halapi
hierarchichalalignmentformatapi
 All Classes Namespaces Functions Pages
Classes | Public Member Functions | Protected Member Functions | List of all members
hal::Sequence Class Referenceabstract

#include <halSequence.h>

Inheritance diagram for hal::Sequence:
hal::SegmentedSequence

Classes

struct  Info
 
struct  UpdateInfo
 

Public Member Functions

virtual std::string getName () const =0
 
virtual std::string getFullName () const =0
 
virtual const GenomegetGenome () const =0
 
virtual GenomegetGenome ()=0
 
virtual hal_index_t getStartPosition () const =0
 
virtual hal_index_t getEndPosition () const =0
 
virtual hal_index_t getArrayIndex () const =0
 
virtual hal_index_t getTopSegmentArrayIndex () const =0
 
virtual hal_index_t getBottomSegmentArrayIndex () const =0
 
- Public Member Functions inherited from hal::SegmentedSequence
virtual hal_size_t getSequenceLength () const =0
 
virtual hal_size_t getNumTopSegments () const =0
 
virtual hal_size_t getNumBottomSegments () const =0
 
virtual TopSegmentIteratorPtr getTopSegmentIterator (hal_index_t position=0)=0
 
virtual TopSegmentIteratorConstPtr getTopSegmentIterator (hal_index_t position=0) const =0
 
virtual TopSegmentIteratorConstPtr getTopSegmentEndIterator () const =0
 
virtual BottomSegmentIteratorPtr getBottomSegmentIterator (hal_index_t position=0)=0
 
virtual
BottomSegmentIteratorConstPtr 
getBottomSegmentIterator (hal_index_t position=0) const =0
 
virtual
BottomSegmentIteratorConstPtr 
getBottomSegmentEndIterator () const =0
 
virtual DNAIteratorPtr getDNAIterator (hal_index_t position=0)=0
 
virtual DNAIteratorConstPtr getDNAIterator (hal_index_t position=0) const =0
 
virtual DNAIteratorConstPtr getDNAEndIterator () const =0
 
virtual ColumnIteratorConstPtr getColumnIterator (const std::set< const Genome * > *targets=NULL, hal_size_t maxInsertLength=0, hal_index_t position=0, hal_index_t lastPosition=NULL_INDEX, bool noDupes=false, bool noAncestors=false, bool reverseStrand=false) const =0
 
virtual void getString (std::string &outString) const =0
 
virtual void setString (const std::string &inString)=0
 
virtual void getSubString (std::string &outString, hal_size_t start, hal_size_t length) const =0
 
virtual void setSubString (const std::string &inString, hal_size_t start, hal_size_t length)=0
 
virtual RearrangementPtr getRearrangement (hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold, bool atomic=false) const =0
 
virtual
GappedTopSegmentIteratorConstPtr 
getGappedTopSegmentIterator (hal_index_t i, hal_size_t gapThreshold, bool atomic=false) const =0
 
virtual
GappedBottomSegmentIteratorConstPtr 
getGappedBottomSegmentIterator (hal_index_t i, hal_size_t childIdx, hal_size_t gapThreshold, bool atomic=false) const =0
 

Protected Member Functions

virtual ~Sequence ()=0
 
- Protected Member Functions inherited from hal::SegmentedSequence
virtual ~SegmentedSequence ()=0
 

Detailed Description

Interface for a sequence of DNA. Note that sequences should not be written to outside of creating new genomes.

Constructor & Destructor Documentation

hal::Sequence::~Sequence ( )
inlineprotectedpure virtual

Destructor

Member Function Documentation

virtual hal_index_t hal::Sequence::getArrayIndex ( ) const
pure virtual

Get the index of the sequence in the sequence array

virtual hal_index_t hal::Sequence::getBottomSegmentArrayIndex ( ) const
pure virtual

Get the index of the sequence in the genome's bottom segment array

virtual hal_index_t hal::Sequence::getEndPosition ( ) const
pure virtual

Get the sequence's end position (start + len - 1) in the genome

virtual std::string hal::Sequence::getFullName ( ) const
pure virtual

Return the sequence's name in genomeName.sequenceName format (which is how it will appear in a MAF)

virtual const Genome* hal::Sequence::getGenome ( ) const
pure virtual

Get the containing (read-only) genome

virtual Genome* hal::Sequence::getGenome ( )
pure virtual

Get the containing genome

virtual std::string hal::Sequence::getName ( ) const
pure virtual

Return the sequence's name

virtual hal_index_t hal::Sequence::getStartPosition ( ) const
pure virtual

Get the sequence's start position in the genome

virtual hal_index_t hal::Sequence::getTopSegmentArrayIndex ( ) const
pure virtual

Get the index of the sequence in the genome's top segment array


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