halapi
hierarchichalalignmentformatapi
Public Member Functions | Protected Attributes
hal::HDF5DNAIterator Class Reference
Inheritance diagram for hal::HDF5DNAIterator:
hal::DNAIterator

List of all members.

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 GenomegetGenome () const
GenomegetGenome ()
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

Member Function Documentation

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)

Parameters:
indexposition 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

Parameters:
cDNA 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.


The documentation for this class was generated from the following files:
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