FileJobOutputter.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/jd2/FileJobOutputter.cc
/// @brief  August 2008 job distributor as planned at RosettaCon08 - FileJobOutputter
/// @author Steven Lewis smlewi@gmail.com

///Unit headers
#include <protocols/jd2/FileJobOutputter.hh>
#include <protocols/jd2/Job.hh>

///Project headers
// AUTO-REMOVED #include <core/pose/Pose.hh>

#include <core/io/raw_data/ScoreFileData.hh>
#include <protocols/jd2/ScoreMap.hh>

///Utility headers
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <utility/io/ozstream.hh>

// option key includes

#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>

#include <utility/vector1.hh>




///C++ headers
//#include <string>
//#include <sstream>

static basic::Tracer TR("protocols.jd2.FileJobOutputter");

namespace protocols {
namespace jd2 {

using namespace basic::options;
using namespace basic::options::OptionKeys;

protocols::jd2::FileJobOutputter::FileJobOutputter() : parent(), write_scorefile_(false), scorefile_name_() {
  TR.Debug << "FileJobOutputter ctor" << std::endl;
  utility::file::FileName default_path( option[ out::path::all ]() );
  if( option[ out::file::scorefile ].user() ){
    write_scorefile_ = true;
    scorefile_name_ = option[ out::file::scorefile ]();
    if ( option[ out::path::score ].user() ) {
      scorefile_name_.path( option[ out::path::score ]().path() );
      }else if (! scorefile_name_.absolute() ) {
          scorefile_name_.path( default_path.path() + "/" + scorefile_name_.path() );
      }
  }else if(option [out::file::score_only].user()){
    write_scorefile_ = true;
    scorefile_name_ = option[out::file::score_only]();
    if (! scorefile_name_.absolute() ) scorefile_name_.path( default_path.path() + "/" + scorefile_name_.path() );
  }else if ( !option[ run::no_scorefile ]() ) {
    write_scorefile_ = true;
    // set up all the information for the scorefile
    utility::file::FileName outfile("score");
    std::ostringstream oss;
    //prefix, suffix
    oss << option[ out::prefix ]() << outfile.base()
        << option[ out::suffix ]();
    outfile.base( oss.str() );
    //path
    if ( option[ out::path::score ].user() ) {
      outfile.path( option[ out::path::score ]().path() );
      outfile.vol( option[ out::path::score ]().vol() );
    } else outfile.path( default_path.path() );
    // determine the extension based on fullatom or centroid; this logic is usually wrong but .sc is okay anyway
    if( option[ out::file::fullatom ] ) {
      outfile.ext( ".fasc" );
    } else {
      outfile.ext( ".sc" );
    }
    scorefile_name_ = outfile.name();
  }
}

protocols::jd2::FileJobOutputter::~FileJobOutputter(){}

void protocols::jd2::FileJobOutputter::scorefile(
  JobCOP job,
  core::pose::Pose const & pose,
  std::string tag,
  std::string scorefile
)
{
  TR.Debug << "FileJobOutputter scorefile" << std::endl;
  if (!write_scorefile_) return;
  core::io::raw_data::ScoreFileData sfd((scorefile.empty() ? scorefile_name_.name() : scorefile));
  std::map < std::string, core::Real > score_map;
    std::map < std::string, std::string > string_map;
  protocols::jd2::ScoreMap::score_map_from_scored_pose( score_map, pose );

  // Adds StringReal job info into the score map for output in the scorefile.
  for( Job::StringRealPairs::const_iterator it(job->output_string_real_pairs_begin()), end(job->output_string_real_pairs_end());
       it != end;
       ++it) {
    score_map[it->first] = it->second;
  }
    
    // Adds StringString job info into a map for output in the scorefile.
  for( Job::StringStringPairs::const_iterator it(job->output_string_string_pairs_begin()), end(job->output_string_string_pairs_end());
        it != end;
        ++it) {
    string_map[it->first] = it->second;
  }

  sfd.write_pose( pose, score_map , (tag+output_name(job)), string_map );
}


///@details this base class implementation will try to _append_ whatever string it gets to a file named after the job, with a user-specified suffix.
void FileJobOutputter::file(
          JobCOP job,
          std::string const & data ){
  TR.Debug << "FileJobOutputter::file" << std::endl;
  if (data.empty()) return; //who needs empty files?

  //this almost certainly needs some sort of error handling - what do you think Andrew?
  utility::io::ozstream out;
  std::string const & miscfile_ext(option[ run::jobdist_miscfile_ext ].value());
  out.open_append( output_name(job) + (miscfile_ext[0] == '.' ? "" : ".") + miscfile_ext );
  out << data << std::flush;
  out.close();
}


//void other_scorefile( std::string const & tag, core::pose::Pose const & pose, std::string const & o_scorefile );

}//jd2
}//protocols