source: trunk/test/alignment.cc @ 2817

// $Id: alignment.cc 2817 2012-08-29 00:38:17Z peter $

/*
  Copyright (C) 2005 Jari Häkkinen, Peter Johansson
  Copyright (C) 2006 Jari Häkkinen
  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
  Copyright (C) 2012 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include "Suite.h"

#include "yat/utility/Aligner.h"
#include "yat/utility/Alignment.h"

#include "yat/utility/Matrix.h"

#include <gsl/gsl_cdf.h>

#include <cassert>
#include <cmath>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>

using namespace theplu::yat;

void read_vector(std::vector<double>& v,std::string& str)
{
  std::istringstream s(str);
  while (!s.eof()) {
    double d;
    s >> d;
    if (!s.fail())
      v.push_back(d);
  }
}

std::istream& operator>>(std::istream& s,
                         std::vector<std::vector<double> >& m)
{
  while (!s.eof()) {
    std::string row;
    char ch;
    while (((ch=s.get())!='\n') && s.good())
      row+=ch;
    if (row.size() || s.good()) { // if stream good, read an empty peak set
      std::vector<double> v;
      read_vector(v,row);
      m.push_back(v);
    }
  }
  return s;
}

double match(const double x, const double y, const double s)
{ 
  return 2*gsl_cdf_gaussian_Q(std::abs(x-y),sqrt(2)*s); 
}
  

double score(const std::vector<double>& l1,
             const std::vector<double>& l2,
             const double sigma, 
             theplu::yat::utility::Matrix& dot_matrix,
             std::vector<std::pair<size_t,size_t> >& path)
{
  dot_matrix.resize(l1.size(),l2.size());
  for (size_t i=0; i<l1.size(); i++) 
    for (size_t j=0; j<l2.size(); j++) {
      assert(i<dot_matrix.rows());
      assert(j<dot_matrix.columns());
      dot_matrix(i,j)=match(l1[i],l2[j],sigma);
    }
  return theplu::yat::utility::NeedlemanWunsch(dot_matrix,path,0);
}


int main(int argc, char* argv[])
{
  test::Suite suite(argc, argv);

  std::ifstream s(test::filename("data/isoform.peaks").c_str());
  std::vector<std::vector<double> > peaksets;
  s >> peaksets;

  for (size_t i=0; i<peaksets.size()-1; i++) 
    for (size_t j=i+1; j<peaksets.size(); j++) {
      utility::Matrix dot_m;
      std::vector<std::pair<size_t,size_t> > path;
      score(peaksets[i], peaksets[j], 1.0, dot_m, path);
    }

  std::string a("AGGUUGUCCGUGGUGAGUUCGCA");
  std::string b("GAGGUUGUCCGUGGUGAGUUCG");
  utility::Matrix m(a.size(), b.size());
  for (size_t j=0; j<a.size(); ++j)
    for (size_t k=0; k<b.size(); ++k)
      m(j,k) = (a[j]==b[k] ? 1 : -1000);
  double score = utility::Aligner(100, 100).smith_waterman(m);
  if (score!=21)
    suite.add(false);

  // testing ssearch
  if (utility::ssearch("Hello", "Hll", 0.0, 1.0)!=2){
    suite.err() << "aligning 'Hello' and 'Hll' gives score " 
                << utility::ssearch("Hello", "Hll", 0.0, 1.0)
                << " expected " << 2 << std::endl;
    suite.add(false);
  }
  if (utility::ssearch("Hello", "Peter said you can't say 'allo", 1, 1)!=3)
    suite.add(false);

  return suite.return_value();
}