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