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         size_t dist = inversionDistance(temp);
  45         while(dist > 0){
  46                 //cout << "Distance: " << inversionDistance(temp) << " : ";
  47                 //copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
  48                 //cout << endl;
  49                 ActionList safe = safeActions(temp);
  50                 if (safe.size() > 0){
  51                         priority_queue<pair<double,SortAction>,vector<pair<double,SortAction> >, ScoreCmp > pq;
  52                         for (ActionList::iterator sa = safe.begin(); sa != safe.end(); ++sa){
  53                                 pq.push(pair<double,SortAction>(m.score(*sa,temp),*sa));
  54                         }
  55                         SortAction sa = pq.top().second;
  56                         sa(temp);
  57                         al.push_back(sa);
  58                         --dist;
  59                 }else
  60                         return ActionList(); //TODO: Need to handle hurdles.
  61         }
  62         return al;
  63 }
  64
  65
  66 GeneSorter::ActionList GeneSorter::safeActions(const GeneOrder& go){
  67         if (countCycles(go) == go.size() - 1)
  68                 return ActionList();
  69         ActionList al;
  70         vector<Interval> intervals = findIntervals(go);
  71         priority_queue<pair<size_t,SortAction>,vector<pair<size_t,SortAction> >, ScoreCmp > pq;
  72         for (size_t i = 0; i < intervals.size(); ++i){
  73                 if (intervals[i].oriented && intervals[i].first != intervals[i].second){
  74                         SortAction sa(new ReverseAction(intervals[i]));
  75                         size_t score = scoreAction(go,sa);
  76                         //cout << "Inversion: " << min(intervals[i].first,intervals[i].second) << ":" << max(intervals[i].first,intervals[i].second)-1 << " Score: " << score <<  endl;
  77                         pq.push(pair<size_t,SortAction>(score,sa));
  78                 }
  79         }
  80         size_t max = pq.top().first;
  81         while (pq.size() > 0 && pq.top().first >= max){
  82                 al.push_back(pq.top().second);
  83                 pq.pop();
  84         }
  85         return al;
  86 }
  87
  88 size_t GeneSorter::scoreAction(const GeneOrder& go, SortAction& sa){
  89         GeneOrder temp(go);
  90         sa(temp);
  91         vector<Interval> intervals = findIntervals(temp);
  92         int o = 0;
  93         for (vector<Interval>::iterator in = intervals.begin(); in != intervals.end(); ++in){
  94                 if (in->oriented)
  95                         ++o;
  96         }
  97         return o;
  98 }
  99