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 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
69 vector<Interval> points;
70 points.push_back(Interval(intervals.size(),intervals.size())); //Dummy interval to match point and index
71 for (size_t p = 1; p <= intervals.size(); ++p){
76 for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
96 points.push_back(Interval(f,s));
102 int countCycles(const GeneOrder& go){
105 vector<Interval> intervals = findIntervals(go);
106 vector<Interval> points = findIntervalsAtPoints(intervals);
107 for (size_t p = 1; p < go.size(); ++p){
108 if (marked.find(p) != marked.end())
110 Interval i = intervals[points[p].first];
111 while (marked.find(p) == marked.end()){
113 if (i == intervals[points[p].first])
114 i = intervals[points[p].second];
116 i = intervals[points[p].first];
128 std::vector<Component> findComponents(const GeneOrder& go){
129 return vector<Component>();
133 * TODO: Think of a better than O(n^2) implementation
134 * Possibly move it to GeneOrder too
136 std::vector<Interval> findIntervals(const GeneOrder& go){
137 vector<Interval> intervals;
138 for (size_t i = 0; i < go.size() - 1; ++i){
143 for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
144 if (static_cast<size_t>(abs(*g)) == i){
152 if(static_cast<size_t>(abs(*g)) == i+1){
161 intervals.push_back(Interval(f,s));