bpp-seq3
3.0.0
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#include <Bpp/Seq/ProbabilisticSite.h>
Public Types | |
typedef std::vector< double > | SymbolType |
typedef Table< double > | DTable |
Public Member Functions | |
ProbabilisticSite (std::shared_ptr< const Alphabet > &alpha) | |
Build a new void ProbabilisticSite object with the specified alphabet. More... | |
ProbabilisticSite (std::shared_ptr< const Alphabet > &alpha, int position) | |
Build a new void ProbabilisticSite object with the specified alphabet and position. More... | |
ProbabilisticSite (const Table< double > &site, std::shared_ptr< const Alphabet > &alpha) | |
Build a new ProbabilisticSite object with the specified alphabet. The content of the site is initialized from a Table<double> object. More... | |
ProbabilisticSite (const Table< double > &site, std::shared_ptr< const Alphabet > &alpha, int position) | |
Build a new ProbabilisticSite object with the specified alphabet and position. The content of the probabilistic site is initialized from a Table<double> object. More... | |
ProbabilisticSite (const ProbabilisticSite &site) | |
The copy constructor. More... | |
ProbabilisticSite (const ProbabilisticSiteInterface &site) | |
ProbabilisticSite & | operator= (const ProbabilisticSite &site) |
The assignment operator. More... | |
ProbabilisticSite & | operator= (const ProbabilisticSiteInterface &site) |
virtual | ~ProbabilisticSite () |
double | getStateValueAt (size_t sequencePosition, int state) const |
get value of a state at a position More... | |
virtual std::shared_ptr< const Alphabet > | getAlphabet () const =0 |
Get the alphabet associated to the list. More... | |
virtual const Alphabet & | alphabet () const =0 |
Get the alphabet associated to the list. More... | |
virtual size_t | size () const =0 |
Get the number of elements in the list. More... | |
virtual std::string | toString () const =0 |
Convert the list as a string. More... | |
virtual double | operator() (size_t position, int state) const =0 |
get value of a state at a position More... | |
virtual const DTable & | getTable () const =0 |
virtual void | setContent (const DTable &list)=0 |
virtual void | setContent (const std::vector< T > &list)=0 |
Set the whole content of the list. More... | |
int | getCoordinate () const override |
Get the coordinate associated to this site. More... | |
void | setCoordinate (int coordinate) override |
Set the position of this site. More... | |
std::shared_ptr< const Alphabet > | getAlphabet () const override |
Get the alphabet associated to the list. More... | |
const Alphabet & | alphabet () const override |
Get the alphabet associated to the list. More... | |
size_t | size () const override |
Get the number of elements in the list. More... | |
void | setContent (const std::vector< std::vector< double >> &list) override |
void | setContent (const DTable &list) override |
std::string | toString () const override |
Convert the list as a string. More... | |
void | addElement (const std::vector< double > &element) override |
void | addElement (size_t pos, const std::vector< double > &element) override |
void | setElement (size_t pos, const std::vector< double > &element) override |
const std::vector< double > & | getElement (size_t pos) const override |
Get the element at position 'pos' as a character. More... | |
virtual void | deleteElement (size_t pos) override |
Remove the element at position 'pos'. More... | |
virtual void | deleteElements (size_t pos, size_t len) override |
Remove the elements at position 'pos'. More... | |
const std::vector< std::vector< double > > & | getContent () const override |
const DTable & | getTable () const override |
const std::vector< double > & | getValue (size_t pos) const override |
checked access to a character in list. More... | |
const std::vector< double > & | operator[] (size_t pos) const override |
Operator [] overloaded for quick access to a character in list. More... | |
std::vector< double > & | operator[] (size_t pos) override |
Operator [] overloaded for quick access to a character in list. More... | |
double | operator() (size_t siteIndex, int state) const override |
get value of a state at a position More... | |
void | shuffle () override |
Randomly shuffle the content of the list, with linear complexity. More... | |
The Clonable interface | |
ProbabilisticSite * | clone () const |
Setting/getting the position of the site. | |
virtual int | getCoordinate () const =0 |
Get the coordinate associated to this site. More... | |
virtual void | setCoordinate (int coordinate)=0 |
Set the position of this site. More... | |
Edition methods. | |
