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// Copyright 2009 Udo Stenzel
// This file is part of ANFO
//
// ANFO is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Anfo is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Anfo. If not, see <http://www.gnu.org/licenses/>.
#ifndef INCLUDED_CONFFILE_H
#define INCLUDED_CONFFILE_H
#include "config.pb.h"
#include <google/protobuf/io/zero_copy_stream_impl.h>
#include <google/protobuf/text_format.h>
#include <fstream>
#include <string>
#include <unistd.h>
/*! \page configuration Configuration Files, Metadata, Output Format
*
* In order to keep configuration files and somewhat complicated,
* persistent data structures in a sensible format and extensible, we
* abuse Google's protocol buffers (http://code.google.com/p/protobuf/)
* for this. Code to handle protocol buffers can be generated for C++,
* Java and Pyhton by the Google toolchain, but also for Haskell
* (http://hackage.haskell.org/cgi-bin/hackage-scripts/package/hprotoc)
* and possibly for more languages. The definition of the possible
* parts of the configuration resides in \c config.proto, we store the
* configuration in a single file using the protobuf text format.
* Metadata for genomes and indices is also defined there, those files
* incorporate their metadata in binary form. If the need arises, we
* can easily move to multiple files, binary files, or a combination of
* both. Text and binary files are interconvertible using \c protoc.
*/
//! \brief reads the configuration from a text file.
//! A text format configuration file is read and parsed into a config
//! object.
//!
//! \param filename filename of configuration file
//! \return parsed configuration
inline config::Config parse_text_config( const std::string& filename )
{
config::Config c ;
std::ifstream config_in( filename.c_str() ) ;
google::protobuf::io::IstreamInputStream fis( &config_in ) ;
if( !google::protobuf::TextFormat::Parse( &fis, &c ) )
throw "parse error reading " + filename ;
return c ;
}
inline config::Config get_default_config( const char* config_file = 0 )
{
if( config_file ) return parse_text_config( config_file ) ;
else if( !access( "anfo.cfg", F_OK ) ) return parse_text_config( "anfo.cfg" ) ;
else if( !access( ".anfo.cfg", F_OK ) ) return parse_text_config( ".anfo.cfg" ) ;
else {
std::string f = getenv( "HOME" ) + std::string( "/.anfo.cfg" ) ;
if( !access( f.c_str(), F_OK ) ) return parse_text_config( f.c_str() ) ;
else throw "no config file found" ;
}
}
#endif
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