OpenStructure
ins_del.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_SEQ_ALG_INS_DEL_HH
20 #define OST_SEQ_ALG_INS_DEL_HH
21 
22 /*
23  Author: Marco Biasini
24  */
28 
29 namespace ost { namespace seq { namespace alg {
30 
44 public:
46  InsDel(const AlignmentHandle& aln, int seq_a=0, int seq_b=1);
48  AlignedRegionList GetInsertions(int ref) const;
50  AlignedRegionList GetDeletions(int ref) const;
51 private:
52  AlignmentHandle aln_;
53  int seq_a_;
54  int seq_b_;
55  AlignedRegionList insdels_;
56 };
57 
58 }}}
59 
60 #endif