bpp-phyl
2.2.0
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Data structure for site patterns. More...
#include <Bpp/Phyl/SitePatterns.h>
Classes | |
class | SortableSite |
Class used for site pattern sorting. More... | |
Public Member Functions | |
SitePatterns (const SiteContainer *sequences, bool own=false) | |
Build a new SitePattern object. More... | |
virtual | ~SitePatterns () |
SitePatterns (const SitePatterns &patterns) | |
SitePatterns & | operator= (const SitePatterns &patterns) |
SitePatterns * | clone () const |
const std::vector< unsigned int > & | getWeights () const |
const std::vector< size_t > & | getIndices () const |
SiteContainer * | getSites () const |
Private Attributes | |
std::vector< std::string > | names_ |
Class used for site pattern sorting. More... | |
std::vector< const Site * > | sites_ |
std::vector< unsigned int > | weights_ |
std::vector< size_t > | indices_ |
const SiteContainer * | sequences_ |
const Alphabet * | alpha_ |
bool | own_ |
Data structure for site patterns.
'names' are the sequence names 'sites' points toward a unique site 'weights' is the number of sites identical to this sites 'indices' are the positions in the original container
Definition at line 69 of file SitePatterns.h.
SitePatterns::SitePatterns | ( | const SiteContainer * | sequences, |
bool | own = false |
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Build a new SitePattern object.
Look for patterns (unique sites) within a site container.
sequences | The container to look in. |
own | Tel is the class own the sequence container. If yes, the sequences wll be deleted together with this instance. |
Definition at line 52 of file SitePatterns.cpp.
References indices_, bpp::SitePatterns::SortableSite::originalPosition, bpp::SitePatterns::SortableSite::siteP, bpp::SitePatterns::SortableSite::siteS, sites_, and weights_.
Referenced by clone().
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inlinevirtual |
Definition at line 129 of file SitePatterns.h.
References own_, and sequences_.
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inline |
Definition at line 134 of file SitePatterns.h.
References own_, and sequences_.
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inline |
Definition at line 165 of file SitePatterns.h.
References SitePatterns().
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inline |
Definition at line 175 of file SitePatterns.h.
References indices_.
Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().
SiteContainer * SitePatterns::getSites | ( | ) | const |
Definition at line 110 of file SitePatterns.cpp.
References alpha_, names_, and sites_.
Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().
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inline |
Definition at line 171 of file SitePatterns.h.
References weights_.
Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().
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inline |
Definition at line 147 of file SitePatterns.h.
References alpha_, indices_, names_, own_, sequences_, sites_, and weights_.
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private |
Definition at line 114 of file SitePatterns.h.
Referenced by getSites(), and operator=().
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private |
Definition at line 112 of file SitePatterns.h.
Referenced by getIndices(), operator=(), and SitePatterns().
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private |
Class used for site pattern sorting.
Definition at line 109 of file SitePatterns.h.
Referenced by getSites(), and operator=().
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private |
Definition at line 115 of file SitePatterns.h.
Referenced by operator=(), SitePatterns(), and ~SitePatterns().
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private |
Definition at line 113 of file SitePatterns.h.
Referenced by operator=(), SitePatterns(), and ~SitePatterns().
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private |
Definition at line 110 of file SitePatterns.h.
Referenced by getSites(), operator=(), and SitePatterns().
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private |
Definition at line 111 of file SitePatterns.h.
Referenced by getWeights(), operator=(), and SitePatterns().