src/genesorter.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 "genesorter.h"
  22
  23 #include "geneorder.h"
  24 #include "sortaction.h"
  25 #include "reverseaction.h"
  26
  27 #include "genealgorithms.h"
  28
  29 #include "model.h"
  30
  31 #include <queue>
  32 using namespace std;
  33
  34 struct ScoreCmp {
  35         template<typename T>
  36         bool operator()(T s1, T s2){
  37                 return s1.first < s2.first;
  38         }
  39 };
  40
  41 GeneSorter::ActionList GeneSorter::sort(const GeneOrder& go, const Model& m){
  42         ActionList al;
  43         GeneOrder temp(go);
  44         while(inversionDistance(temp) > 0){
  45                 //cout << "Distance: " << inversionDistance(temp) << " : ";
  46                 //copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
  47                 //cout << endl;
  48                 ActionList safe = safeActions(temp);
  49                 if (safe.size() > 0){
  50                         priority_queue<pair<double,SortAction>,vector<pair<double,SortAction> >, ScoreCmp > pq;
  51                         for (ActionList::iterator sa = safe.begin(); sa != safe.end(); ++sa){
  52                                 pq.push(pair<double,SortAction>(m.score(*sa,temp),*sa));
  53                         }
  54                         SortAction sa = pq.top().second;
  55                         sa(temp);
  56                         al.push_back(sa);
  57                 }else
  58                         return ActionList(); //TODO: Need to handle hurdles.
  59         }
  60         return al;
  61 }
  62
  63
  64 GeneSorter::ActionList GeneSorter::safeActions(const GeneOrder& go){
  65         if (countCycles(go) == go.size() - 1)
  66                 return ActionList();
  67         ActionList al;
  68         vector<Interval> intervals = findIntervals(go);
  69         priority_queue<pair<size_t,SortAction>,vector<pair<size_t,SortAction> >, ScoreCmp > pq;
  70         for (size_t i = 0; i < intervals.size(); ++i){
  71                 if (intervals[i].oriented && intervals[i].first != intervals[i].second){
  72                         SortAction sa(new ReverseAction(intervals[i]));
  73                         size_t score = scoreAction(go,sa);
  74                         //cout << "Inversion: " << min(intervals[i].first,intervals[i].second) << ":" << max(intervals[i].first,intervals[i].second)-1 << " Score: " << score <<  endl;
  75                         pq.push(pair<size_t,SortAction>(score,sa));
  76                 }
  77         }
  78         size_t max = pq.top().first;
  79         while (pq.size() > 0 && pq.top().first >= max){
  80                 al.push_back(pq.top().second);
  81                 pq.pop();
  82         }
  83         return al;
  84 }
  85
  86 size_t GeneSorter::scoreAction(const GeneOrder& go, SortAction& sa){
  87         GeneOrder temp(go);
  88         sa(temp);
  89         vector<Interval> intervals = findIntervals(temp);
  90         int o = 0;
  91         for (vector<Interval>::iterator in = intervals.begin(); in != intervals.end(); ++in){
  92                 if (in->oriented)
  93                         ++o;
  94         }
  95         return o;
  96 }
  97