src/modelidentifier.cpp

   1 /***************************************************************************
   2  *   Copyright (C) 2006 by Michael Andreen                                 *
   3  *   andreen@student.chalmers.se                                           *
   4  *                                                                         *
   5  *   This program is free software; you can redistribute it and/or modify  *
   6  *   it under the terms of the GNU General Public License as published by  *
   7  *   the Free Software Foundation; either version 2 of the License, or     *
   8  *   (at your option) any later version.                                   *
   9  *                                                                         *
  10  *   This program is distributed in the hope that it will be useful,       *
  11  *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  12  *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  13  *   GNU General Public License for more details.                          *
  14  *                                                                         *
  15  *   You should have received a copy of the GNU General Public License     *
  16  *   along with this program; if not, write to the                         *
  17  *   Free Software Foundation, Inc.,                                       *
  18  *   51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA          *
  19  ***************************************************************************/
  20
  21 #include "modelidentifier.h"
  22 #include "genealgorithms.h"
  23
  24 #include <doublefann.h>
  25 #include "models.h"
  26 #include "model.h"
  27
  28 using namespace std;
  29
  30 ModelIdentifier::ModelIdentifier(std::string ann){
  31         _ann = fann_create_from_file(ann.c_str());
  32         if(!_ann){
  33                 throw invalid_argument("Could not create network");
  34         }
  35 }
  36
  37 ModelIdentifier::~ModelIdentifier(){
  38         fann_destroy(_ann);
  39 }
  40
  41 priority_queue<pair<double,Model> > ModelIdentifier::identify(const GeneOrder& go){
  42         int pos = 0;
  43         int neg = 0;
  44         for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g){
  45                 if (*g >= 0)
  46                         ++pos;
  47                 else
  48                         ++neg;
  49         }
  50         double length = go.size();
  51         vector<double> input(8);
  52         input[0] = pos/length;
  53         input[1] = neg/length;
  54
  55         pair<int,int> seqs = longestSequences(go);
  56
  57         input[2] = seqs.first/length;
  58         input[3] = seqs.second/length;
  59
  60         double cycles = countCycles(go);
  61         input[4] = cycles/length;
  62
  63         vector<Component> comps = findComponents(go);
  64
  65         pos = 0;
  66         neg = 0;
  67         int un = 0;
  68         for (vector<Component>::iterator c = comps.begin(); c != comps.end(); ++c){
  69                 if (c->sign > 0)
  70                         ++pos;
  71                 else if (c->sign < 0)
  72                         ++neg;
  73                 else
  74                         ++un;
  75         }
  76
  77         input[5] = un/cycles;
  78         input[6] = pos/cycles;
  79         input[7] = neg/cycles;
  80
  81         double *output = fann_run(_ann,&input[0]);
  82
  83         priority_queue<pair<double,Model> > scores;
  84         scores.push(pair<double,Model>(output[0],Model(new Models::X)));
  85         scores.push(pair<double,Model>(output[1],Model(new Models::Zipper)));
  86         scores.push(pair<double,Model>(output[2],Model(new Models::ModelImpl)));
  87         scores.push(pair<double,Model>(output[3],Model(new Models::FatX)));
  88         scores.push(pair<double,Model>(output[4],Model(new Models::Cloud)));
  89         return scores;
  90 }