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SequenceSet.h

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00001 /* seqpp/SequenceSet.h
00002  *
00003  * Copyright (C) 2003 Laboratoire Statistique & Génome
00004  *
00005  * This program is free software; you can redistribute it and/or modify
00006  * it under the terms of the GNU General Public License as published by
00007  * the Free Software Foundation; either version 2 of the License, or (at
00008  * your option) any later version.
00009  *
00010  * This program is distributed in the hope that it will be useful, but
00011  * WITHOUT ANY WARRANTY; without even the implied warranty of
00012  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
00013  * General Public License for more details.
00014  *
00015  * You should have received a copy of the GNU General Public License
00016  * along with this program; if not, write to the Free Software
00017  * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
00018  */
00028 #ifndef SEQPP_SEQUENCESET_H
00029 #define SEQPP_SEQUENCESET_H
00030 
00031 #include <seqpp/PrimarySequenceSet.h>
00032 #include <iomanip>
00043 class SequenceSet : public PrimarySequenceSet<Sequence>, public PrimaryCount
00044 {
00045   private :
00046 
00048    int _tmp_nb_seqmax;
00049 
00051    int read_fasta( ifstream & f,  const string & name_file ="noname");
00053    int read_genbank( ifstream & f, const string & name_file ="noname" );
00054 
00056    virtual unsigned long tell_max_count() const{
00057      return _total_length;
00058    }
00059    virtual void compute_count( unsigned long * * extern_count, 
00060                                short phase,
00061                                short initial_phase,
00062                                unsigned long beg,
00063                                unsigned long end ) const;
00064 
00065    public :
00066      
00068 
00074      SequenceSet ( const string & seq_list_file,
00075                    const string & alpha_file, 
00076                    short order,
00077                    int nbseq = BUFFERSEQ );
00078      
00080 
00088      SequenceSet ( const string & seq_list_file, 
00089                     short mode, 
00090                     const string & line2parse,
00091                     bool case_sensitivity,
00092                     short order,
00093                     int nbseq = BUFFERSEQ ); 
00094 
00095      // copy constructor 
00096      //SequenceSet( const SequenceSet & set );
00097      
00098      // destructor
00099      virtual ~SequenceSet() {};  
00100 }; 
00101 #endif // SEQPP_SEQUENCESET_H



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