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 __GENEORDER_H__
22 #define __GENEORDER_H__
30 * Stores a gene order permutation and ensures that all genes are present and not duplicated.
31 * \author Michael Andreen
36 typedef std::vector<long> GeneList;
37 typedef GeneList::size_type size_type;
40 * Creates a copy of the given gene order
42 GeneOrder(const GeneOrder& go);
45 * Creates a gene order from a given list.
47 * \throws invalid_argument if the list is not a valid permutation.
50 GeneOrder(T begin, T end);
53 * Destroyes the gene order.
58 * Copies the given gene order.
60 const GeneOrder& operator=(const GeneOrder& go);
63 * Returns the gene at the given index.
65 * \throws out_of_range if i is smaller than 0 or too big.
67 const Gene& operator[](size_type i) const;
70 * Returns the size of the permutation.
75 * Returns the vector containing the gene order permutation.
77 const GeneList& list() const;
83 * pads the permutation with 0 in front and n+1 at the end if needed
88 * Verifies that the permutation starts with 0, ends with n+1 and that all genes i, 0 < i < n+1
89 * are present, without duplication.
96 * Put all the genes in the list, check that all genes are included, pad with 0 and n+1 if needed.
97 * TODO: This is far from done atm
100 GeneOrder::GeneOrder(T begin, T end): _geneorder(begin,end){