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Version 4.1.5 |
#include <seqpp/PrimarySequence.h>
Inheritance diagram for PrimarySequence:
Public Member Functions | |
virtual | ~PrimarySequence ()=0 |
Destructor. | |
const Translator & | ref_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 |
Note that a Primarysequence is associated with a Translator object.
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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin |