halapi
hierarchichalalignmentformatapi
Public Member Functions | Protected Attributes
hal::Hdf5DnaArray Class Reference

#include <hdf5DnaArray.h>

List of all members.

Public Member Functions

 Hdf5DnaArray ()
virtual ~Hdf5DnaArray ()
void create (H5File *file, const std::string &path, hsize_t size, const H5::DSetCreatPropList &cparms=H5::DSetCreatPropList::DEFAULT)
void open (H5File *file, const std::string &path)
void write ()
Hdf5DnaIterator getDnaIterator (hsize_t offset=0)
Hdf5DnaConstIterator getDnaConstIterator (hsize_t offset=0)
hsize_t size ()

Protected Attributes

RawH5ExternalArray _array

Detailed Description

Wraps the RawH5ExternalArray with interface tailored to storing and accessing only DNA characters


Constructor & Destructor Documentation

hal::Hdf5DnaArray::Hdf5DnaArray ( )

Constructor

virtual hal::Hdf5DnaArray::~Hdf5DnaArray ( ) [virtual]

Destructor


Member Function Documentation

void hal::Hdf5DnaArray::create ( H5File *  file,
const std::string &  path,
hsize_t  size,
const H5::DSetCreatPropList &  cparms = H5::DSetCreatPropList::DEFAULT 
)

Create a new array (overloads method in parent)

Parameters:
fileHDF5 file in which to add new array dataset
pathlocation of new array in file
sizeFixed length of the new array
cparamsCreation parameters for new array (chunking, zipping)
Hdf5DnaConstIterator hal::Hdf5DnaArray::getDnaConstIterator ( hsize_t  offset = 0)

Get read-only iterator

Parameters:
offsetposition of iterator in array
hal::Hdf5DnaArray::getDnaIterator ( hsize_t  offset = 0) [inline]

Get read/write iterator

Parameters:
offsetposition of iterator in array
void hal::Hdf5DnaArray::open ( H5File *  file,
const std::string &  path 
)

Open an existing array

Parameters:
fileHDF5 file containing array to open
pathlocation of array in file
hsize_t hal::Hdf5DnaArray::size ( )

Get size of array

void hal::Hdf5DnaArray::write ( )

Write any unsaved buffer contents back to the file


The documentation for this class was generated from the following file:
 All Classes Namespaces Functions Variables Friends