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 using namespace std;
  28
  29 std::pair<int,int> longestSequences(const GeneOrder& go){
  30         vector<vector<int> > v = robinsonSchensted(go);
  31         return pair<int,int>(v[0].size(),v.size());
  32 }
  33
  34 std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go){
  35         vector<vector<int> > v;
  36         for (GeneOrder::iterator i = go.begin(); i != go.end(); ++i){
  37                 int n = abs(*i);
  38                 bool added = false;
  39                 for (vector<vector<int> >::iterator vs = v.begin();
  40                                 vs != v.end(); ++vs){
  41                         vector<int>::iterator bigger = upper_bound(vs->begin(),vs->end(),n);
  42                         if ( bigger == vs->end()){
  43                                 vs->push_back(n);
  44                                 added = true;
  45                                 break;
  46                         }else{
  47                                 swap(n,*bigger);
  48                         }
  49                 }
  50                 if (!added){
  51                         v.push_back(vector<int>());
  52                         v.back().push_back(n);
  53                 }
  54         }
  55         return v;
  56 }
  57
  58 int countCycles(const GeneOrder& go){
  59         int cycles = 0;
  60         set<size_t> marked;
  61         for (size_t p = 1; p < go.size() - 1; ++p){
  62                 if (marked.find(p) != marked.end())
  63                         continue;
  64         }
  65         return cycles;
  66 }
  67
  68 std::vector<Component> findComponents(const GeneOrder& go){
  69         return vector<Component>();
  70 }
  71
  72 std::vector<Interval> findIntervals(const GeneOrder& go){
  73         return vector<Interval>();
  74 }