stage/include/ost/io/fasta_io_handler.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_IO_FASTA_HANDLER_HH 00020 #define OST_IO_FASTA_HANDLER_HH 00021 /* 00022 Author: Marco Biasini 00023 */ 00024 #include <ost/io/module_config.hh> 00025 #include "sequence_io_handler.hh" 00026 00027 namespace ost { namespace io { 00028 00029 class DLLEXPORT_OST_IO FastaIOHandler : public SequenceIOHandler { 00030 public: 00031 virtual void Import(seq::SequenceList& aln, 00032 const boost::filesystem::path& loc); 00033 00034 virtual void Export(const seq::ConstSequenceList& aln, 00035 const boost::filesystem::path& loc) const; 00036 00037 virtual void Import(seq::SequenceList& aln, 00038 std::istream& instream); 00039 00040 virtual void Export(const seq::ConstSequenceList& aln, 00041 std::ostream& ostream) const; 00042 00043 static bool ProvidesImport(const boost::filesystem::path& loc, 00044 const String& format="auto"); 00045 static bool ProvidesExport(const boost::filesystem::path& loc, 00046 const String& format="auto"); 00047 static String GetFormatName() { return String("Fasta"); } 00048 static String GetFormatDescription() { return String("Sequence format originally used by the Fasta suite of programs"); } 00049 00050 private: 00051 }; 00052 00053 typedef SequenceIOHandlerFactory<FastaIOHandler> FastaIOHandlerFactory; 00054 }} 00055 00056 #endif
