mems::gnAlignedSequences Class Reference

gnAlignedSequences allows for the manipulation of aligned sequence data. More...

#include <gnAlignedSequences.h>

List of all members.

Public Member Functions
void	addSequence (genome::gnSequence &seqToAdd, std::string &seqName)
	Adds a sequence to the alignment.
void	addSequence (std::string &seqToAdd, std::string &seqName)
	Adds a sequence to the alignment.
gnSeqI	alignedSeqsSize () const
	Returns the size of each sequence in the alignment (all are identical).
void	assignFileName (std::string name)
	Assigns a file name to the alignment data for purposes of output.
bool	collapseIdenticalSequences ()
	Collapses the alignment accross all sequences.
void	concatenateAlignedSequences (gnAlignedSequences toConcat)
	Concatenates 2 alignmnets.
void	constructFromClustalW (std::string alignedFileName)
	Loads the data held in file alignedFileName (in ClustalW format).
void	constructFromMega (std::string alignedFileName)
	Loads the data held in file alignedFileName (in Mega format).
void	constructFromMSF (std::string alignedFileName)
	Loads the data held in file alignedFileName (in MSF format).
void	constructFromNexus (std::string alignedFileName)
	Loads the data held in file alignedFileName (in Nexus format).
void	constructFromPhylip (std::string alignedFileName)
	Loads the data held in file alignedFileName (in Phylip format).
void	constructFromRelaxedNexus (std::istream &align_stream)
	Reads a single sequence entry in relaxed NEXUS format.
void	extractVariableSites (gnAlignedSequences &variableSites, bool countGapsAsMismatches)
	Extracts the variable sites from *this.
gnAlignedSequences	getAlignedSegment (unsigned start, unsigned stop)
	Create a new alignment that is comprised of all of the segments in the initial alignment from start to stop (inclusive) if stop == 0, the alignment ends at the end.
std::string	getAlignedSequenceFileName ()
	Returns the name of the file associated with this gnAlignedSequences.
gnAlignedSequences	getCodons (int readingFrame, int startCodon, int codonMultiple)
	Extracts every codonMultiple-th codon in the reading frame readingFrame beginning with startCodon reading frames supported: 1, 2 & 3 (no reverse complementing).
	gnAlignedSequences (const gnAlignedSequences &toCopy)
	Copy Constructor, creates a copy of toCopy.
	gnAlignedSequences ()
	Empty Constructor, creates a default gnAlignedSequences.
std::vector< char >	operator[] (const int offset)
	Accesses the alignment and returns the bases at that position in all sequences.
void	output (const std::string &format_name, std::ostream &os) const
	Writes out this sequence alignment in the specified format, assuming the format is supported.
bool	outputClustalW (std::ostream &os) const
	Writes alignment using the given output stream (in ClustalW format).
bool	outputCodon (std::ostream &os) const
	Writes alignment in 3-base, codon segments using the given output stream (in Phylip format).
bool	outputMega (std::ostream &os) const
	Writes alignment using the given output stream (in Mega format).
bool	outputMSF (std::ostream &os) const
	Writes alignment using the given output stream (in MSF format).
bool	outputNexus (std::ostream &os) const
	Writes alignment using the given output stream (in Nexus format).
