src/genealgorithms.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 "genealgorithms.h"
  22 #include "geneorder.h"
  23
  24 #include <algorithm>
  25 #include <set>
  26 #include <cstdlib>
  27 #include <iostream>
  28 using namespace std;
  29
  30 std::pair<int,int> longestSequences(const GeneOrder& go){
  31         vector<vector<int> > v = robinsonSchensted(go);
  32         return pair<int,int>(v[0].size(),v.size());
  33 }
  34
  35 std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go){
  36         vector<vector<int> > v;
  37         for (GeneOrder::iterator i = go.begin(); i != go.end(); ++i){
  38                 int n = abs(*i);
  39                 bool added = false;
  40                 for (vector<vector<int> >::iterator vs = v.begin();
  41                                 vs != v.end(); ++vs){
  42                         vector<int>::iterator bigger = upper_bound(vs->begin(),vs->end(),n);
  43                         if ( bigger == vs->end()){
  44                                 vs->push_back(n);
  45                                 added = true;
  46                                 break;
  47                         }else{
  48                                 swap(n,*bigger);
  49                         }
  50                 }
  51                 if (!added){
  52                         v.push_back(vector<int>());
  53                         v.back().push_back(n);
  54                 }
  55         }
  56         return v;
  57 }
  58
  59 struct FindP{
  60         size_t p;
  61         FindP(size_t p) : p(p) {}
  62         bool operator()(Interval i){
  63                 return (i.first == p || i.second == p);
  64         }
  65 };
  66
  67
  68 int countCycles(const GeneOrder& go){
  69         int cycles = 0;
  70         set<size_t> marked;
  71         vector<Interval> intervals = findIntervals(go);
  72         vector<Interval> points = findIntervalsAtPoints(intervals);
  73         for (size_t p = 1; p < go.size(); ++p){
  74                 if (marked.find(p) != marked.end())
  75                         continue;
  76                 Interval i = intervals[points[p].first];
  77                 while (marked.find(p) == marked.end()){
  78                         marked.insert(p);
  79                         if (i == intervals[points[p].first])
  80                                 i = intervals[points[p].second];
  81                         else
  82                                 i = intervals[points[p].first];
  83
  84                         if (p == i.first)
  85                                 p = i.second;
  86                         else
  87                                 p = i.first;
  88                 }
  89                 ++cycles;
  90         }
  91         return cycles;
  92 }
  93
  94 std::vector<Component> findComponents(const GeneOrder& go){
  95         return vector<Component>();
  96 }
  97
  98 /**
  99  *
 100  */
 101 std::vector<Interval> findIntervals(const GeneOrder& go){
 102         vector<Interval> intervals(go.size()-1,Interval(go.size(),go.size()));
 103         size_t n = 0;
 104         for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
 105                         size_t i = abs(*g);
 106                         if (i < go.size() - 1)
 107                                 intervals[i].first = n + (*g >= 0 ? 1 : 0);
 108                         if (i > 0)
 109                                 intervals[i-1].second = n + (*g < 0 ? 1 : 0);
 110         }
 111         return intervals;
 112 }
 113
 114 /**
 115  * TODO: Think of a better than O(n^2) implementation.
 116  * Possibly move to cache result
 117  */
 118 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
 119         size_t max = intervals.size()+1;
 120         vector<Interval> points(max,Interval(max,max));
 121         size_t n = 0;
 122         for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
 123                 if (points[i->first].first == max){
 124                         points[i->first].first = n;
 125                 }else
 126                         points[i->first].second = n;
 127
 128                 if (points[i->second].first == max){
 129                         points[i->second].first = n;
 130                 }else
 131                         points[i->second].second = n;
 132         }
 133         return points;
 134
 135 }