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<Gene> GeneList;
37 typedef GeneList::size_type size_type;
38 typedef GeneList::const_iterator iterator;
41 * Creates a copy of the given gene order
43 GeneOrder(const GeneOrder& go);
46 * Creates a gene order from a given list, using STL-type iterators.
48 * The given permutation needs to contain all genes 1 to n, if 0 is
49 * included it has to be the first item, if it is not present it will
50 * be added automatically. Similarily, if n is not the last item, then
51 * n+1 will be added to the end.
53 * \param begin iterator to the first element in the list, from begin()
54 * on stl collections and pointer to first item on plain arrays.
56 * \param end iterator to the element behind the last, from end() in
57 * stl collections or pointer to first element+size on plain arrays.
59 * \throws std::invalid_argument if the list is not a valid permutation.
62 GeneOrder(T begin, T end);
65 * Destroyes the gene order.
70 * Copies the given gene order.
72 const GeneOrder& operator=(const GeneOrder& go);
75 * Returns the gene at the given index.
77 * \throws std::out_of_range if i is smaller than 0 or bigger than n.
79 const Gene& operator[](size_type i) const;
82 * Returns the size of the permutation.
84 size_type size() const;
87 * Returns the vector containing the gene order permutation.
89 const GeneList& list() const;
92 * Returns the start iterator for the permutation.
93 * To be used with STL style functions.
97 iterator begin() const;
100 * Returns the end iterator for the permutation.
101 * To be used with STL style functions.
105 iterator end() const;
111 * pads the permutation with 0 in front and n+1 at the end if needed
116 * Verifies that the permutation starts with 0, ends with n+1 and that all genes i, 0 < i < n+1
117 * are present, without duplication.
124 * Put all the genes in the list, check that all genes are included, pad with 0 and n+1 if needed.
125 * TODO: This is far from done atm
128 GeneOrder::GeneOrder(T begin, T end): _geneorder(begin,end){