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PrimarySequence Class Reference

Virtual class corresponding to a generic sequence. More...

#include <seqpp/PrimarySequence.h>

Inheritance diagram for PrimarySequence:

Sequence List of all members.

Public Member Functions

virtual ~PrimarySequence ()=0
 Destructor.
const Translatorref_translator () const
 allows a const access to the alphabet
short tell_alphabet_size () const
 returns the alphabet size
short tell_nb_inv () const
 returns the nber of invalid codes in alphabet
virtual unsigned long tell_length () const
 returns the length
string tell_seq_name () const
 return the sequence name
string tell_file_name () const
 return the file name
void set_pos (unsigned long t)
 sets the current position
unsigned long tell_pos ()
 returns the current position
virtual short tell_int (unsigned long pos) const =0
 returns the int value of the single letter on position pos
short tell_int ()
 Return the code on current position.
short tell_int_compl (unsigned long pos) const
 Returns the complementary code on position i.
short tell_int_compl () const
 Returns the complementary code on position i.
string tell_pattern (unsigned long pos) const
 returns the pattern for a position
string tell_pattern_compl (unsigned long pos)
 returns complementary pattern on position pos
string tell_patterns (unsigned long beg, unsigned long stop) const
 returns the patterns between position beg and stop
string tell_label (unsigned long pos) const
 return the label(if defined in the alphabet) for a position
string tell_labels (unsigned long beg, unsigned long stop) const
 returns the label(if defined in the alphabet)-sequence between position beg and stop
const string strseq () const
 returns the sequence as a string
void print (const string &file, ios_base::openmode mode=ios::out) const
 print the sequence to file in fasta format

Protected Attributes

const Translator_transl
 a Translator alphabet pointer
short _sizecode
 the number of char for a letter of the alphabet (alphabet mode)
short _nmodal
 number of possible observable value
long * _obs
 Vector of the observed datas.
unsigned long _length
 length of the sequence
unsigned long _ipos
 current position
string _name
 name of the sequence
string _name_file
 name of the file

Detailed Description

Virtual class corresponding to a generic sequence.

Note that a Primarysequence is associated with a Translator object.


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



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Generated on Thu Aug 4 18:34:05 2005 for seqpp by doxygen 1.3.9.1