00001 //------------------------------------------------------------------------------ 00002 // This file is part of the OpenStructure project <www.openstructure.org> 00003 // 00004 // Copyright (C) 2008-2011 by the OpenStructure authors 00005 // 00006 // This library is free software; you can redistribute it and/or modify it under 00007 // the terms of the GNU Lesser General Public License as published by the Free 00008 // Software Foundation; either version 3.0 of the License, or (at your option) 00009 // any later version. 00010 // This library is distributed in the hope that it will be useful, but WITHOUT 00011 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 00012 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more 00013 // details. 00014 // 00015 // You should have received a copy of the GNU Lesser General Public License 00016 // along with this library; if not, write to the Free Software Foundation, Inc., 00017 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 00018 //------------------------------------------------------------------------------ 00019 #ifndef OST_SEQ_ALG_INS_DEL_HH 00020 #define OST_SEQ_ALG_INS_DEL_HH 00021 00022 /* 00023 Author: Marco Biasini 00024 */ 00025 #include <ost/seq/aligned_region.hh> 00026 #include <ost/seq/alignment_handle.hh> 00027 #include <ost/seq/alg/module_config.hh> 00028 00029 namespace ost { namespace seq { namespace alg { 00030 00043 class DLLEXPORT_OST_SEQ_ALG InsDel { 00044 public: 00046 InsDel(const AlignmentHandle& aln, int seq_a=0, int seq_b=1); 00048 AlignedRegionList GetInsertions(int ref) const; 00050 AlignedRegionList GetDeletions(int ref) const; 00051 private: 00052 AlignmentHandle aln_; 00053 int seq_a_; 00054 int seq_b_; 00055 AlignedRegionList insdels_; 00056 }; 00057 00058 }}} 00059 00060 #endif