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 #ifndef __GENEALGORITHMS_H__
22 #define __GENEALGORITHMS_H__
29 Component(int b,int e,int s):begin(b),end(e),sign(s){}
30 bool operator==(const Component& c){
31 return begin == c.begin && end == c.end && sign == c.sign;
39 Interval(size_t f,size_t s,bool o = false):first(f),second(s),oriented(o){}
40 bool operator==(const Interval& i){
41 return first == i.first && second == i.second && oriented == i.oriented;
49 * Returns the length of the longest increasing sequence and the longest
50 * decreasing sequence.
52 std::pair<int,int> longestSequences(const GeneOrder& go);
56 std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go);
59 * Counts the number of cycles in the gene order.
61 size_t countCycles(const GeneOrder& go);
64 * Calculates the inversion distance for this gene order
66 size_t inversionDistance(const GeneOrder& go);
69 * Finds the components in the gene order.
71 std::vector<Component> findComponents(const GeneOrder& go);
76 std::vector<Interval> findIntervals(const GeneOrder& go);
79 * Creates a list with the intervals at each point.
81 std::vector<Interval> findIntervalsAtPoints(const std::vector<Interval>& intervals);