aa33715685
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
89 lines
3.7 KiB
C++
89 lines
3.7 KiB
C++
/***************************************************************************
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* Copyright (C) 2005 by Waldo Cancino *
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* wcancino@icmc.usp.br *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#ifndef SEQUENCES_H
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#define SEQUENCES_H
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#include <vector>
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#include <string>
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#include <iostream>
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#include <fstream>
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#include <cstring>
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// class to store the sequences in a file
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struct PatternInfo
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{
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int idx;
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int count;
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};
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class Sequences
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{
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private:
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//enum nucleotides = { A, C, G, T};
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unsigned int num_patterns;
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unsigned int num_inf_sites;
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unsigned int numseqs;
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unsigned int seqlen;
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unsigned char *seqs;
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std::vector<std::string> seqnames;
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std::vector<struct PatternInfo> patterns;
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std::vector<unsigned int> inf_sites;
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unsigned char meaning[12][5];
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double freqs[4];
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bool is_informative(unsigned int col) const;
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public:
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inline unsigned char* operator[](int n) const { return &(seqs[n*seqlen]); }
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Sequences(const char *filename);
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~Sequences() {
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delete [] seqs;
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}
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inline unsigned char seq_pos( int i, int j) const { return (*this)[i][j]; }
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inline unsigned char pattern_pos(int i, int j) const
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{ return seq_pos( j, patterns[i].idx); }
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inline unsigned char infsite_pos(int i, int j) const
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{ return pattern_pos( inf_sites[i], j); }
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std::string position(int i);
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inline int num_seqs() const { return numseqs; }
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inline int seq_len() const { return seqlen; }
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inline int pattern_count() const { return num_patterns; }
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inline int pattern_count(int i) const { return patterns[i].count; }
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inline int infsite_count() const { return num_inf_sites; }
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inline int infsite_count(int i) const { return patterns[inf_sites[i]].count; }
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inline double *frequences() { return freqs; }
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inline double frequence(int i) const { return freqs[i]; }
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inline std::string seqname(int i) const { return seqnames.at(i); }
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inline bool is_defined(short int l) const { return l<4; }
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inline bool is_ambiguous(short int l) const { return (l>3 && l<14); }
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inline bool is_gap(short int l) const { return (l == 14); }
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inline bool is_undefined(short int l) const { return (l ==15); }
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inline std::vector<struct PatternInfo>& get_patterns() { return patterns; }
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inline unsigned char* ambiguos_meaning(short int l) const { return
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(unsigned char*) meaning[l-4]; }
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void list_taxons() const;
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int search_taxon_name(std::string &s) const;
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void calculate_patterns();
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void calculate_frequences();
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void save_seq_data(std::ostream &of);
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};
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#endif
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