halapi
hierarchichalalignmentformatapi
Public Member Functions | Static Public Member Functions | Static Protected Member Functions | Protected Attributes | Static Protected Attributes | Friends
hal::HDF5BottomSegment Class Reference
Inheritance diagram for hal::HDF5BottomSegment:
hal::BottomSegment hal::Segment

List of all members.

Public Member Functions

 HDF5BottomSegment (HDF5Genome *genome, HDF5ExternalArray *array, hal_index_t index)
 ~HDF5BottomSegment ()
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_size_t getNumChildren () const
hal_index_t getChildIndex (hal_size_t i) const
void setChildIndex (hal_size_t i, hal_index_t childIndex)
hal_bool_t getChildReversed (hal_size_t i) const
void setChildReversed (hal_size_t child, hal_bool_t isReversed)
hal_index_t getTopParseIndex () const
void setTopParseIndex (hal_index_t parseIndex)
hal_offset_t getTopParseOffset () const
void setTopParseOffset (hal_offset_t parseOffset)
hal_index_t getArrayIndex () const

Static Public Member Functions

static H5::CompType dataType (hal_size_t numChildren)
static hal_size_t numChildrenFromDataType (const H5::DataType &dataType)

Static Protected Member Functions

static const size_t totalSize (hal_size_t numChildren)

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 topIndexOffset = lengthOffset + sizeof(hal_size_t)
static const size_t topOffsetOffset = topIndexOffset + sizeof(hal_index_t)
static const size_t parIndexOffset = topOffsetOffset + sizeof(hal_offset_t)
static const size_t firstChildOffset = parIndexOffset + sizeof(hal_index_t)

Friends

class HDF5TopSegmentIterator
class HDF5BottomSegmentIterator

Constructor & Destructor Documentation

HDF5BottomSegment::HDF5BottomSegment ( 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
HDF5BottomSegment::~HDF5BottomSegment ( )

Destructor


Member Function Documentation

hal_index_t hal::HDF5BottomSegment::getArrayIndex ( ) const [inline, virtual]

Get the index of the segment in the segment array

Implements hal::Segment.

hal_index_t hal::HDF5BottomSegment::getChildIndex ( hal_size_t  i) const [inline, virtual]

Get the index of a child segment (OR NULL_INDEX if none)

Parameters:
iindex of child to query

Implements hal::BottomSegment.

hal_bool_t hal::HDF5BottomSegment::getChildReversed ( hal_size_t  i) const [inline, virtual]

Get whether descent segment for ith child is mapped to the reverse complement of this segment

Parameters:
iindex of child to query

Implements hal::BottomSegment.

const Genome * hal::HDF5BottomSegment::getGenome ( ) const [inline, virtual]

Get the containing (read-only) genome

Implements hal::Segment.

Genome * hal::HDF5BottomSegment::getGenome ( ) [inline, virtual]

Get the containing genome

Implements hal::Segment.

hal_size_t hal::HDF5BottomSegment::getLength ( ) const [inline, virtual]

Get the length of the segment (number of bases)

Implements hal::Segment.

hal_index_t hal::HDF5BottomSegment::getNextParalogyIndex ( ) const [inline, virtual]

Get index of the next paralogous segment in the genome

Implements hal::Segment.

hal_size_t hal::HDF5BottomSegment::getNumChildren ( ) const [inline, virtual]

Get the number of child genomes (note this is a number of slots and that the current segment could actually have fewer children)

Implements hal::BottomSegment.

hal_index_t hal::HDF5BottomSegment::getStartPosition ( ) const [inline, virtual]

Get the segment's start position in the genome

Implements hal::Segment.

hal_index_t hal::HDF5BottomSegment::getTopParseIndex ( ) const [inline, virtual]

Get index of top segment in samge genome that contains this segment's start coordinate

Implements hal::BottomSegment.

hal_offset_t hal::HDF5BottomSegment::getTopParseOffset ( ) const [inline, virtual]

Get offset in associated top segment of start coordinate of this segment

Implements hal::BottomSegment.

void hal::HDF5BottomSegment::setChildIndex ( hal_size_t  i,
hal_index_t  childIndex 
) [inline, virtual]

Set the index of a child segment (OR NULL_INDEX if none)

Parameters:
iindex of child to set
childIndexindex of segment in child to set

Implements hal::BottomSegment.

void hal::HDF5BottomSegment::setChildReversed ( hal_size_t  child,
hal_bool_t  isReversed 
) [inline, virtual]

Set whether descent segment for ith child is mapped to the reverse complement of this segment

Parameters:
iindex of child to set
isReverseflag

Implements hal::BottomSegment.

void hal::HDF5BottomSegment::setLength ( hal_size_t  length) [inline, virtual]

Set the length of the segment

Parameters:
lengthNew length of segment

Implements hal::Segment.

void hal::HDF5BottomSegment::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::HDF5BottomSegment::setStartPosition ( hal_index_t  startPos) [inline, virtual]

Set the segment's start position in the genome

Parameters:
startPosStart position

Implements hal::Segment.

void hal::HDF5BottomSegment::setTopParseIndex ( hal_index_t  parseIndex) [inline, virtual]

Set index of top segment in samge genome that contains this segment's start coordinate

Parameters:
parParseIndexindex

Implements hal::BottomSegment.

void hal::HDF5BottomSegment::setTopParseOffset ( hal_offset_t  parseOffset) [inline, virtual]

Set offset in associated top segment of start coordinate of this segment

Parameters:
parpArseOffsetoffset in parent

Implements hal::BottomSegment.


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