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Version 4.2.0 |
#include <seqpp/PrimarySequence.h>
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 |
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