bool	outputPhylip (std::ostream &os) const
	Writes alignment using the given output stream (in Phylip format).
bool	outputWithConsensus (std::ostream &os)
	Writes alignment with consensus using the given output stream (in Phylip format).
bool	removeAlignedSeq (unsigned index)
	Removes a single sequence from the alignment.
bool	removeAlignedSeq (std::string seqName)
	Removes a single sequence from the alignment.
void	seq (uint seqI)
	~gnAlignedSequences ()
	Destructor, frees the memory used.
Static Public Member Functions
const std::vector< std::string > &	getSupportedFormats ()
	Returns a vector of supported format names.
boolean	isSupportedFormat (const std::string &format_name)
	Checks whether a particular format name is supported.
Public Attributes
std::list< std::pair< std::string *, std::string * > >	alignedSequences
std::vector< std::string >	names
std::vector< int64 >	positions
	If this is part of a larger alignment this vector stores start positions within that alignment.
std::vector< std::string >	sequences
Private Member Functions
void	addAllSegments (gnAlignedSequences &alignment, unsigned start, unsigned stop)
	Adds all segments in *this to the given alignment.
void	addAllSegmentsReplaceGaps (gnAlignedSequences &alignment, unsigned start, unsigned stop)
	Adds all segments in *this to the given alignment - replaces gaps with consensus data.
void	addSequence (genome::gnSequence seqToAdd, std::string seqName, int consensusStart, std::string originalConsensus)
	Adds a sequence to the alignment.
bool	buildConsensus ()
	Reads all sequences in the alignment and creates a consensus.
bool	constructClustalWAlignedSequenceList (std::ifstream &alignmentFile)
	Aids readClustalWAlignment.
bool	constructMegaAlignedSequenceList (std::ifstream &alignmentFile)
	Aids readMegaAlignment.
bool	constructMSFAlignedSequenceList (std::ifstream &alignmentFile)
	Aids readMSFAlignment.
bool	constructNexusAlignedSequenceList (std::ifstream &alignmentFile)
	Aids readNexusAlignment.
bool	constructPhylipAlignedSequenceList (std::ifstream &alignmentFile)
	Aids readPhylipAlignment.
bool	coordinates (std::string line)
	Searches given line for coordinates.
int	determineBaseIndex (char base)
	Computes an index for a given base (0-25: a-z).
bool	readClustalWAlignment ()
	Aids constructFromClustalW.
bool	readMegaAlignment ()
	Aids constructFromMega.
bool	readMSFAlignment ()
	Aids constructFromMSF.
bool	readNexusAlignment ()
	Aids constructFromNexus.
bool	readPhylipAlignment ()
	Aids constructFromPhylip.
bool	readRelaxedNexusAlignment (std::istream &align_stream)
	This function assumes that the #NEXUS at the beginning of the file has been read off already.
void	removeAllSegments (unsigned start, unsigned stop)
	Removes all segments across all sequences in *this.
int	sequenceNameInList (std::string &sequenceName)
	Determines whether a sequence of the given name is present in the list.
bool	sequenceNameInList (std::string sequenceName, std::list< std::pair< std::string *, std::string * > >::iterator &sequenceItr)
	Determines whether a sequence of the given name is present in the list..
Private Attributes
std::string	alignedSequenceFileName
std::string	consensus
std::vector< int >	indexPositions

