bpp-seq3  3.0.0
bpp::OrderedValuesContainer Class Referenceabstract

The Container of Ordered Values interface. More...

#include <Bpp/Seq/Container/OrderedValuesContainer.h>

+ Inheritance diagram for bpp::OrderedValuesContainer:
+ Collaboration diagram for bpp::OrderedValuesContainer:

Public Member Functions

 OrderedValuesContainer ()
 
virtual ~OrderedValuesContainer ()
 
OrderedValuesContainerclone () const =0
 
virtual std::string toString (size_t sequenceIndex) const =0
 
virtual const std::string & getName (size_t sequenceIndex) const =0
 Get the name of a particular row of the alignement (aka sequence). More...
 
virtual size_t getSequencePosition (const std::string &name) const =0
 Get the position of a sequence in sequence container from its name. More...
 
virtual double getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const =0
 
virtual double operator() (size_t siteIndex, size_t sequenceIndex, int state) const =0
 
virtual const CommentsgetComments (size_t sequenceIndex) const =0
 
virtual void setComments (size_t sequenceIndex, const Comments &comments)=0
 
virtual std::string toString (const std::string &name) const=0
 Convert a particular sequence to a string. More...
 
virtual double getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const=0
 get value of a state in a position More...
 
virtual const CommentsgetComments (const std::string &name) const=0
 Get comments of a particular sequence. More...
 
virtual void setComments (const std::string &name, const Comments &comments)=0
 Set the comments of a particular sequence. More...
 
virtual const AlphabetgetAlphabet () const =0
 Get container's alphabet. More...
 
virtual std::string toString (const std::string &name) const =0
 Convert a particular sequence to a string. More...
 
virtual bool hasSequence (const std::string &name) const =0
 Check if a sequence with a given name is present in the container. More...
 
virtual size_t getNumberOfSequences () const =0
 Get the number of sequences in the container. More...
 
virtual std::vector< std::string > getSequenceNames () const =0
 Get all the names of the sequences in the container. More...
 
virtual void setSequenceNames (const std::vector< std::string > &names, bool checkNames)=0
 Set all sequence names. More...
 
virtual double getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const =0
 get value of a state in a position More...
 
virtual double operator() (size_t siteIndex, const std::string &sequenceName, int state) const =0
 
virtual const CommentsgetComments (const std::string &name) const =0
 Get comments of a particular sequence. More...
 
virtual void setComments (const std::string &name, const Comments &comments)=0
 Set the comments of a particular sequence. More...
 
virtual const CommentsgetGeneralComments () const =0
 Get the comments of this container. More...
 
virtual void setGeneralComments (const Comments &comments)=0
 Set the comments of this container. More...
 
virtual void deleteGeneralComments ()=0
 Delete the comments associated to this container. More...
 
virtual void clear ()=0
 Delete all data in the container. More...
 
virtual SequencedValuesContainercreateEmptyContainer () const =0
 Return a copy of this container, but with no data inside. More...
 

Detailed Description

The Container of Ordered Values interface.

Container implementing the OrderedValuesContainer interface deal with named and indexed. This interface provides access methods to the doubles stored in the data.

Definition at line 62 of file OrderedValuesContainer.h.

Constructor & Destructor Documentation

◆ OrderedValuesContainer()

bpp::OrderedValuesContainer::OrderedValuesContainer ( )
inline

Definition at line 66 of file OrderedValuesContainer.h.

◆ ~OrderedValuesContainer()

virtual bpp::OrderedValuesContainer::~OrderedValuesContainer ( )
inlinevirtual

Definition at line 67 of file OrderedValuesContainer.h.

Member Function Documentation

◆ clear()

virtual void bpp::SequencedValuesContainer::clear ( )
pure virtualinherited

◆ clone()

◆ createEmptyContainer()

virtual SequencedValuesContainer* bpp::SequencedValuesContainer::createEmptyContainer ( ) const
pure virtualinherited

Return a copy of this container, but with no data inside.

This method creates a new SequencedValuesContainer objet. The class of this container depends on the derivative class.

Returns
A new empty container, with the same alphabet as this one.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

◆ deleteGeneralComments()

virtual void bpp::SequencedValuesContainer::deleteGeneralComments ( )
pure virtualinherited

Delete the comments associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ getAlphabet()

virtual const Alphabet* bpp::SequencedValuesContainer::getAlphabet ( ) const
pure virtualinherited

Get container's alphabet.

