1 /***************************************************************************
2 * Copyright (C) 2006 by Michael Andreen *
3 * andreen@student.chalmers.se *
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. *
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. *
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 ***************************************************************************/
21 #include "genealgorithms.h"
22 #include "geneorder.h"
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());
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){
40 for (vector<vector<int> >::iterator vs = v.begin();
42 vector<int>::iterator bigger = upper_bound(vs->begin(),vs->end(),n);
43 if ( bigger == vs->end()){
52 v.push_back(vector<int>());
53 v.back().push_back(n);
61 FindP(size_t p) : p(p) {}
62 bool operator()(Interval i){
63 return (i.first == p || i.second == p);
68 int countCycles(const GeneOrder& go){
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())
76 Interval i = intervals[points[p].first];
77 while (marked.find(p) == marked.end()){
79 if (i == intervals[points[p].first])
80 i = intervals[points[p].second];
82 i = intervals[points[p].first];
94 std::vector<Component> findComponents(const GeneOrder& go){
95 return vector<Component>();
101 std::vector<Interval> findIntervals(const GeneOrder& go){
102 vector<Interval> intervals(go.size()-1,Interval(go.size(),go.size()));
104 for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
106 if (i < go.size() - 1)
107 intervals[i].first = n + (*g >= 0 ? 1 : 0);
109 intervals[i-1].second = n + (*g < 0 ? 1 : 0);
115 * TODO: Think of a better than O(n^2) implementation.
116 * Possibly move to cache result
118 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
119 size_t max = intervals.size()+1;
120 vector<Interval> points(max,Interval(max,max));
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;
126 points[i->first].second = n;
128 if (points[i->second].first == max){
129 points[i->second].first = n;
131 points[i->second].second = n;