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  * TODO: Think of a better than O(n^2) implementation
 100  * Possibly move it to GeneOrder too
 101  */
 102 std::vector<Interval> findIntervals(const GeneOrder& go){
 103         vector<Interval> intervals;
 104         for (size_t i = 0; i < go.size() - 1; ++i){
 105                 size_t f = 0;
 106                 size_t s = 0;
 107                 bool found = false;
 108                 size_t n = 0;
 109                 for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
 110                         if (static_cast<size_t>(abs(*g)) == i){
 111                                 f = n;
 112                                 if (*g >= 0)
 113                                         ++f;
 114                                 if (found)
 115                                         break;
 116                                 found = true;
 117                         }
 118                         if(static_cast<size_t>(abs(*g)) == i+1){
 119                                 s = n;
 120                                 if (*g < 0)
 121                                         ++s;
 122                                 if (found)
 123                                         break;
 124                                 found = true;
 125                         }
 126                 }
 127                 intervals.push_back(Interval(f,s));
 128         }
 129         return intervals;
 130 }
 131
 132 /**
 133  * TODO: Think of a better than O(n^2) implementation.
 134  * Possibly move to cache result
 135  */
 136 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
 137         vector<Interval> points;
 138         points.push_back(Interval(intervals.size(),intervals.size())); //Dummy interval to match point and index
 139         for (size_t p = 1; p <= intervals.size(); ++p){
 140                 size_t f = 0;
 141                 size_t s = 0;
 142                 bool found = false;
 143                 size_t n = 0;
 144                 for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
 145                         if (i->first == p){
 146                                 if (!found){
 147                                         f = n;
 148                                         found = true;
 149                                 }else{
 150                                         s = n;
 151                                         break;
 152                                 }
 153                         }
 154                         if (i->second == p){
 155                                 if (!found){
 156                                         f = n;
 157                                         found = true;
 158                                 }else{
 159                                         s = n;
 160                                         break;
 161                                 }
 162                         }
 163                 }
 164                 points.push_back(Interval(f,s));
 165         }
 166         return points;
 167
 168 }