bpp-phyl
2.2.0
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General interface for storing reward mapping data. More...
#include <Bpp/Phyl/Mapping/RewardMapping.h>
Public Member Functions | |
RewardMapping () | |
virtual | ~RewardMapping () |
RewardMapping * | clone () const =0 |
virtual double & | operator() (size_t nodeIndex, size_t siteIndex)=0 |
virtual const double & | operator() (size_t nodeIndex, size_t siteIndex) const =0 |
virtual const Tree & | getTree () const =0 |
virtual bool | isEmpty () const =0 |
virtual size_t | getNumberOfSites () const =0 |
virtual size_t | getNumberOfBranches () const =0 |
virtual int | getSitePosition (size_t index) const =0 |
virtual std::vector< double > | getBranchLengths () const =0 |
virtual size_t | getNodeIndex (int nodeId) const =0 throw (NodeNotFoundException) |
virtual void | setSitePosition (size_t index, int position)=0 |
Set the position of a given site. More... | |
General interface for storing reward mapping data.
Since only probabilistic reward mapping is implemented for now, the basal interface only contains a few methods. More methods are expected to be added later.
Definition at line 62 of file RewardMapping.h.
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inline |
Definition at line 67 of file RewardMapping.h.
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inlinevirtual |
Definition at line 68 of file RewardMapping.h.
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pure virtual |
Implements bpp::Mapping.
Implemented in bpp::ProbabilisticRewardMapping, and bpp::AbstractRewardMapping.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
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pure virtualinherited |
nodeId | An id of the node to look for in the map. |
Implemented in bpp::AbstractMapping.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
Referenced by bpp::SubstitutionMappingTools::computeNormForSite(), bpp::RewardMappingTools::computeSumForSite(), bpp::SubstitutionMappingTools::computeSumForSite(), and bpp::SubstitutionMappingTools::computeTotalSubstitutionVectorForSite().
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
Referenced by bpp::RewardMappingTools::computeSumForBranch(), and bpp::SubstitutionMappingTools::computeSumForBranch().
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pure virtualinherited |
index | The site index. |
Implemented in bpp::AbstractMapping.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
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pure virtual |
Implemented in bpp::ProbabilisticRewardMapping.
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pure virtual |
Implemented in bpp::ProbabilisticRewardMapping.
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pure virtualinherited |
Set the position of a given site.
index | The site index. |
position | The position of the site. |
Implemented in bpp::AbstractMapping.