First commit of PhyloMOEO files with some additions to Paradiseo-MOEO
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
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wcancino
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contribution/branches/PhyloMOEA/PhyloMOEA/Sequences.cpp
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276
contribution/branches/PhyloMOEA/PhyloMOEA/Sequences.cpp
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/***************************************************************************
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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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#include <Sequences.h>
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#include <iostream>
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#include <fstream>
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#include <map>
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#include "assert.h"
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#include <ExceptionManager.h>
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void Sequences::list_taxons() const {
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std::cout << "lista de taxons" << std::endl;
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for(int i=0; i< seqnames.size(); i++)
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std::cout << seqnames[i] << std::endl;
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}
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using namespace std;
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Sequences::Sequences(const char *fn)
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{
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numseqs = 0;
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seqlen = 0;
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seqs = NULL;
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fstream fin;
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string tmpseq;
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// ambiguos characters
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meaning[0][0] = meaning[0][1] = 1; meaning[0][2] = meaning[0][3] = meaning[0][4] = 0; // M
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meaning[1][0] = meaning[1][2] = 1; meaning[1][1] = meaning[1][3] = meaning[1][4] = 0; // R
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meaning[2][0] = meaning[2][3] = 1; meaning[2][1] = meaning[2][2] = meaning[2][4] = 0; // W
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meaning[3][1] = meaning[3][2] = 1; meaning[3][0] = meaning[3][3] = meaning[3][4] = 0; // S
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meaning[4][1] = meaning[4][3] = 1; meaning[4][0] = meaning[4][2] = meaning[4][4] = 0; // Y
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meaning[5][2] = meaning[5][3] = 1; meaning[5][0] = meaning[5][1] = meaning[5][4] = 0; // K
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meaning[6][0] = meaning[6][1] = meaning[6][2] = 1 ; meaning[6][3] = meaning[6][4] = 0; // V
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meaning[7][0] = meaning[7][1] = meaning[7][3] = 1 ; meaning[7][2] = meaning[7][4] = 0; // H
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meaning[8][0] = meaning[8][2] = meaning[8][3] = 1 ; meaning[8][1] = meaning[8][4] = 0; // D
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meaning[9][1] = meaning[9][2] = meaning[9][3] = 1 ; meaning[9][0] = meaning[9][4] = 0; // B
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meaning[10][1] = meaning[10][2] = meaning[10][3] = meaning[10][0] = 0; meaning[10][4] = 1; // gap
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meaning[11][1] = meaning[11][2] = meaning[11][3] = meaning[11][0] = 1; meaning[11][4] = 0; // undefined
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// open the file for reading
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try{
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fin.open(fn, ios::in);
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if(!fin.is_open())
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{
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cout << "\n" << fn << endl;
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throw ExceptionManager(10);
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}
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// read numseq and seqlen
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if(!(fin >> numseqs >> seqlen))
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{
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throw ExceptionManager(11);
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}
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seqs = new unsigned char[numseqs*seqlen];
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seqnames.resize(numseqs);
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for(int i=0; i < numseqs; i++)
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{
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fin >> seqnames[i];
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fin >> tmpseq;
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for(int j=0; j<seqlen; j++)
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{
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switch(toupper(tmpseq[j]))
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{
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case 'A': seqs[i*seqlen+j] = 0; break;
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case 'C': seqs[i*seqlen+j] = 1; break;
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case 'G': seqs[i*seqlen+j] = 2; break;
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case 'T': seqs[i*seqlen+j] = 3; break;
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case 'M': seqs[i*seqlen+j] = 4; break;
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case 'R': seqs[i*seqlen+j] = 5; break;
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case 'W': seqs[i*seqlen+j] = 6; break;
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case 'S': seqs[i*seqlen+j] = 7; break;
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case 'Y': seqs[i*seqlen+j] = 8; break;
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case 'K': seqs[i*seqlen+j] = 9; break;
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case 'V': seqs[i*seqlen+j] = 10; break;
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case 'H': seqs[i*seqlen+j] = 11; break;
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case 'D': seqs[i*seqlen+j] = 12; break;
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case 'B': seqs[i*seqlen+j] = 13; break;
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case '-': seqs[i*seqlen+j] = 14; break; // gap character
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case '?':
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case 'X':
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case 'N' :
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case 'O' : seqs[i*seqlen+j] = 15; break; // undefined character
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default :
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{
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cout << "invalid character:" << tmpseq[j] << " seq:" << seqnames[i] << " column " << j << endl;
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throw ExceptionManager(11);
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assert(1==0); break; // invalid character
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}
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}
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}
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}
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}
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catch( ExceptionManager e)
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{
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e.Report();
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}
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fin.close();
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}
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int Sequences::search_taxon_name(std::string &s) const
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{
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int i;
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for(i=numseqs-1; i>=0 && seqnames[i].substr(0,10)!=s; i--);
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return i;
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}
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// return true is the site is informative
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bool Sequences::is_informative(unsigned int col) const
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{
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unsigned char temp[16];
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int sum = 0;
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memset( temp, 0, 16*sizeof(unsigned char));
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for(int j=0; j< numseqs; j++)
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{
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// check if the site is repeated
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unsigned char l = (*this)[j][col]; //SeqData->pattern_pos(i,j);
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if( temp[l] == 0)