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Detailed Description

gnAlignedSequences allows for the manipulation of aligned sequence data.

Definition at line 48 of file gnAlignedSequences.h.

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Constructor & Destructor Documentation

mems::gnAlignedSequences::gnAlignedSequences (   )

Empty Constructor, creates a default gnAlignedSequences. Definition at line 20 of file gnAlignedSequences.cpp. References alignedSequenceFileName.

mems::gnAlignedSequences::gnAlignedSequences (  const gnAlignedSequences &  toCopy  )

Copy Constructor, creates a copy of toCopy. Definition at line 28 of file gnAlignedSequences.cpp. References alignedSequenceFileName, consensus, names, positions, and sequences.

mems::gnAlignedSequences::~gnAlignedSequences (   )  [inline]

Destructor, frees the memory used. Definition at line 399 of file gnAlignedSequences.h.

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Member Function Documentation

void mems::gnAlignedSequences::addAllSegments (  gnAlignedSequences &  alignment, unsigned  start, unsigned  stop )  [private]

Adds all segments in *this to the given alignment. Parameters: alignment  sequences to add. start  segment start point. stop  segment stop point. Definition at line 1503 of file gnAlignedSequences.cpp. References addSequence(), names, sequences, and uint. Referenced by extractVariableSites(), and getAlignedSegment().

void mems::gnAlignedSequences::addAllSegmentsReplaceGaps (  gnAlignedSequences &  alignment, unsigned  start, unsigned  stop )  [private]

Adds all segments in *this to the given alignment - replaces gaps with consensus data. Parameters: alignment  sequences to add. start  segment start point. stop  segment stop point. Definition at line 1515 of file gnAlignedSequences.cpp. References addSequence(), alignedSequences, and consensus. Referenced by getCodons().

void mems::gnAlignedSequences::addSequence (  genome::gnSequence  seqToAdd, std::string  seqName, int  consensusStart, std::string  originalConsensus )  [private]

Adds a sequence to the alignment. Parameters: seqToAdd  the sequence data. seqName  the sequence's name. consensusStart  position in consensus to add sequence. originalConsensus  the alignment's consensus. Definition at line 1466 of file gnAlignedSequences.cpp. References alignedSequences, and sequenceNameInList().

void mems::gnAlignedSequences::addSequence (  genome::gnSequence &  seqToAdd, std::string &  seqName )

Adds a sequence to the alignment. Parameters: seqToAdd  the sequence data. seqName  the sequence's name. Definition at line 1441 of file gnAlignedSequences.cpp. References names, and sequences.

void mems::gnAlignedSequences::addSequence (  std::string &  seqToAdd, std::string &  seqName )

Adds a sequence to the alignment. Parameters: seqToAdd  the sequence data. seqName  the sequence's name. Definition at line 1434 of file gnAlignedSequences.cpp. References names, and sequences. Referenced by addAllSegments(), and addAllSegmentsReplaceGaps().

gnSeqI mems::gnAlignedSequences::alignedSeqsSize (   )  const

Returns the size of each sequence in the alignment (all are identical). Returns: the size of the aligned sequences. Definition at line 705 of file gnAlignedSequences.cpp. References sequences. Referenced by outputClustalW(), mems::simpleFindBackbone(), and mems::simpleFindIslands().

void mems::gnAlignedSequences::assignFileName (  std::string  name  )  [inline]

Assigns a file name to the alignment data for purposes of output. Parameters: name  the name of the file. Definition at line 402 of file gnAlignedSequences.h. References alignedSequenceFileName.

bool mems::gnAlignedSequences::buildConsensus (   )  [private]

Reads all sequences in the alignment and creates a consensus. Returns: true if successful. Definition at line 1377 of file gnAlignedSequences.cpp. References alignedSequences, consensus, and determineBaseIndex(). Referenced by concatenateAlignedSequences(), constructFromClustalW(), constructFromMega(), constructFromMSF(), constructFromNexus(), constructFromPhylip(), extractVariableSites(), getAlignedSegment(), and getCodons().

bool mems::gnAlignedSequences::collapseIdenticalSequences (   )

Collapses the alignment accross all sequences. Sequences are compared in terms of base content - if the sequences of base pairs of equal, the sequences are identical Returns: true if there exist identical sequences that are collapsed. Definition at line 846 of file gnAlignedSequences.cpp. References alignedSequences.

void mems::gnAlignedSequences::concatenateAlignedSequences (  gnAlignedSequences  toConcat  )

Concatenates 2 alignmnets. Parameters: toConcat  the sequence which is appended to *this. Definition at line 750 of file gnAlignedSequences.cpp. References alignedSequences, and buildConsensus().

bool mems::gnAlignedSequences::constructClustalWAlignedSequenceList (  std::ifstream &  alignmentFile  )  [private]

Aids readClustalWAlignment. Parameters: alignmentFile  the file that contains the alignment. Returns: true if successful. Definition at line 1083 of file gnAlignedSequences.cpp. References alignedSequences, and sequenceNameInList(). Referenced by readClustalWAlignment().

void mems::gnAlignedSequences::constructFromClustalW (  std::string  alignedFileName  )

Loads the data held in file alignedFileName (in ClustalW format). Parameters: alignedFileName  name of a file containing an alignment. Definition at line 39 of file gnAlignedSequences.cpp. References alignedSequenceFileName, buildConsensus(), consensus, indexPositions, and readClustalWAlignment().

