halapi
hierarchichalalignmentformatapi
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Public Member Functions | |
HDF5Sequence (HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index) | |
~HDF5Sequence () | |
std::string | getName () const |
const Genome * | getGenome () const |
Genome * | getGenome () |
hal_size_t | getStartPosition () const |
hal_index_t | getArrayIndex () const |
hal_size_t | getSequenceLength () const |
hal_size_t | getNumTopSegments () const |
hal_size_t | getNumBottomSegments () const |
TopSegmentIteratorPtr | getTopSegmentIterator (hal_index_t position) |
TopSegmentIteratorConstPtr | getTopSegmentIterator (hal_index_t position) const |
BottomSegmentIteratorPtr | getBottomSegmentIterator (hal_index_t position) |
BottomSegmentIteratorConstPtr | getBottomSegmentIterator (hal_index_t position) const |
void | getString (std::string &outString) const |
void | setString (const std::string &inString) |
void | getSubString (std::string &outString, hal_size_t start, hal_size_t length) const |
void | setSubString (const std::string &intString, hal_size_t start, hal_size_t length) |
void | set (hal_size_t startPosition, const Sequence::Info &sequenceInfo) |
Static Public Member Functions | |
static H5::CompType | dataType (hal_size_t maxNameLength) |
Protected Attributes | |
HDF5ExternalArray * | _array |
hal_index_t | _index |
HDF5Genome * | _genome |
Static Protected Attributes | |
static const size_t | startOffset = 0 |
static const size_t | lengthOffset = sizeof(hal_size_t) |
static const size_t | numTopSegmentsOffset = lengthOffset + sizeof(hal_size_t) |
static const size_t | numBottomSegmentsOffset = numTopSegmentsOffset + sizeof(hal_size_t) |
static const size_t | nameOffset = numBottomSegmentsOffset + sizeof(hal_size_t) |
Friends | |
class | HDF5SequenceIterator |
HDF5Sequence::HDF5Sequence | ( | 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 |
HDF5Sequence::~HDF5Sequence | ( | ) |
Destructor
hal_index_t HDF5Sequence::getArrayIndex | ( | ) | const [virtual] |
Get the index of the sequence in the sequence array
Implements hal::Sequence.
BottomSegmentIteratorPtr HDF5Sequence::getBottomSegmentIterator | ( | hal_index_t | position | ) | [virtual] |
Get a bottom segment iterator
position | Index in segment array of returned iterator |
Implements hal::SegmentedSequence.
BottomSegmentIteratorConstPtr HDF5Sequence::getBottomSegmentIterator | ( | hal_index_t | position | ) | const [virtual] |
Get a const bottom segment iterator
position | Index in segment array of returned iterator |
Implements hal::SegmentedSequence.
const Genome * HDF5Sequence::getGenome | ( | ) | const [virtual] |
Get the containing (read-only) genome
Implements hal::Sequence.
Genome * HDF5Sequence::getGenome | ( | ) | [virtual] |
Get the containing genome
Implements hal::Sequence.
hal_size_t HDF5Sequence::getNumBottomSegments | ( | ) | const [virtual] |
Get the number of bottom segments (which form blocks with the children) in the sequence
Implements hal::SegmentedSequence.
hal_size_t HDF5Sequence::getNumTopSegments | ( | ) | const [virtual] |
Get the number of top segements (which form blocks with ancestor and siblings) in the sequence
Implements hal::SegmentedSequence.
hal_size_t HDF5Sequence::getSequenceLength | ( | ) | const [virtual] |
Get the total length of the DNA sequence in the sequence
Implements hal::SegmentedSequence.
hal_size_t HDF5Sequence::getStartPosition | ( | ) | const [virtual] |
Get the sequence's start position in the genome
Implements hal::Sequence.
void HDF5Sequence::getString | ( | std::string & | outString | ) | const [virtual] |
Get the character string underlying the segmented sequence
outString | String object into which we copy the result |
Implements hal::SegmentedSequence.
void HDF5Sequence::getSubString | ( | std::string & | outString, |
hal_size_t | start, | ||
hal_size_t | length | ||
) | const [virtual] |
Get the substring of character string underlying the segmented sequence
outString | String object into which we copy the result |
start | First position of substring |
length | Length of substring |
Implements hal::SegmentedSequence.
TopSegmentIteratorPtr HDF5Sequence::getTopSegmentIterator | ( | hal_index_t | position | ) | [virtual] |
Get a top segment iterator
position | Index in segment array of returned iterator |
Implements hal::SegmentedSequence.
TopSegmentIteratorConstPtr HDF5Sequence::getTopSegmentIterator | ( | hal_index_t | position | ) | const [virtual] |
Get a const top segment iterator
position | Index in segment array of returned iterator |
Implements hal::SegmentedSequence.
void HDF5Sequence::setString | ( | const std::string & | inString | ) | [virtual] |
Set the character string underlying the segmented sequence
inString | input string to copy |
Implements hal::SegmentedSequence.
void HDF5Sequence::setSubString | ( | const std::string & | inString, |
hal_size_t | start, | ||
hal_size_t | length | ||
) | [virtual] |
Set the character string underlying the segmented sequence
inString | input string to copy |
start | First position of substring |
length | Length of substring |
Implements hal::SegmentedSequence.