13 #include "halSegmentedSequence.h"
14 #include "halSequence.h"
28 virtual const std::string&
getName()
const = 0;
42 const std::vector<hal::Sequence::Info>& sequenceDimensions,
43 bool storeDNAArrays =
true) = 0;
51 const std::vector<hal::Sequence::UpdateInfo>& sequenceDimensions) = 0;
59 const std::vector<hal::Sequence::UpdateInfo>& sequenceDimensions) = 0;
79 hal_index_t position = 0) = 0;
84 hal_index_t position = 0)
const = 0;
virtual hal_index_t getChildIndex(const Genome *child) const =0
Definition: halGenome.h:24
virtual void updateBottomDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0
virtual hal_size_t getNumSequences() const =0
virtual Sequence * getSequenceBySite(hal_size_t position)=0
virtual SequenceIteratorPtr getSequenceIterator(hal_index_t position=0)=0
virtual bool containsDNAArray() const =0
virtual Genome * getParent()=0
Definition: halSegmentedSequence.h:23
virtual const std::string & getName() const =0
virtual ~Genome()=0
Definition: halGenome.h:132
virtual SequenceIteratorConstPtr getSequenceEndIterator() const =0
virtual void updateTopDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0
virtual const Alignment * getAlignment() const =0
virtual Sequence * getSequence(const std::string &name)=0
virtual MetaData * getMetaData()=0
virtual hal_size_t getNumChildren() const =0
virtual void setDimensions(const std::vector< hal::Sequence::Info > &sequenceDimensions, bool storeDNAArrays=true)=0
Definition: halSequence.h:20
Definition: halAlignment.h:21
virtual Genome * getChild(hal_size_t childIdx)=0