void mems::gnAlignedSequences::constructFromMega (  std::string  alignedFileName  )

Loads the data held in file alignedFileName (in Mega format). Parameters: alignedFileName  name of a file containing an alignment. Definition at line 100 of file gnAlignedSequences.cpp. References alignedSequenceFileName, buildConsensus(), consensus, indexPositions, and readMegaAlignment().

void mems::gnAlignedSequences::constructFromMSF (  std::string  alignedFileName  )

Loads the data held in file alignedFileName (in MSF format). Parameters: alignedFileName  name of a file containing an alignment. Definition at line 65 of file gnAlignedSequences.cpp. References alignedSequenceFileName, buildConsensus(), consensus, indexPositions, and readMSFAlignment().

void mems::gnAlignedSequences::constructFromNexus (  std::string  alignedFileName  )

Loads the data held in file alignedFileName (in Nexus format). Parameters: alignedFileName  name of a file containing an alignment. Definition at line 87 of file gnAlignedSequences.cpp. References alignedSequenceFileName, buildConsensus(), consensus, indexPositions, and readNexusAlignment().

void mems::gnAlignedSequences::constructFromPhylip (  std::string  alignedFileName  )

Loads the data held in file alignedFileName (in Phylip format). Parameters: alignedFileName  name of a file containing an alignment. Definition at line 52 of file gnAlignedSequences.cpp. References alignedSequenceFileName, buildConsensus(), consensus, indexPositions, and readPhylipAlignment().

void mems::gnAlignedSequences::constructFromRelaxedNexus (  std::istream &  align_stream  )

Reads a single sequence entry in relaxed NEXUS format. Assumes that the #NEXUS has already been read off. Parameters: align_stream  The stream to read data from Definition at line 78 of file gnAlignedSequences.cpp. References readRelaxedNexusAlignment().

bool mems::gnAlignedSequences::constructMegaAlignedSequenceList (  std::ifstream &  alignmentFile  )  [private]

Aids readMegaAlignment. Parameters: alignmentFile  the file that contains the alignment. Returns: true if successful. Definition at line 1289 of file gnAlignedSequences.cpp. References alignedSequences, and sequenceNameInList(). Referenced by readMegaAlignment().

bool mems::gnAlignedSequences::constructMSFAlignedSequenceList (  std::ifstream &  alignmentFile  )  [private]

Aids readMSFAlignment. Parameters: alignmentFile  the file that contains the alignment. Returns: true if successful. Definition at line 1189 of file gnAlignedSequences.cpp. References alignedSequences, coordinates(), and sequenceNameInList(). Referenced by readMSFAlignment().

bool mems::gnAlignedSequences::constructNexusAlignedSequenceList (  std::ifstream &  alignmentFile  )  [private]

Aids readNexusAlignment. Parameters: alignmentFile  the file that contains the alignment. Returns: true if successful. Definition at line 1240 of file gnAlignedSequences.cpp. References alignedSequences, and sequenceNameInList(). Referenced by readNexusAlignment().

bool mems::gnAlignedSequences::constructPhylipAlignedSequenceList (  std::ifstream &  alignmentFile  )  [private]

Aids readPhylipAlignment. Parameters: alignmentFile  the file that contains the alignment. Returns: true if successful. Definition at line 1132 of file gnAlignedSequences.cpp. References alignedSequences. Referenced by readPhylipAlignment().

bool mems::gnAlignedSequences::coordinates (  std::string  line  )  [private]

Searches given line for coordinates. Parameters: line  line to search. Returns: true if coordinates. Definition at line 1554 of file gnAlignedSequences.cpp. Referenced by constructMSFAlignedSequenceList().

int mems::gnAlignedSequences::determineBaseIndex (  char  base  )  [private]

Computes an index for a given base (0-25: a-z). Parameters: base  base to be converted. Returns: an index. Definition at line 1544 of file gnAlignedSequences.cpp. Referenced by buildConsensus().

void mems::gnAlignedSequences::extractVariableSites (  gnAlignedSequences &  variableSites, bool  countGapsAsMismatches )

