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
  26 using namespace std;
  27
  28 ModelIdentifier::ModelIdentifier(std::string ann){
  29         _ann = fann_create_from_file(ann.c_str());
  30         if(!_ann){
  31                 throw invalid_argument("Could not create network");
  32         }
  33 }
  34
  35 ModelIdentifier::~ModelIdentifier(){
  36         fann_destroy(_ann);
  37 }
  38
  39 std::map<ModelIdentifier::Model,double> ModelIdentifier::identify(const GeneOrder& go){
  40         int pos = 0;
  41         int neg = 0;
  42         for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g){
  43                 if (*g >= 0)
  44                         ++pos;
  45                 else
  46                         ++neg;
  47         }
  48         double length = go.size();
  49         vector<double> input(8);
  50         input[0] = pos/length;
  51         input[1] = neg/length;
  52
  53         pair<int,int> seqs = longestSequences(go);
  54
  55         input[2] = seqs.first/length;
  56         input[3] = seqs.second/length;
  57
  58         double cycles = countCycles(go);
  59         input[4] = cycles/length;
  60
  61         vector<Component> comps = findComponents(go);
  62
  63         pos = 0;
  64         neg = 0;
  65         int un = 0;
  66         for (vector<Component>::iterator c = comps.begin(); c != comps.end(); ++c){
  67                 if (c->sign > 0)
  68                         ++pos;
  69                 else if (c->sign < 0)
  70                         ++neg;
  71                 else
  72                         ++un;
  73         }
  74
  75         input[5] = un/cycles;
  76         input[6] = pos/cycles;
  77         input[7] = neg/cycles;
  78
  79         double *output = fann_run(_ann,&input[0]);
  80
  81         map<Model,double> scores;
  82         scores[X] = output[0];
  83         scores[Zipper] = output[1];
  84         scores[Whirl] = output[2];
  85         scores[FatX] = output[3];
  86         scores[Cloud] = output[4];
  87         return scores;
  88 }