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 int countCycles(const GeneOrder& go){
  60         int cycles = 0;
  61         set<size_t> marked;
  62         for (size_t p = 1; p < go.size() - 1; ++p){
  63                 if (marked.find(p) != marked.end())
  64                         continue;
  65         }
  66         return cycles;
  67 }
  68
  69 std::vector<Component> findComponents(const GeneOrder& go){
  70         return vector<Component>();
  71 }
  72
  73 //TODO: Think of a better than O(n^2) implementation
  74 std::vector<Interval> findIntervals(const GeneOrder& go){
  75         vector<Interval> intervals;
  76         for (size_t i = 0; i < go.size() - 1; ++i){
  77                 size_t f = 0;
  78                 size_t s = 0;
  79                 bool found = false;
  80                 size_t n = 0;
  81                 for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
  82                         if (static_cast<size_t>(abs(*g)) == i){
  83                                 f = n;
  84                                 if (*g >= 0)
  85                                         ++f;
  86                                 if (found)
  87                                         break;
  88                                 found = true;
  89                         }
  90                         if(static_cast<size_t>(abs(*g)) == i+1){
  91                                 s = n;
  92                                 if (*g < 0)
  93                                         ++s;
  94                                 if (found)
  95                                         break;
  96                                 found = true;
  97                         }
  98                 }
  99                 intervals.push_back(Interval(f,s));
 100         }
 101         return intervals;
 102 }