Extracts the variable sites from *this. Parameters: variableSites  the alignment consisting of all variable sites. countGapsAsMismatches  true if gaps are to be considered mismatches. Definition at line 783 of file gnAlignedSequences.cpp. References addAllSegments(), alignedSequences, buildConsensus(), and indexPositions.

gnAlignedSequences mems::gnAlignedSequences::getAlignedSegment (  unsigned  start, unsigned  stop )

Create a new alignment that is comprised of all of the segments in the initial alignment from start to stop (inclusive) if stop == 0, the alignment ends at the end. Parameters: start  the beginning point of the segment. stop  the end point of the segment. Returns: the new gnAlignedSequences that is created Definition at line 680 of file gnAlignedSequences.cpp. References addAllSegments(), and buildConsensus().

std::string mems::gnAlignedSequences::getAlignedSequenceFileName (   )  [inline]

Returns the name of the file associated with this gnAlignedSequences. Returns: the alignment file name. Definition at line 405 of file gnAlignedSequences.h. References alignedSequenceFileName.

gnAlignedSequences mems::gnAlignedSequences::getCodons (  int  readingFrame, int  startCodon, int  codonMultiple )

Extracts every codonMultiple-th codon in the reading frame readingFrame beginning with startCodon reading frames supported: 1, 2 & 3 (no reverse complementing). Parameters: readingFrame  the codon reading frame. startCodon  the number codon in readingFrame with which to begin. codonMultiple  the multiple with which codons in readingFrame are selected. Returns: the new gnAlignedSequences that is created Definition at line 691 of file gnAlignedSequences.cpp. References addAllSegmentsReplaceGaps(), alignedSequences, and buildConsensus().

const vector< string > & mems::gnAlignedSequences::getSupportedFormats (   )  [static]

Returns a vector of supported format names. Definition at line 112 of file gnAlignedSequences.cpp. Referenced by isSupportedFormat().

boolean mems::gnAlignedSequences::isSupportedFormat (  const std::string &  format_name  )  [static]

Checks whether a particular format name is supported. Definition at line 126 of file gnAlignedSequences.cpp. References getSupportedFormats().

vector< char > mems::gnAlignedSequences::operator[] (  const int  offset  )

Accesses the alignment and returns the bases at that position in all sequences. Parameters: offset  the position in the alignment to access. Returns: a vector of characters at position offset. Definition at line 871 of file gnAlignedSequences.cpp. References alignedSequences.

void mems::gnAlignedSequences::output (  const std::string &  format_name, std::ostream &  os )  const

Writes out this sequence alignment in the specified format, assuming the format is supported. Definition at line 135 of file gnAlignedSequences.cpp. References outputClustalW(), outputCodon(), outputMega(), outputMSF(), outputNexus(), and outputPhylip().

bool mems::gnAlignedSequences::outputClustalW (  std::ostream &  os  )  const

Writes alignment using the given output stream (in ClustalW format). Parameters: os  the output stream. Returns: true if successful. Definition at line 205 of file gnAlignedSequences.cpp. References alignedSeqsSize(), mems::countGaps(), names, positions, sequences, and uint. Referenced by output().

bool mems::gnAlignedSequences::outputCodon (  std::ostream &  os  )  const

Writes alignment in 3-base, codon segments using the given output stream (in Phylip format). Parameters: os  the output stream. Returns: true if successful. Definition at line 554 of file gnAlignedSequences.cpp. References alignedSequences. Referenced by output().

bool mems::gnAlignedSequences::outputMega (  std::ostream &  os  )  const

Writes alignment using the given output stream (in Mega format). Parameters: os  the output stream. Returns: true if successful. Definition at line 512 of file gnAlignedSequences.cpp. References alignedSequences, and mems::MEGA_ALIGN_COLUMNS. Referenced by output().

bool mems::gnAlignedSequences::outputMSF (  std::ostream &  os  )  const

Writes alignment using the given output stream (in MSF format). Parameters: os  the output stream. Returns: true if successful. Definition at line 267 of file gnAlignedSequences.cpp. References alignedSequences. Referenced by output().

