00001 //------------------------------------------------------------------------------ 00002 // This file is part of the OpenStructure project <www.openstructure.org> 00003 // 00004 // Copyright (C) 2008-2010 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_LOCAL_ALIGN_HH 00020 #define OST_SEQ_LOCAL_ALIGN_HH 00021 00022 00023 #include <ost/seq/alignment_handle.hh> 00024 #include <ost/seq/alg/module_config.hh> 00025 #include <ost/seq/alg/alignment_opts.hh> 00026 #include <ost/seq/alg/subst_weight_matrix.hh> 00027 /* 00028 Author: Marco Biasini 00029 */ 00030 00031 namespace ost { namespace seq { namespace alg { 00032 00034 struct DLLEXPORT_OST_SEQ_ALG AlignedPatch { 00036 int offset_a; 00038 int offset_b; 00040 AlignmentHandle alignment; 00041 bool operator==(const AlignedPatch& rhs) const { 00042 return offset_a==rhs.offset_a && offset_b==rhs.offset_b && 00043 rhs.alignment==alignment; 00044 } 00045 bool operator!=(const AlignedPatch& rhs) const { 00046 return !this->operator==(rhs); 00047 } 00048 }; 00049 00050 typedef std::vector<AlignedPatch> AlignedPatchList; 00051 00065 AlignedPatchList DLLEXPORT_OST_SEQ_ALG 00066 LocalSequenceAlign(const SequenceHandle& seq_a, const SequenceHandle& seq_b, 00067 const AlignmentOpts& opts); 00068 }}} 00069 00070 #endif
1.5.8