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__
30 * Simple interval struct, holds the indexes + information if the interval is
34 Interval(size_t f,size_t s,bool o = false):first(f),second(s),oriented(o){}
35 bool operator==(const Interval& i){
36 return first == i.first && second == i.second && oriented == i.oriented;
44 * Returns the length of the longest increasing sequence and the longest
45 * decreasing sequence.
47 std::pair<int,int> longestSequences(const GeneOrder& go);
50 * Uses the Robinson-Schensted algorithm on the gene order. Gives the longest
51 * increasing and decreasing subsequences.
53 std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go);
56 * Counts the number of cycles in the gene order.
58 size_t countCycles(const GeneOrder& go);
61 * Calculates the inversion distance for this gene order
63 size_t inversionDistance(const GeneOrder& go);
66 * Finds the components in the gene order.
68 std::vector<Component> findComponents(const GeneOrder& go);
73 std::vector<Interval> findIntervals(const GeneOrder& go);
76 * Creates a list with the intervals at each point.
78 std::vector<Interval> findIntervalsAtPoints(const std::vector<Interval>& intervals);