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PrimarySequenceSet< TSequence > Class Template Reference

Class corresponding to a generic sequence set. More...

#include <seqpp/PrimarySequenceSet.h>

List of all members.

Public Member Functions

 PrimarySequenceSet ()
 default constructor
virtual ~PrimarySequenceSet ()
 destructor
const Translatorget_translator () const
 allows a const access to the alphabet via a reference
short tell_alphabet_size () const
 returns the alphabet size
short tell_nb_inv () const
 returns the nber of invalid codes
TSequence & get_sequence (int i) const
 allows a const access to ith sequence via a reference
TSequence & operator() (int i) const
 allows a const access to ith sequence via a reference
int tell_nb_sequence () const
 returns the number of sequences
virtual unsigned long tell_length () const
 returns the total length
unsigned long tell_length_max () const
 returns the length max
unsigned long tell_length_seq (int i) const
 returns the length of sequence i
string tell_seq_name (int i) const
 gives the name oh the ith file
string tell_file_name (int i) const
 gives the name oh the ith file
void weight_matrix (double **wmat) const
 compute the weight matrix associated to the sequences wmat[token][position in the sequence]

Protected Attributes

const Translator_transl
 Associated alphabet.
short _nmodal
 number of possible observable value
int _nb_seq
 Number of sequences in the array.
unsigned long _total_length
 Total length.
unsigned long _length_max
 Maximum length of a sequence.
TSequence ** _array_seq
 Array of sequences.


Detailed Description

template<class TSequence>
class PrimarySequenceSet< TSequence >

Class corresponding to a generic sequence set.


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



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