stage/include/ost/seq/aligned_region.hh
Go to the documentation of this file.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_ALIGNED_REGION_HH 00020 #define OST_SEQ_ALIGNED_REGION_HH 00021 00022 /* 00023 Author: Marco Biasini 00024 */ 00025 #include <ost/seq/module_config.hh> 00026 #include <ost/seq/alignment_handle.hh> 00027 #include <ost/seq/aligned_column_iterator.hh> 00028 00029 namespace ost { namespace seq { 00030 00031 00038 class DLLEXPORT_OST_SEQ AlignedRegion { 00039 public: 00040 typedef AlignedColumnIterator iterator; 00041 AlignedRegion(const AlignmentHandle& aln, 00042 int start, int end, int master=-1); 00043 00045 int GetEnd() const; 00047 int GetStart() const; 00048 int GetMaster() const; 00049 void SetMaster(int master); 00051 void Delete(); 00054 void Replace(const AlignedRegion& aln_r); 00055 00058 void ShiftLeft(int n); 00059 00063 void ShiftRight(int n); 00064 00068 int GetLength() const; 00069 00071 AlignmentHandle GetAlignmentHandle() const; 00072 00076 AlignedColumn operator[](int index) const; 00077 00079 AlignedColumnIterator begin(); 00081 AlignedColumnIterator end(); 00082 00083 bool operator==(const AlignedRegion& rhs) const; 00084 bool operator!=(const AlignedRegion& rhs) const; 00085 private: 00086 AlignmentHandle aln_; 00087 int start_; 00088 int end_ ; 00089 int master_; 00090 }; 00091 00092 typedef std::vector<AlignedRegion> AlignedRegionList; 00093 00094 }} 00095 00096 #endif
