bpp-phyl
2.2.0
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Partial implementation of the substitution mapping interface. More...
#include <Bpp/Phyl/Mapping/SubstitutionMapping.h>
Public Member Functions | |
AbstractSubstitutionMapping (const Tree &tree) | |
AbstractSubstitutionMapping (const AbstractSubstitutionMapping &absm) | |
AbstractSubstitutionMapping * | clone () const =0 |
AbstractSubstitutionMapping & | operator= (const AbstractSubstitutionMapping &absm) |
virtual | ~AbstractSubstitutionMapping () |
virtual size_t | getNumberOfSubstitutionTypes () const =0 |
virtual double & | operator() (size_t nodeIndex, size_t siteIndex, size_t type)=0 |
virtual const double & | operator() (size_t nodeIndex, size_t siteIndex, size_t type) 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... | |
bool | isEmpty () const |
const TreeTemplate< Node > & | getTree () const throw (Exception) |
void | setTree (const Tree &tree) |
int | getSitePosition (size_t index) const throw (Exception) |
void | setSitePosition (size_t index, int position) throw (Exception) |
Set the position of a given site. More... | |
size_t | getNumberOfSites () const |
size_t | getNumberOfBranches () const |
virtual const Node * | getNode (size_t nodeIndex) const |
virtual void | setNumberOfSites (size_t numberOfSites) |
virtual std::vector< double > | getBranchLengths () const |
virtual size_t | getNodeIndex (int nodeId) const throw (NodeNotFoundException) |
Partial implementation of the substitution mapping interface.
This implementation copies the input tree in a TreeTemplate<Node> object.
Definition at line 94 of file SubstitutionMapping.h.
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inline |
Definition at line 101 of file SubstitutionMapping.h.
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inline |
Definition at line 103 of file SubstitutionMapping.h.
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inlinevirtual |
Definition at line 116 of file SubstitutionMapping.h.
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pure virtual |
Implements bpp::AbstractMapping.
Implemented in bpp::ProbabilisticSubstitutionMapping.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
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inlinevirtualinherited |
Implements bpp::Mapping.
Definition at line 222 of file Mapping.h.
References bpp::AbstractMapping::nbBranches_, and bpp::AbstractMapping::nodes_.
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inlinevirtualinherited |
Definition at line 212 of file Mapping.h.
References bpp::AbstractMapping::nodes_.
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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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inlinevirtualinherited |
nodeId | An id of the node to look for in the map. |
Implements bpp::Mapping.
Definition at line 230 of file Mapping.h.
References bpp::AbstractMapping::nbBranches_, and bpp::AbstractMapping::nodes_.
Referenced by bpp::SubstitutionMappingTools::getCountsPerBranch(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutions(), bpp::ProbabilisticRewardMapping::getReward(), bpp::SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite(), and bpp::SubstitutionMappingTools::outputTotalCountsPerBranchPerSite().
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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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inlinevirtualinherited |
Implements bpp::Mapping.
Definition at line 210 of file Mapping.h.
References bpp::AbstractMapping::nbBranches_.
Referenced by bpp::ProbabilisticRewardMapping::setNumberOfSites(), bpp::ProbabilisticSubstitutionMapping::setNumberOfSites(), bpp::ProbabilisticRewardMapping::setTree(), and bpp::ProbabilisticSubstitutionMapping::setTree().
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
Referenced by bpp::RewardMappingTools::computeSumForBranch(), and bpp::SubstitutionMappingTools::computeSumForBranch().
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inlinevirtualinherited |
Implements bpp::Mapping.
Definition at line 208 of file Mapping.h.
References bpp::AbstractMapping::nbSites_.
Referenced by bpp::SubstitutionMappingTools::getCountsPerBranch(), bpp::SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite(), bpp::SubstitutionMappingTools::outputTotalCountsPerBranchPerSite(), bpp::ProbabilisticRewardMapping::setTree(), and bpp::ProbabilisticSubstitutionMapping::setTree().
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pure virtualinherited |
Implemented in bpp::ProbabilisticSubstitutionMapping.
Referenced by bpp::SubstitutionMappingTools::computeNormForSite(), bpp::SubstitutionMappingTools::computeSumForBranch(), bpp::SubstitutionMappingTools::computeSumForSite(), and bpp::SubstitutionMappingTools::computeTotalSubstitutionVectorForSite().
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pure virtualinherited |
index | The site index. |
Implemented in bpp::AbstractMapping.
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inlinevirtualinherited |
index | The site index. |
Implements bpp::Mapping.
Definition at line 196 of file Mapping.h.
References bpp::AbstractMapping::isEmpty(), and bpp::AbstractMapping::sitesPositions_.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
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inlinevirtualinherited |
Implements bpp::Mapping.
Definition at line 182 of file Mapping.h.
References bpp::AbstractMapping::isEmpty(), and bpp::AbstractMapping::tree_.
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pure virtualinherited |
Implemented in bpp::AbstractMapping.
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inlinevirtualinherited |
Implements bpp::Mapping.
Definition at line 180 of file Mapping.h.
References bpp::AbstractMapping::tree_.
Referenced by bpp::AbstractMapping::getSitePosition(), bpp::AbstractMapping::getTree(), and bpp::AbstractMapping::setSitePosition().
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pure virtualinherited |
Implemented in bpp::ProbabilisticSubstitutionMapping.
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pure virtualinherited |
Implemented in bpp::ProbabilisticSubstitutionMapping.
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inline |
Definition at line 110 of file SubstitutionMapping.h.
References bpp::AbstractMapping::operator=().
Referenced by bpp::ProbabilisticSubstitutionMapping::operator=().
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inlinevirtualinherited |
Reimplemented in bpp::ProbabilisticSubstitutionMapping, and bpp::ProbabilisticRewardMapping.
Definition at line 214 of file Mapping.h.
References bpp::AbstractMapping::nbSites_, and bpp::AbstractMapping::sitesPositions_.
Referenced by bpp::ProbabilisticRewardMapping::setNumberOfSites(), and bpp::ProbabilisticSubstitutionMapping::setNumberOfSites().
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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.
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inlinevirtualinherited |
Set the position of a given site.
index | The site index. |
position | The position of the site. |
Implements bpp::Mapping.
Definition at line 202 of file Mapping.h.
References bpp::AbstractMapping::isEmpty(), and bpp::AbstractMapping::sitesPositions_.
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inlineinherited |
Definition at line 188 of file Mapping.h.
References bpp::AbstractMapping::nbBranches_, bpp::AbstractMapping::nodes_, and bpp::AbstractMapping::tree_.
Referenced by bpp::ProbabilisticRewardMapping::setTree(), and bpp::ProbabilisticSubstitutionMapping::setTree().