bool mems::gnAlignedSequences::outputNexus (  std::ostream &  os  )  const

Writes alignment using the given output stream (in Nexus format). Parameters: os  the output stream. Returns: true if successful. Definition at line 351 of file gnAlignedSequences.cpp. References alignedSequences, names, names, and sequences. Referenced by output().

bool mems::gnAlignedSequences::outputPhylip (  std::ostream &  os  )  const

Writes alignment using the given output stream (in Phylip format). Parameters: os  the output stream. Returns: true if successful. Definition at line 162 of file gnAlignedSequences.cpp. References names, sequences, and uint. Referenced by output().

bool mems::gnAlignedSequences::outputWithConsensus (  std::ostream &  os  )

Writes alignment with consensus using the given output stream (in Phylip format). Parameters: os  the output stream. Returns: true if successful. Definition at line 606 of file gnAlignedSequences.cpp. References alignedSequences, and consensus.

bool mems::gnAlignedSequences::readClustalWAlignment (   )  [private]

Aids constructFromClustalW. Returns: true if successful. Definition at line 883 of file gnAlignedSequences.cpp. References alignedSequenceFileName, and constructClustalWAlignedSequenceList(). Referenced by constructFromClustalW().

bool mems::gnAlignedSequences::readMegaAlignment (   )  [private]

Aids constructFromMega. Returns: true if successful. Definition at line 1053 of file gnAlignedSequences.cpp. References alignedSequenceFileName, and constructMegaAlignedSequenceList(). Referenced by constructFromMega().

bool mems::gnAlignedSequences::readMSFAlignment (   )  [private]

Aids constructFromMSF. Returns: true if successful. Definition at line 943 of file gnAlignedSequences.cpp. References alignedSequenceFileName, and constructMSFAlignedSequenceList(). Referenced by constructFromMSF().

bool mems::gnAlignedSequences::readNexusAlignment (   )  [private]

Aids constructFromNexus. Returns: true if successful. Definition at line 1022 of file gnAlignedSequences.cpp. References alignedSequenceFileName, and constructNexusAlignedSequenceList(). Referenced by constructFromNexus().

bool mems::gnAlignedSequences::readPhylipAlignment (   )  [private]

Aids constructFromPhylip. Returns: true if successful. Definition at line 914 of file gnAlignedSequences.cpp. References alignedSequenceFileName, and constructPhylipAlignedSequenceList(). Referenced by constructFromPhylip().

bool mems::gnAlignedSequences::readRelaxedNexusAlignment (  std::istream &  align_stream  )  [private]

This function assumes that the #NEXUS at the beginning of the file has been read off already. Returns: true if successful. Definition at line 978 of file gnAlignedSequences.cpp. References names, sequences, and uint. Referenced by constructFromRelaxedNexus().

bool mems::gnAlignedSequences::removeAlignedSeq (  unsigned  index  )

Removes a single sequence from the alignment. Parameters: index  the position in the of the sequence to be removed. Returns: true if successful (a sequence at index exists). Definition at line 730 of file gnAlignedSequences.cpp. References alignedSequences.

bool mems::gnAlignedSequences::removeAlignedSeq (  std::string  seqName  )

Removes a single sequence from the alignment. Parameters: seqName  the name of the sequence to remove. Returns: true if successful (a sequence called seqName exists). Definition at line 713 of file gnAlignedSequences.cpp. References alignedSequences.

void mems::gnAlignedSequences::removeAllSegments (  unsigned  start, unsigned  stop )  [private]

Removes all segments across all sequences in *this. Parameters: start  segment start point. stop  segment stop point. Definition at line 1529 of file gnAlignedSequences.cpp. References alignedSequences.

void mems::gnAlignedSequences::seq (  uint  seqI  )

int mems::gnAlignedSequences::sequenceNameInList (  std::string &  sequenceName  )  [private]

