halapi
hierarchichalalignmentformatapi
Public Member Functions | Static Public Member Functions | Protected Attributes | Static Protected Attributes | Friends
hal::HDF5TopSegment Class Reference
Inheritance diagram for hal::HDF5TopSegment:
hal::TopSegment hal::Segment

List of all members.

Public Member Functions

 HDF5TopSegment (HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index)
 ~HDF5TopSegment ()
hal_size_t getLength () const
void setLength (hal_size_t length)
const GenomegetGenome () const
GenomegetGenome ()
hal_index_t getStartPosition () const
void setStartPosition (hal_index_t startPos)
hal_index_t getNextParalogyIndex () const
void setNextParalogyIndex (hal_index_t parIdx)
hal_index_t getParentIndex () const
void setParentIndex (hal_index_t parIdx)
hal_bool_t getParentReversed () const
void setParentReversed (hal_bool_t isReversed)
hal_index_t getBottomParseIndex () const
void setBottomParseIndex (hal_index_t botParseIdx)
hal_offset_t getBottomParseOffset () const
void setBottomParseOffset (hal_offset_t botParseOffset)
hal_index_t getArrayIndex () const

Static Public Member Functions

static H5::CompType dataType ()

Protected Attributes

HDF5ExternalArray_array
hal_index_t _index
HDF5Genome_genome

Static Protected Attributes

static const size_t genomeIndexOffset = 0
static const size_t lengthOffset = sizeof(hal_index_t)
static const size_t bottomIndexOffset = lengthOffset + sizeof(hal_size_t)
static const size_t bottomOffsetOffset = bottomIndexOffset + sizeof(hal_index_t)
static const size_t parIndexOffset = bottomOffsetOffset + sizeof(hal_offset_t)
static const size_t parentIndexOffset = parIndexOffset + sizeof(hal_index_t)
static const size_t parentReversedOffset = parentIndexOffset + sizeof(hal_index_t)
static const size_t totalSize = parentReversedOffset + sizeof(hal_bool_t)

Friends

class HDF5TopSegmentIterator
class HDF5BottomSegmentIterator

Constructor & Destructor Documentation

HDF5TopSegment::HDF5TopSegment ( 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
HDF5TopSegment::~HDF5TopSegment ( )

Destructor


Member Function Documentation

hal_index_t hal::HDF5TopSegment::getArrayIndex ( ) const [inline, virtual]

Get the index of the segment in the segment array

Implements hal::Segment.

hal_index_t hal::HDF5TopSegment::getBottomParseIndex ( ) const [inline, virtual]

Get the index of the bottom segment in genome that contains the start coordinate of this top segment

Implements hal::TopSegment.

hal_offset_t hal::HDF5TopSegment::getBottomParseOffset ( ) const [inline, virtual]

Get the offset in the bottom parse segment that aligns with the start coordinate of this segment

Implements hal::TopSegment.

const Genome * hal::HDF5TopSegment::getGenome ( ) const [inline, virtual]

Get the containing (read-only) genome

Implements hal::Segment.

Genome * hal::HDF5TopSegment::getGenome ( ) [inline, virtual]

Get the containing genome

Implements hal::Segment.

hal_size_t hal::HDF5TopSegment::getLength ( ) const [inline, virtual]

Get the length of the segment (number of bases)

Implements hal::Segment.

hal_index_t hal::HDF5TopSegment::getNextParalogyIndex ( ) const [inline, virtual]

Get index of the next paralogous segment in the genome

Implements hal::Segment.

hal_index_t hal::HDF5TopSegment::getParentIndex ( ) const [inline, virtual]

Get index of the homologous segmenet in the ancestral genome

Implements hal::TopSegment.

hal_bool_t hal::HDF5TopSegment::getParentReversed ( ) const [inline, virtual]

Check whether segment is mapped to parent's reverse complement

Implements hal::TopSegment.

hal_index_t hal::HDF5TopSegment::getStartPosition ( ) const [inline, virtual]

Get the segment's start position in the genome

Implements hal::Segment.

void hal::HDF5TopSegment::setBottomParseIndex ( hal_index_t  botParseIdx) [inline, virtual]

Set the index of the bototm segment in the genome that contains the start coordinate of this top segment

Parameters:
botParseIndxindex to set

Implements hal::TopSegment.

void hal::HDF5TopSegment::setBottomParseOffset ( hal_offset_t  botParseOffset) [inline, virtual]

Set the offset in the bottom parse segment that aligns with the start coordinate of this segment

Parameters:
botParseOffsetoffset

Implements hal::TopSegment.

void hal::HDF5TopSegment::setLength ( hal_size_t  length) [inline, virtual]

Set the length of the segment

Parameters:
lengthNew length of segment

Implements hal::Segment.

void hal::HDF5TopSegment::setNextParalogyIndex ( hal_index_t  parIdx) [inline, virtual]

Set index of the next paralogous segment in the genome

Parameters:
parIdxof next segment in same genome that is homologous to this segment

Implements hal::Segment.

void hal::HDF5TopSegment::setParentIndex ( hal_index_t  parIdx) [inline, virtual]

Set the index of the homologous segment in the ancestra genome

Parameters:
parIdxparent index to set

Implements hal::TopSegment.

void hal::HDF5TopSegment::setParentReversed ( hal_bool_t  isReversed) [inline, virtual]

Set whether segment is mapped to parent's reverse complement

Parameters:
isReversedFlag

Implements hal::TopSegment.

void hal::HDF5TopSegment::setStartPosition ( hal_index_t  startPos) [inline, virtual]

Set the segment's start position in the genome

Parameters:
startPosStart position

Implements hal::Segment.


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