virtual void | deleteElement (size_t pos)=0 |
Remove the element at position 'pos'. More... | |
virtual void | deleteElements (size_t pos, size_t len)=0 |
Remove the elements at position 'pos'. More... | |
Provide direct access to the list content. | |
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virtual void | shuffle ()=0 |
Randomly shuffle the content of the list, with linear complexity. More... | |
Acting on the content of the list. | |
virtual void | setContent (const std::vector< T > &list)=0 |
Set the whole content of the list. More... | |
virtual const std::vector< T > & | getContent () const =0 |
Edition methods. | |
virtual void | addElement (const T &c)=0 |
Add a character to the end of the list. More... | |
virtual void | addElement (size_t pos, const T &c)=0 |
Add a character at a certain position in the list. More... | |
virtual void | setElement (size_t pos, const T &c)=0 |
Set the element at position 'pos' to character 'c'. More... | |
virtual const T & | getElement (size_t pos) const =0 |
Get the element at position 'pos' as a character. More... | |
Provide direct access to the list content. | |
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virtual const T & | getValue (size_t pos) const =0 |
checked access to a character in list. More... | |
virtual const T & | operator[] (size_t pos) const =0 |
Operator [] overloaded for quick access to a character in list. More... | |
virtual T & | operator[] (size_t pos)=0 |
Operator [] overloaded for quick access to a character in list. More... | |
Protected Attributes | |
DTable | content_ |
The list content. More... | |
Private Attributes | |
int | coordinate_ |
The position associated with this site. More... | |
std::shared_ptr< const Alphabet > | alphabet_ |
The Alphabet attribute must be initialized in the constructor and then can never be changed. More... | |
Definition at line 35 of file ProbabilisticSite.h.
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inherited |
Definition at line 35 of file ProbabilisticSymbolList.h.
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inherited |
Definition at line 34 of file ProbabilisticSymbolList.h.
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inline |
Build a new void ProbabilisticSite object with the specified alphabet.
alpha | The alphabet to use. |
Definition at line 46 of file ProbabilisticSite.h.
Referenced by clone().
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inline |
Build a new void ProbabilisticSite object with the specified alphabet and position.
alpha | The alphabet to use. |
position | The position attribute for this probabilistic site. |
Definition at line 58 of file ProbabilisticSite.h.
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inline |
Build a new ProbabilisticSite object with the specified alphabet. The content of the site is initialized from a Table<double> object.
site | The content of the probabilist site. |
alpha | The alphabet to use. |
Exception | If the content does not match the specified alphabet or is internally inconsistent. |
Definition at line 72 of file ProbabilisticSite.h.
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inline |
Build a new ProbabilisticSite object with the specified alphabet and position. The content of the probabilistic site is initialized from a Table<double> object.
site | The content of the probabilistic site. |
alpha | The alphabet to use. |
position | The position attribute for this site. |
Exception | If the content does not match the specified alphabet or is internally insconsistent. |
Definition at line 87 of file ProbabilisticSite.h.
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inline |
The copy constructor.
Definition at line 96 of file ProbabilisticSite.h.
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inline |
Definition at line 102 of file ProbabilisticSite.h.
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inlinevirtual |
Definition at line 137 of file ProbabilisticSite.h.
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overrideinherited |
Definition at line 146 of file ProbabilisticSymbolList.cpp.
References bpp::Table< class >::addColumn(), bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getNumberOfRows().
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pure virtualinherited |
Add a character to the end of the list.
c | The character to add. |
Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.
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overrideinherited |
Definition at line 171 of file ProbabilisticSymbolList.cpp.
References bpp::Table< class >::addColumn(), bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getNumberOfRows().
