aa33715685
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
54 lines
2.6 KiB
C++
54 lines
2.6 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 PATTERNS_H
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#define PATTERNS_H
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#include <Sequences.h>
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#include <vector>
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#include <string>
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class Patterns
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{
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private:
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int num_patterns;
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double freqs[4];
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std::vector<unsigned char*> pattern;
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std::vector<int> pattern_count;
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Sequences &seqs;
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public:
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// return a pattern content
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Patterns(Sequences &S);
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~Patterns();
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unsigned char* operator[](int n) const { return pattern[n]; }
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inline int count(int n) const { return pattern_count[n]; }
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inline int count() const { return num_patterns; }
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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 pattern_name(int i) const { return seqs.seqname(i); }
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inline int search_taxon_name(std::string &s) const { return seqs.search_taxon_name(s); }
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inline bool is_ambiguous(short int l) const { return seqs.is_ambiguous(l); }
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inline bool is_gap(short int l) const { return seqs.is_gap(l); }
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inline bool is_undefined(short int l) const { return seqs.is_undefined(l); }
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inline unsigned char* ambiguos_meaning(short int l) const { return seqs.ambiguos_meaning(l); }
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void calculate_frequences();
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int num_sequences();
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};
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#endif
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