halapi
hierarchichalalignmentformatapi
|
Public Member Functions | |
HDF5DNAIterator (HDF5Genome *genome, hal_index_t index) | |
hal_dna_t | getChar () const |
hal_dna_t | getCompChar () const |
void | setChar (hal_dna_t c) |
void | toLeft () const |
void | toRight () const |
void | jumpTo (hal_size_t index) const |
const Genome * | getGenome () const |
Genome * | getGenome () |
hal_index_t | getArrayIndex () const |
void | readString (std::string &outString, hal_size_t length, hal_bool_t reversed=false) const |
void | writeString (const std::string &inString, hal_size_t length, hal_bool_t reversed=false) |
bool | inRange () const |
Protected Attributes | |
hal_index_t | _index |
HDF5Genome * | _genome |
hal_index_t hal::HDF5DNAIterator::getArrayIndex | ( | ) | const [inline, virtual] |
Get the index of the segment in the segment array
Implements hal::DNAIterator.
hal_dna_t hal::HDF5DNAIterator::getChar | ( | ) | const [inline, virtual] |
Get the DNA character at this position
Implements hal::DNAIterator.
hal_dna_t hal::HDF5DNAIterator::getCompChar | ( | ) | const [inline, virtual] |
Get the reverse Complemenet of the DNA character at this position
Implements hal::DNAIterator.
const Genome * hal::HDF5DNAIterator::getGenome | ( | ) | const [inline, virtual] |
Get the containing (read-only) genome
Implements hal::DNAIterator.
Genome * hal::HDF5DNAIterator::getGenome | ( | ) | [inline, virtual] |
Get the containing genome
Implements hal::DNAIterator.
void hal::HDF5DNAIterator::jumpTo | ( | hal_size_t | index | ) | const [inline, virtual] |
Jump to any point on the genome (can lead to inefficient paging from disk if used irresponsibly)
index | position in array to jump to |
Implements hal::DNAIterator.
void hal::HDF5DNAIterator::setChar | ( | hal_dna_t | c | ) | [inline, virtual] |
Set the DNA character at this position
c | DNA character to set |
Implements hal::DNAIterator.
void hal::HDF5DNAIterator::toLeft | ( | ) | const [inline, virtual] |
Move to previous position
Implements hal::DNAIterator.
void hal::HDF5DNAIterator::toRight | ( | ) | const [inline, virtual] |
Move to next position
Implements hal::DNAIterator.