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pure virtualinherited |
Add a character at a certain position in the list.
pos | The position where to insert the element. |
c | The character to add. |
Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.
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pure virtualinherited |
Get the alphabet associated to the list.
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::concatenate(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::invertComplement(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), and bpp::AbstractTransliterator::translate().
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inlineoverridevirtualinherited |
Get the alphabet associated to the list.
Implements bpp::CruxSymbolListInterface.
Definition at line 144 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::alphabet_.
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inlinevirtual |
Implements bpp::ProbabilisticSiteInterface.
Definition at line 130 of file ProbabilisticSite.h.
References ProbabilisticSite().
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inlineoverridevirtualinherited |
Remove the element at position 'pos'.
pos | The position of the element to remove. |
Implements bpp::CruxSymbolListInterface.
Definition at line 172 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::deleteColumn().
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pure virtualinherited |
Remove the element at position 'pos'.
pos | The position of the element to remove. |
Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
Referenced by bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), and bpp::SequenceTools::removeStops().
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inlineoverridevirtualinherited |
Remove the elements at position 'pos'.
pos | The position of the first element to remove. |
len | The length of the region to remove. |
Implements bpp::CruxSymbolListInterface.
Definition at line 177 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::deleteColumns().
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pure virtualinherited |
Remove the elements at position 'pos'.
pos | The position of the first element to remove. |
len | The length of the region to remove. |
Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
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pure virtualinherited |
Get the alphabet associated to the list.
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
Referenced by bpp::Sequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceWithQualityTools::complement(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::getComplement(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::jointEntropy(), bpp::SequenceWithAnnotation::merge(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::ProbabilisticSymbolList::operator=(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::SequenceWithQualityTools::reverseTranscript(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SequenceWithQualityTools::transcript(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::WordAlphabet::translate(), and bpp::SymbolListTools::variabilityShannon().
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inlineoverridevirtualinherited |
Get the alphabet associated to the list.
Implements bpp::CruxSymbolListInterface.
Definition at line 142 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::alphabet_.
Referenced by bpp::ProbabilisticSymbolList::getStateValueAt(), bpp::Pasta::nextSequence(), bpp::ProbabilisticSymbolList::operator()(), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), and bpp::Pasta::writeSequence().
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pure virtualinherited |
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
Referenced by bpp::Sequence::append(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::SequenceWithAnnotation::merge(), bpp::ProbabilisticSymbolList::operator=(), and bpp::Sequence::operator=().
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inlineoverridevirtualinherited |
Implements bpp::TemplateCoreSymbolListInterface< T >.
Definition at line 182 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getData().
Referenced by bpp::Pasta::writeSequence().
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pure virtualinherited |
Get the coordinate associated to this site.
Implemented in bpp::AbstractCoreSite.
Referenced by bpp::SiteInterface::operator<(), bpp::AbstractCoreSite::operator=(), and bpp::SiteInterface::operator==().
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inlineoverridevirtualinherited |
Get the coordinate associated to this site.
Implements bpp::CoreSiteInterface.
Definition at line 144 of file CoreSite.h.
References bpp::AbstractCoreSite::coordinate_.
Referenced by bpp::SiteContainerTools::resolveDottedAlignment().
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pure virtualinherited |
Get the element at position 'pos' as a character.
pos | The position of the character to retrieve. |
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
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inlineoverridevirtualinherited |
Get the element at position 'pos' as a character.
pos | The position of the character to retrieve. |
Implements bpp::TemplateCoreSymbolListInterface< T >.
Definition at line 167 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getColumn().
Referenced by bpp::ProbabilisticSymbolList::getValue().
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inlinevirtual |
get value of a state at a position
sequencePosition | index of the looked value in the site |
state | state in the alphabet |
Implements bpp::CoreSiteInterface.
Definition at line 139 of file ProbabilisticSite.h.
References bpp::ProbabilisticSymbolList::size().
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pure virtualinherited |
Implemented in bpp::ProbabilisticSymbolList.
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inlineoverridevirtualinherited |
Implements bpp::ProbabilisticSymbolListInterface.
Definition at line 187 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_.
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pure virtualinherited |
checked access to a character in list.
pos | The position to retrieve. |
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::findFirstOf(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().
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inlineoverridevirtualinherited |
checked access to a character in list.
pos | The position to retrieve. |
Implements bpp::TemplateCoreSymbolListInterface< T >.
Definition at line 192 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::getElement().
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pure virtualinherited |
get value of a state at a position
Short-cut for getStateValueAt.
position | position in the list |
state | state in the alphabet |
Implemented in bpp::ProbabilisticSymbolList, and bpp::IntSymbolList.
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inlineoverridevirtualinherited |
get value of a state at a position
Short-cut for getStateValueAt.
position | position in the list |
state | state in the alphabet |
Implements bpp::CruxSymbolListInterface.
Definition at line 214 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, bpp::ProbabilisticSymbolList::getAlphabet(), and bpp::Table< class >::getColumn().
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inline |
The assignment operator.
Definition at line 111 of file ProbabilisticSite.h.
References bpp::AbstractCoreSite::operator=(), and bpp::ProbabilisticSymbolList::operator=().
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inline |
Definition at line 118 of file ProbabilisticSite.h.
References bpp::AbstractCoreSite::operator=(), and bpp::ProbabilisticSymbolList::operator=().
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pure virtualinherited |
Operator [] overloaded for quick access to a character in list.
pos | The position to retrieve. |
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
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inlineoverridevirtualinherited |
Operator [] overloaded for quick access to a character in list.
pos | The position to retrieve. |
Implements bpp::TemplateCoreSymbolListInterface< T >.
Definition at line 197 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getColumn().
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inlineoverridevirtualinherited |
Operator [] overloaded for quick access to a character in list.
pos | The position to retrieve. |
Implements bpp::TemplateCoreSymbolListInterface< T >.
Definition at line 202 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getColumn().
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pure virtualinherited |
Operator [] overloaded for quick access to a character in list.
pos | The position to retrieve. |
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
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overridevirtualinherited |
Implements bpp::ProbabilisticSymbolListInterface.
Definition at line 76 of file ProbabilisticSymbolList.cpp.
References bpp::ProbabilisticSymbolList::alphabet_, bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::getNumberOfRows(), bpp::Table< class >::getRowNames(), bpp::Table< class >::hasRowNames(), bpp::Table< class >::setRowNames(), bpp::ProbabilisticSymbolList::size(), and bpp::TextTools::toString().
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pure virtualinherited |
Implemented in bpp::ProbabilisticSymbolList.
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overrideinherited |
Definition at line 132 of file ProbabilisticSymbolList.cpp.
References bpp::ProbabilisticSymbolList::alphabet_, bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::setRowNames(), and bpp::ProbabilisticSymbolList::size().
Referenced by bpp::Pasta::nextSequence().
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pure virtualinherited |
Set the whole content of the list.
list | The new content of the list. |
Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.
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inherited |
Set the whole content of the list.
list | The new content of the list. |
Referenced by bpp::ProbabilisticSymbolList::operator=(), and bpp::ProbabilisticSymbolList::ProbabilisticSymbolList().
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inlineoverridevirtualinherited |
Set the position of this site.
coordinate | The new position of the site. |
Implements bpp::CoreSiteInterface.
Definition at line 146 of file CoreSite.h.
References bpp::AbstractCoreSite::coordinate_.
Referenced by bpp::CompressedVectorSiteContainer::reindexSites(), and bpp::CompressedVectorSiteContainer::setSiteCoordinates().
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pure virtualinherited |
Set the position of this site.
coordinate | The new position of the site. |
Implemented in bpp::AbstractCoreSite.
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overrideinherited |
Definition at line 188 of file ProbabilisticSymbolList.cpp.
References bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::getNumberOfRows(), and bpp::Table< class >::setColumn().
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pure virtualinherited |
Set the element at position 'pos' to character 'c'.
pos | The position of the character to set. |
c | The value of the element. |
Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.
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inlineoverridevirtualinherited |
Randomly shuffle the content of the list, with linear complexity.
Implements bpp::CruxSymbolListInterface.
Definition at line 219 of file ProbabilisticSymbolList.h.
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pure virtualinherited |
Randomly shuffle the content of the list, with linear complexity.
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
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pure virtualinherited |
Get the number of elements in the list.
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.
Referenced by bpp::AbstractTemplateSymbolList< T >::AbstractTemplateSymbolList(), bpp::SequenceWithQuality::addElement(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getFrequencies(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getMajorAllele(), bpp::SymbolListTools::getMajorAlleleFrequency(), bpp::SymbolListTools::getMinorAllele(), bpp::SymbolListTools::getMinorAlleleFrequency(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SymbolListTools::getNumberOfDistinctCharacters(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasSingleton(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SymbolListTools::heterozygosity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isDoubleton(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::isParsimonyInformativeSite(), bpp::SymbolListTools::isTriplet(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), bpp::SymbolListTools::jointEntropy(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SiteInterface::operator==(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceWalker::SequenceWalker(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::SymbolListTools::variabilityFactorial(), and bpp::SymbolListTools::variabilityShannon().
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inlineoverridevirtualinherited |
Get the number of elements in the list.
Implements bpp::CruxSymbolListInterface.
Definition at line 146 of file ProbabilisticSymbolList.h.
References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getNumberOfColumns().
Referenced by bpp::SequenceContainerTools::getFrequencies(), getStateValueAt(), bpp::ProbabilisticSequence::getStateValueAt(), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), and bpp::ProbabilisticSymbolList::setContent().
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pure virtualinherited |
Convert the list as a string.
This method is useful for dumping a list to a file or to the screen for display.
Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, bpp::Sequence, bpp::ProbabilisticSymbolList, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.
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overridevirtualinherited |
Convert the list as a string.
This method is useful for dumping a list to a file or to the screen for display.
Implements bpp::CruxSymbolListInterface.
Definition at line 108 of file ProbabilisticSymbolList.cpp.
References bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::getNumberOfColumns(), bpp::Table< class >::getNumberOfRows(), and bpp::Table< class >::getRowName().
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privateinherited |
The Alphabet attribute must be initialized in the constructor and then can never be changed.
To apply another alphabet to the list requires creating another list.
Definition at line 71 of file ProbabilisticSymbolList.h.
Referenced by bpp::ProbabilisticSymbolList::alphabet(), bpp::ProbabilisticSymbolList::getAlphabet(), bpp::ProbabilisticSymbolList::operator=(), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), and bpp::ProbabilisticSymbolList::setContent().
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protectedinherited |
The list content.
Definition at line 77 of file ProbabilisticSymbolList.h.
Referenced by bpp::ProbabilisticSymbolList::addElement(), bpp::ProbabilisticSymbolList::deleteElement(), bpp::ProbabilisticSymbolList::deleteElements(), bpp::ProbabilisticSymbolList::getContent(), bpp::ProbabilisticSymbolList::getElement(), bpp::ProbabilisticSymbolList::getStateValueAt(), bpp::ProbabilisticSymbolList::getTable(), bpp::ProbabilisticSymbolList::operator()(), bpp::ProbabilisticSymbolList::operator=(), bpp::ProbabilisticSymbolList::operator[](), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), bpp::ProbabilisticSymbolList::setContent(), bpp::ProbabilisticSymbolList::setElement(), bpp::ProbabilisticSymbolList::size(), and bpp::ProbabilisticSymbolList::toString().
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The position associated with this site.
Definition at line 85 of file CoreSite.h.
Referenced by bpp::AbstractCoreSite::getCoordinate(), bpp::AbstractCoreSite::operator=(), and bpp::AbstractCoreSite::setCoordinate().