Returns
The alphabet associated to this container.

Implemented in bpp::AbstractValuesContainer.

Referenced by bpp::Clustal::appendAlignmentFromStream(), bpp::DCSE::appendAlignmentFromStream(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), bpp::GenBank::appendSequencesFromStream(), bpp::Mase::appendSequencesFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getConsensus(), bpp::SequenceContainerTools::getFrequencies(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSequences(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::SequenceContainerTools::merge(), bpp::SiteContainerTools::merge(), bpp::AbstractSequenceContainer::operator=(), bpp::Phylip::readInterleaved(), bpp::Phylip::readSequential(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SiteContainerTools::sampleSites(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

◆ getComments() [1/3]

virtual const Comments& bpp::SequencedValuesContainer::getComments ( const std::string &  name) const
pure virtualinherited

Get comments of a particular sequence.

Parameters
nameThe name of the sequence.
Returns
The comments associated to sequence with name 'name'.
Exceptions
SequenceNotFoundExceptionIf the name does not match any sequence in the container.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::SequenceContainerTools::getCodonPosition(), and bpp::Mase::writeSequences().

◆ getComments() [2/3]

virtual const Comments& bpp::SequencedValuesContainer::getComments

Get comments of a particular sequence.

Parameters
sequenceIndexThe position of the sequence.
Returns
The comments associated to sequence at position 'sequenceIndex'.
Exceptions
IndexOutOfBoundsExceptionIf the position does not match any sequence in the container.

◆ getComments() [3/3]

virtual const Comments& bpp::OrderedValuesContainer::getComments ( size_t  sequenceIndex) const
pure virtual

◆ getGeneralComments()

◆ getName()

virtual const std::string& bpp::OrderedValuesContainer::getName ( size_t  sequenceIndex) const
pure virtual

Get the name of a particular row of the alignement (aka sequence).

Parameters
sequenceIndexThe position of the sequence.
Returns
The name of the sequence at position 'sequenceIndex'.
Exceptions
IndexOutOfBoundsExceptionIf the position does not match any sequence in the container.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::VectorSiteContainer::VectorSiteContainer().

◆ getNumberOfSequences()

virtual size_t bpp::SequencedValuesContainer::getNumberOfSequences ( ) const
pure virtualinherited

Get the number of sequences in the container.

Returns
The number of sequences in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SimpleSequenceContainerIterator::hasMoreSequences(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Clustal::writeAlignment(), bpp::Phylip::writeAlignment(), bpp::Stockholm::writeAlignment(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

◆ getSequenceNames()

virtual std::vector<std::string> bpp::SequencedValuesContainer::getSequenceNames ( ) const
pure virtualinherited

Get all the names of the sequences in the container.

Returns
A vector of strings with all sequence names.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::SequenceContainerTools::append(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SiteContainerTools::getCompleteSites(), bpp::SequenceContainerTools::getCounts(), bpp::SequenceContainerTools::getFrequencies(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::SequenceContainerTools::keepOnlySelectedSequences(), bpp::SequenceContainerTools::merge(), bpp::SiteContainerTools::merge(), bpp::VectorSequenceContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SequenceApplicationTools::restrictSelectedSequencesByName(), bpp::SiteContainerTools::sampleSites(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Pasta::writeAlignedValues(), bpp::Stockholm::writeAlignment(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequences(), bpp::Mase::writeSequences(), and bpp::Phylip::writeSequential().

◆ getSequencePosition()

virtual size_t bpp::OrderedValuesContainer::getSequencePosition ( const std::string &  name) const
pure virtual

Get the position of a sequence in sequence container from its name.

Parameters
nameThe name of the sequence.
Returns
The position of the sequence with name 'name', if it exists.
Exceptions
SequenceNotFoundExceptionIf no sequence with name 'name' could be found.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::AbstractProbabilisticSequenceContainer::setComments(), bpp::AbstractSequenceContainer::setComments(), and bpp::AbstractValuesContainer::setComments().

