) const |
void | setChildIndex (hal_size_t i, hal_index_t childIndex) |
hal_bool_t | getChildReversed (hal_size_t i) const |
void | setChildReversed (hal_size_t child, hal_bool_t isReversed) |
hal_index_t | getTopParseIndex () const |
void | setTopParseIndex (hal_index_t parseIndex) |
hal_offset_t | getTopParseOffset () const |
void | setTopParseOffset (hal_offset_t parseOffset) |
hal_index_t | getArrayIndex () const |
Static Public Member Functions | |
static H5::CompType | dataType (hal_size_t numChildren) |
static hal_size_t | numChildrenFromDataType (const H5::DataType &dataType) |
Static Protected Member Functions | |
static const size_t | totalSize (hal_size_t numChildren) |
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 | topIndexOffset = lengthOffset + sizeof(hal_size_t) |
static const size_t | topOffsetOffset = topIndexOffset + sizeof(hal_index_t) |
static const size_t | parIndexOffset = topOffsetOffset + sizeof(hal_offset_t) |
static const size_t | firstChildOffset = parIndexOffset + sizeof(hal_index_t) |
Friends | |
class | HDF5TopSegmentIterator |
class | HDF5BottomSegmentIterator |
HDF5BottomSegment::HDF5BottomSegment | ( | 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 |
HDF5BottomSegment::~HDF5BottomSegment | ( | ) |
Destructor
hal_index_t hal::HDF5BottomSegment::getArrayIndex | ( | ) | const [inline, virtual] |
Get the index of the segment in the segment array
Implements hal::Segment.
hal_index_t hal::HDF5BottomSegment::getChildIndex | ( | hal_size_t | i | ) | const [inline, virtual] |
Get the index of a child segment (OR NULL_INDEX if none)
i | index of child to query |
Implements hal::BottomSegment.
hal_bool_t hal::HDF5BottomSegment::getChildReversed | ( | hal_size_t | i | ) | const [inline, virtual] |
Get whether descent segment for ith child is mapped to the reverse complement of this segment
i | index of child to query |
Implements hal::BottomSegment.
const Genome * hal::HDF5BottomSegment::getGenome | ( | ) | const [inline, virtual] |
Get the containing (read-only) genome
Implements hal::Segment.
Genome * hal::HDF5BottomSegment::getGenome | ( | ) | [inline, virtual] |
Get the containing genome
Implements hal::Segment.
hal_size_t hal::HDF5BottomSegment::getLength | ( | ) | const [inline, virtual] |
Get the length of the segment (number of bases)
Implements hal::Segment.
hal_index_t hal::HDF5BottomSegment::getNextParalogyIndex | ( | ) | const [inline, virtual] |
Get index of the next paralogous segment in the genome
Implements hal::Segment.
hal_size_t hal::HDF5BottomSegment::getNumChildren | ( | ) | const [inline, virtual] |
Get the number of child genomes (note this is a number of slots and that the current segment could actually have fewer children)
Implements hal::BottomSegment.
hal_index_t hal::HDF5BottomSegment::getStartPosition | ( | ) | const [inline, virtual] |
Get the segment's start position in the genome
Implements hal::Segment.
hal_index_t hal::HDF5BottomSegment::getTopParseIndex | ( | ) | const [inline, virtual] |
Get index of top segment in samge genome that contains this segment's start coordinate
Implements hal::BottomSegment.
hal_offset_t hal::HDF5BottomSegment::getTopParseOffset | ( | ) | const [inline, virtual] |
Get offset in associated top segment of start coordinate of this segment
Implements hal::BottomSegment.
void hal::HDF5BottomSegment::setChildIndex | ( | hal_size_t | i, |
hal_index_t | childIndex | ||
) | [inline, virtual] |
Set the index of a child segment (OR NULL_INDEX if none)
i | index of child to set |
childIndex | index of segment in child to set |
Implements hal::BottomSegment.
void hal::HDF5BottomSegment::setChildReversed | ( | hal_size_t | child, |
hal_bool_t | isReversed | ||
) | [inline, virtual] |
Set whether descent segment for ith child is mapped to the reverse complement of this segment
i | index of child to set |
isReverse | flag |
Implements hal::BottomSegment.
void hal::HDF5BottomSegment::setLength | ( | hal_size_t | length | ) | [inline, virtual] |
void hal::HDF5BottomSegment::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::HDF5BottomSegment::setStartPosition | ( | hal_index_t | startPos | ) | [inline, virtual] |
Set the segment's start position in the genome
startPos | Start position |
Implements hal::Segment.
void hal::HDF5BottomSegment::setTopParseIndex | ( | hal_index_t | parseIndex | ) | [inline, virtual] |
Set index of top segment in samge genome that contains this segment's start coordinate
parParseIndex | index |
Implements hal::BottomSegment.
void hal::HDF5BottomSegment::setTopParseOffset | ( | hal_offset_t | parseOffset | ) | [inline, virtual] |
Set offset in associated top segment of start coordinate of this segment
parpArseOffset | offset in parent |
Implements hal::BottomSegment.