#include <halBottomSegment.h>
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class | counted_ptr< BottomSegment > |
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class | counted_ptr< const BottomSegment > |
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Interface for a bottom segment of DNA
virtual hal_index_t hal::BottomSegment::getChildIndex |
( |
hal_size_t |
i | ) |
const |
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pure virtual |
Get the index of a child segment (OR NULL_INDEX if none)
- Parameters
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virtual hal_index_t hal::BottomSegment::getChildIndexG |
( |
const Genome * |
childGenome | ) |
const |
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pure virtual |
Get the index of a child segment (OR NULL_INDEX if none)
- Parameters
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childGenome | genome of child to query |
virtual bool hal::BottomSegment::getChildReversed |
( |
hal_size_t |
i | ) |
const |
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pure virtual |
Get whether descent segment for ith child is mapped to the reverse complement of this segment
- Parameters
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virtual hal_index_t hal::BottomSegment::getLeftChildIndex |
( |
hal_size_t |
i | ) |
const |
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pure virtual |
Get the index of the child of the left neighbour of this segment in the genome (use isLeft first to check if the left neighbour is in the same sequence)
- Parameters
-
i | index of child genome to query |
virtual hal_size_t hal::BottomSegment::getNumChildren |
( |
| ) |
const |
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pure virtual |
Get the number of child genomes (note this is a number of slots and that the current segment could actually have fewer children)
virtual hal_index_t hal::BottomSegment::getRightChildIndex |
( |
hal_size_t |
i | ) |
const |
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pure virtual |
Get the right of the child of the left neighbour of this segment in the genome (use isRight first to check if the right neighbour is in the same sequence)
- Parameters
-
i | index of child genome to query |
virtual hal_index_t hal::BottomSegment::getTopParseIndex |
( |
| ) |
const |
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pure virtual |
Get index of top segment in samge genome that contains this segment's start coordinate
virtual hal_offset_t hal::BottomSegment::getTopParseOffset |
( |
| ) |
const |
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pure virtual |
Get offset in associated top segment of start coordinate of this segment
virtual bool hal::BottomSegment::hasChild |
( |
hal_size_t |
child | ) |
const |
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pure virtual |
Test if child segment exists
- Parameters
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child | index of child genome |
virtual bool hal::BottomSegment::hasChildG |
( |
const Genome * |
childGenome | ) |
const |
|
pure virtual |
Test if child segment exists
- Parameters
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virtual bool hal::BottomSegment::hasParseUp |
( |
| ) |
const |
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pure virtual |
Test if there is a top parse segment in the genome that contains the start positon of the current iterator (should be true if not in root
virtual void hal::BottomSegment::setChildIndex |
( |
hal_size_t |
i, |
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hal_index_t |
childIndex |
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) |
| |
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pure virtual |
Set the index of a child segment (OR NULL_INDEX if none)
- Parameters
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i | index of child to set |
childIndex | index of segment in child to set |
virtual void hal::BottomSegment::setChildReversed |
( |
hal_size_t |
child, |
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bool |
isReversed |
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) |
| |
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pure virtual |
Set whether descent segment for ith child is mapped to the reverse complement of this segment
- Parameters
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i | index of child to set |
isReverse | flag |
virtual void hal::BottomSegment::setTopParseIndex |
( |
hal_index_t |
parseIndex | ) |
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pure virtual |
Set index of top segment in samge genome that contains this segment's start coordinate
- Parameters
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The documentation for this class was generated from the following file: