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seq::NTSequence Class Reference

A nucleotide sequence. More...

#include <NTSequence.h>

List of all members.

Public Member Functions

 NTSequence ()
 Create an empty nucleotide sequence with emtpy name and empty description.
 NTSequence (unsigned size)
 Create a nucleotide sequence of length size, filled with Nucleotide::N, with empty name and emtpy description.
 NTSequence (const std::string name, const std::string description, const std::string aSeqString, bool sampleAmbiguities=false) throw (ParseException)
 Create a nucleotide sequence with given name and description, and with the given sequence string.
 NTSequence (const const_iterator first, const const_iterator last)
 Create a nucleotide sequence with empty name and emtpy description, and copy the sequence data from the range [first, last[.
void sampleAmbiguities ()
 Remove ambiguity nucleotide symbols by replacing them by sampling a random non-ambiguous nucleotide that is represented by the ambiguity symbol.
void nonAmbiguousSequences (std::vector< NTSequence > &result) const
 Add all the possible non-ambiguous sequences possibly represented by this sequence to result.
std::string asString () const
 Represent the sequence data as a string.
std::string name () const
 Get the name.
std::string description () const
 Get the description.
void setName (std::string name)
 Set the name.
void setDescription (std::string description)
 Set the description.


Detailed Description

A nucleotide sequence.

The sequence may have a name and a description.

The sequence data is stored by publicly inheriting std::vector<Nucleotide>, so you can use all std::vector manipulations to access the nucleotide data.


Constructor & Destructor Documentation

seq::NTSequence::NTSequence  ) 
 

Create an empty nucleotide sequence with emtpy name and empty description.

seq::NTSequence::NTSequence unsigned  size  ) 
 

Create a nucleotide sequence of length size, filled with Nucleotide::N, with empty name and emtpy description.

seq::NTSequence::NTSequence const std::string  name,
const std::string  description,
const std::string  aSeqString,
bool  sampleAmbiguities = false
throw (ParseException)
 

Create a nucleotide sequence with given name and description, and with the given sequence string.

Each character in the sequence string will be interpreted as a Nucleotide using the Nucleotide::Nucleotide(char) constructor.

If sampleAmbiguities = true, then sampleAmbiguities() is performed during construction.

See also:
sampleAmbiguities()

seq::NTSequence::NTSequence const const_iterator  first,
const const_iterator  last
 

Create a nucleotide sequence with empty name and emtpy description, and copy the sequence data from the range [first, last[.


Member Function Documentation

std::string seq::NTSequence::asString  )  const
 

Represent the sequence data as a string.

std::string seq::NTSequence::description  )  const [inline]
 

Get the description.

std::string seq::NTSequence::name  )  const [inline]
 

Get the name.

void seq::NTSequence::nonAmbiguousSequences std::vector< NTSequence > &  result  )  const
 

Add all the possible non-ambiguous sequences possibly represented by this sequence to result.

void seq::NTSequence::sampleAmbiguities  ) 
 

Remove ambiguity nucleotide symbols by replacing them by sampling a random non-ambiguous nucleotide that is represented by the ambiguity symbol.

See also:
Nucleotide::sampleAmbiguity()

void seq::NTSequence::setDescription std::string  description  )  [inline]
 

Set the description.

void seq::NTSequence::setName std::string  name  )  [inline]
 

Set the name.


The documentation for this class was generated from the following file:
Generated on Fri Jul 14 15:30:43 2006 for libseq by  doxygen 1.4.4