Determines whether a sequence of the given name is present in the list. Parameters: sequenceName  the name to be found. Returns: the index in the list or -1 if not present Definition at line 1357 of file gnAlignedSequences.cpp. References names, and uint.

bool mems::gnAlignedSequences::sequenceNameInList (  std::string  sequenceName, std::list< std::pair< std::string *, std::string * > >::iterator &  sequenceItr )  [private]

Determines whether a sequence of the given name is present in the list.. Parameters: sequenceName  the name to be found. sequenceItr  the list iterator to be employed. Returns: true if sequenceName is present. Definition at line 1365 of file gnAlignedSequences.cpp. References alignedSequences. Referenced by addSequence(), constructClustalWAlignedSequenceList(), constructMegaAlignedSequenceList(), constructMSFAlignedSequenceList(), and constructNexusAlignedSequenceList().

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Member Data Documentation

std::string mems::gnAlignedSequences::alignedSequenceFileName [private]

Definition at line 390 of file gnAlignedSequences.h. Referenced by assignFileName(), constructFromClustalW(), constructFromMega(), constructFromMSF(), constructFromNexus(), constructFromPhylip(), getAlignedSequenceFileName(), gnAlignedSequences(), readClustalWAlignment(), readMegaAlignment(), readMSFAlignment(), readNexusAlignment(), and readPhylipAlignment().

std::list<std::pair <std::string*, std::string*> > mems::gnAlignedSequences::alignedSequences

Definition at line 254 of file gnAlignedSequences.h. Referenced by addAllSegmentsReplaceGaps(), addSequence(), buildConsensus(), collapseIdenticalSequences(), concatenateAlignedSequences(), constructClustalWAlignedSequenceList(), constructMegaAlignedSequenceList(), constructMSFAlignedSequenceList(), constructNexusAlignedSequenceList(), constructPhylipAlignedSequenceList(), extractVariableSites(), getCodons(), operator[](), outputCodon(), outputMega(), outputMSF(), outputNexus(), outputWithConsensus(), removeAlignedSeq(), removeAllSegments(), and sequenceNameInList().

std::string mems::gnAlignedSequences::consensus [private]

Definition at line 392 of file gnAlignedSequences.h. Referenced by addAllSegmentsReplaceGaps(), buildConsensus(), constructFromClustalW(), constructFromMega(), constructFromMSF(), constructFromNexus(), constructFromPhylip(), gnAlignedSequences(), and outputWithConsensus().

std::vector<int> mems::gnAlignedSequences::indexPositions [private]

Definition at line 393 of file gnAlignedSequences.h. Referenced by constructFromClustalW(), constructFromMega(), constructFromMSF(), constructFromNexus(), constructFromPhylip(), and extractVariableSites().

std::vector< std::string > mems::gnAlignedSequences::names

Definition at line 256 of file gnAlignedSequences.h. Referenced by addAllSegments(), addSequence(), mems::GenericInterval< GappedBaseImpl >::GetAlignedSequences(), gnAlignedSequences(), outputClustalW(), outputNexus(), outputPhylip(), readRelaxedNexusAlignment(), and sequenceNameInList().

std::vector< int64 > mems::gnAlignedSequences::positions

If this is part of a larger alignment this vector stores start positions within that alignment. Definition at line 257 of file gnAlignedSequences.h. Referenced by mems::GenericInterval< GappedBaseImpl >::GetAlignedSequences(), gnAlignedSequences(), and outputClustalW().

std::vector< std::string > mems::gnAlignedSequences::sequences

Definition at line 255 of file gnAlignedSequences.h. Referenced by addAllSegments(), addSequence(), alignedSeqsSize(), mems::GenericInterval< GappedBaseImpl >::GetAlignedSequences(), gnAlignedSequences(), outputClustalW(), outputNexus(), outputPhylip(), readRelaxedNexusAlignment(), mems::simpleFindBackbone(), and mems::simpleFindIslands().

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

• libMems/gnAlignedSequences.h
• libMems/gnAlignedSequences.cpp

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