halapi
hierarchichalalignmentformatapi
Public Member Functions | Static Public Member Functions | Protected Attributes | Static Protected Attributes | Friends
hal::HDF5Sequence Class Reference
Inheritance diagram for hal::HDF5Sequence:
hal::Sequence hal::SegmentedSequence

List of all members.

Public Member Functions

 HDF5Sequence (HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index)
 ~HDF5Sequence ()
std::string getName () const
const GenomegetGenome () const
GenomegetGenome ()
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

Constructor & Destructor Documentation

HDF5Sequence::HDF5Sequence ( HDF5Genome genome,
HDF5ExternalArray array,
hal_index_t  index 
)

Constructor

Parameters:
genomeSmart pointer to genome to which segment belongs
arrayHDF5 array containg segment
indexIndex of segment in the array
HDF5Sequence::~HDF5Sequence ( )

Destructor


Member Function Documentation

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

Parameters:
positionIndex in segment array of returned iterator

Implements hal::SegmentedSequence.

BottomSegmentIteratorConstPtr HDF5Sequence::getBottomSegmentIterator ( hal_index_t  position) const [virtual]

Get a const bottom segment iterator

Parameters:
positionIndex 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

Parameters:
outStringString 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

Parameters:
outStringString object into which we copy the result
startFirst position of substring
lengthLength of substring

Implements hal::SegmentedSequence.

TopSegmentIteratorPtr HDF5Sequence::getTopSegmentIterator ( hal_index_t  position) [virtual]

Get a top segment iterator

Parameters:
positionIndex in segment array of returned iterator

Implements hal::SegmentedSequence.

TopSegmentIteratorConstPtr HDF5Sequence::getTopSegmentIterator ( hal_index_t  position) const [virtual]

Get a const top segment iterator

Parameters:
positionIndex 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

Parameters:
inStringinput 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

Parameters:
inStringinput string to copy
startFirst position of substring
lengthLength of substring

Implements hal::SegmentedSequence.


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