source: trunk/yat/microarray/DataSet.cc @ 720

// $Id: DataSet.cc 720 2006-12-26 18:21:36Z jari $

/*
  Copyright (C) The authors contributing to this file.

  This file is part of the yat library, http://lev.thep.lu.se/trac/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 2 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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
  02111-1307, USA.
*/

#include "DataSet.h"

#include <set>

namespace theplu {
namespace yat {
namespace microarray {

  DataSet::DataSet(const classifier::MatrixLookup& data, 
                   const classifier::Target& target,
                   const std::vector<std::string>& probe)
    : data_(data), probe_(probe), target_(target)
  {
  }

  
  DataSet::DataSet(const DataSet& first, 
                   const std::vector<std::string>& probes)
    : data_(classifier::MatrixLookup(0,0)), target_(first.target())
  {
    using std::vector;
    using std::string;
    std::set<std::string> probe_set;
    std::vector<size_t> index;
    
    typedef std::set<std::string>::iterator ProbeIter; 
        
    // making a probe_set and checking for duplicates
    for (vector<string>::const_iterator i=probes.begin(); i!=probes.end();++i){
      ProbeIter iter = probe_set.lower_bound((*i));
      if (iter!=probe_set.end() && (*iter) == (*i)){
        std::cerr << "DataSet: Error: " << (*iter) << "found twice.\n";
      }
      probe_set.insert(iter, *i);
    }

    std::vector<size_t> new_index;
    std::set<std::string> probe_set2;
    for (size_t i = 0; i<first.probe().size(); ++i){
      ProbeIter iter = probe_set.find(first.probe()[i]);
      if (iter!=probe_set.end()) {
        ProbeIter iter = probe_set2.lower_bound(first.probe()[i]);
        if (iter!=probe_set2.end() && (*iter) == first.probe()[i]){
          std::cerr << "DataSet: Warning: " << (*iter) << "found twice.\n";
        }
        else {
          probe_set2.insert(iter, first.probe()[i]);
          new_index.push_back(i);
          probe_.push_back(first.probe()[i]);
        }
      }
    }
    data_ = classifier::MatrixLookup(first.data(),new_index,true);
  }


  const classifier::MatrixLookup& DataSet::data(void) const
  {
    return data_;
  }


  const std::vector<std::string>& DataSet::probe(void) const
  {
    return probe_;
  }


  const classifier::Target& DataSet::target(void) const
  {
    return target_;
  }

}}} // end of namespace microarray, yat, and theplu