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{
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temp[l] = 1; sum++;
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}
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}
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// informative sites have at least two differents chars
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return(sum > 1);
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}
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void Sequences::calculate_patterns()
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{
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// map pattern and index in the vector pattern
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num_patterns=num_inf_sites=0;
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map<string, int> pattern_map;
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struct PatternInfo p;
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string s;
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for(int i=0; i< seqlen; i++)
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{
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s = position(i);
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//if(s.find('?',0)== string::npos)cout << i << endl;
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// new pattern
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if( pattern_map.find(s) == pattern_map.end() )
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{
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pattern_map[s] = num_patterns;
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p.idx = i;
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p.count = 1;
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patterns.push_back(p);
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// calculate informative site
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if( is_informative(i) )
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{
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inf_sites.push_back(num_patterns);
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num_inf_sites++;
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}
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num_patterns++;
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}
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// old pattern
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else
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patterns[ pattern_map[s] ].count++;
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}
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//cout << "Padrones reconhecidos:" << num_patterns << endl;
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//cout << "Sites informativos :" << num_inf_sites << endl;
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}
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void Sequences::calculate_frequences()
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{
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long num_undefined = 0; // number of undefined positions
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freqs[0] = freqs[1] = freqs[2] = freqs[3] = 0.25;
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double tmp[4];
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double divisor;
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// i don't know why most program do this
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for(int m=0; m<8; m++)
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{
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tmp[0] = tmp[1] = tmp[2] = tmp[3] = 0;
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for(int i=0; i< num_patterns; i++)
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for(int j=0; j< numseqs; j++)
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{
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unsigned char l = pattern_pos(i,j);
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if ( is_ambiguous(l) )
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{
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divisor = 0;
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for(int k=0; k<4; k++)
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divisor += ambiguos_meaning(l)[k] * freqs[k];
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for(int k=0; k<4; k++)
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tmp[k] +=
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(ambiguos_meaning(l)[k]*freqs[k]/divisor)*
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patterns[i].count;
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}
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else if( is_undefined(l) || is_gap(l) )
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for(int k=0; k<4; k++) tmp[k] += freqs[k]*patterns[i].count;
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else
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tmp[l] += patterns[i].count;
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}
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for(int k=0; k<4; k++) freqs[k] = tmp[k] / (tmp[0]+tmp[1]+tmp[2]+tmp[3]);
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}
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// final frequences
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//for(int i=0; i<4; i++){
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// cout << "frequencia de " << i << " -->:" << freqs[i] << endl;
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//}
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// cout << "suma de frequencias:" << freqs[0] + freqs[1] + freqs[2] + freqs[3] << endl;
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}
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// get the
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string Sequences::position(int pos)
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{
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string column;
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unsigned char c;
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char nucleotide;
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for(int i=0; i < numseqs; i++)
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{
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c = seq_pos(i, pos);
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switch(c)
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{
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case 0: nucleotide = 'A'; break;
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case 1: nucleotide = 'C'; break;
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case 2: nucleotide = 'G'; break;
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case 3: nucleotide = 'T'; break;
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case 4: nucleotide = 'M'; break;
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case 5: nucleotide = 'R'; break;
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case 6: nucleotide = 'W'; break;
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case 7: nucleotide = 'S'; break;
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case 8: nucleotide = 'Y'; break;
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case 9: nucleotide = 'K'; break;
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case 10: nucleotide = 'V'; break;
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case 11: nucleotide = 'H'; break;
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case 12: nucleotide = 'D'; break;
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case 13: nucleotide = 'B'; break;
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case 14: nucleotide = '-'; break;
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case 15: nucleotide = '?'; break;
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default: assert(1==0); break;
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}
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column+=nucleotide;
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}
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return column;
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}
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void Sequences::save_seq_data(ostream &of=cout)
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{
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of << "\nSequence Datafile Statistics\n";
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of << "----------------------------------------------\n";
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of << "Number of Sequences : " << this->numseqs << endl;
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of << "Sequence Length : " << this->seqlen << endl;
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of << "Number of Patterns : " << this->num_patterns << endl;
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of << "Frequency A : " << this->freqs[0] << endl;
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of << "Frequency C : " << this->freqs[1] << endl;
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of << "Frequency G : " << this->freqs[2] << endl;
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of << "Frequency T : " << this->freqs[3] << endl;
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}
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