◆ getStateValueAt() [1/3]

virtual double bpp::SequencedValuesContainer::getStateValueAt ( size_t  siteIndex,
const std::string &  sequenceName,
int  state 
) const
pure virtualinherited

get value of a state in a position

Parameters
siteIndexindex of the site
sequenceNamename of the sequence in the container
statestate in the alphabet

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ getStateValueAt() [2/3]

virtual double bpp::SequencedValuesContainer::getStateValueAt

get value of a state in a position

Parameters
siteIndexindex of the site
sequenceNamename of the sequence in the container
statestate in the alphabet

◆ getStateValueAt() [3/3]

virtual double bpp::OrderedValuesContainer::getStateValueAt ( size_t  siteIndex,
size_t  sequenceIndex,
int  state 
) const
pure virtual

◆ hasSequence()

virtual bool bpp::SequencedValuesContainer::hasSequence ( const std::string &  name) const
pure virtualinherited

Check if a sequence with a given name is present in the container.

Parameters
nameThe name of the sequence.
Returns
True if a sequence with the given name is present in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::SequenceContainerTools::getSelectedSequences().

◆ operator()() [1/2]

virtual double bpp::SequencedValuesContainer::operator() ( size_t  siteIndex,
const std::string &  sequenceName,
int  state 
) const
pure virtualinherited

◆ operator()() [2/2]

virtual double bpp::OrderedValuesContainer::operator() ( size_t  siteIndex,
size_t  sequenceIndex,
int  state 
) const
pure virtual

◆ setComments() [1/3]

virtual void bpp::SequencedValuesContainer::setComments

Set the comments of a particular sequence.

Parameters
sequenceIndexThe position of the sequence.
commentsThe comments to set to sequence with position 'i'.
Exceptions
IndexOutOfBoundsExceptionIf the position does not match any sequence in the container.

Referenced by bpp::AbstractProbabilisticSequenceContainer::setComments(), bpp::AbstractValuesContainer::setComments(), and bpp::VectorProbabilisticSequenceContainer::setComments().

◆ setComments() [2/3]

virtual void bpp::SequencedValuesContainer::setComments ( const std::string &  name,
const Comments comments 
)
pure virtualinherited

Set the comments of a particular sequence.

Parameters
nameThe name of the sequence.
commentsThe comments to set to sequence with name 'name'.
Exceptions
SequenceNotFoundExceptionIf the name does not match any sequence in the container.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractValuesContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ setComments() [3/3]

◆ setGeneralComments()

virtual void bpp::SequencedValuesContainer::setGeneralComments ( const Comments comments)
pure virtualinherited

Set the comments of this container.

Parameters
commentsThe comments to be associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::Clustal::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), and bpp::Mase::appendSequencesFromStream().

◆ setSequenceNames()

virtual void bpp::SequencedValuesContainer::setSequenceNames ( const std::vector< std::string > &  names,
bool  checkNames 
)
pure virtualinherited

Set all sequence names.

Parameters
namesA vector of strings with all sequence names. Its size must be strictly equal to the the size of the container (the number of sequences).
checkNamesTell if the container must check if the name of the sequence is already used in the container before adding it.
Exceptions
ExceptionIf there are redundant names in the input vector.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::SequenceContainerTools::createContainerWithSequenceNames(), bpp::SiteContainerTools::getCompleteSites(), and bpp::SiteContainerTools::getSitesWithoutGaps().

◆ toString() [1/3]

virtual std::string bpp::SequencedValuesContainer::toString ( const std::string &  name) const
pure virtualinherited

Convert a particular sequence to a string.

Parameters
nameThe name of the sequence.
Returns
A string describing the content of the sequence.
Exceptions
SequenceNotFoundExceptionIf the name does not match any sequence in the container.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::SequenceContainerTools::convertAlphabet(), bpp::Phylip::writeInterleaved(), bpp::Mase::writeSequences(), and bpp::Phylip::writeSequential().

◆ toString() [2/3]

virtual std::string bpp::SequencedValuesContainer::toString

Convert a particular sequence to a string.

Parameters
sequenceIndexThe position of the sequence.
Returns
A string describing the content of the sequence.
Exceptions
IndexOutOfBoundsExceptionIf the position does not match any sequence in the container.

◆ toString() [3/3]

virtual std::string bpp::OrderedValuesContainer::toString ( size_t  sequenceIndex) const
pure virtual

The documentation for this class was generated from the following file: