JobOutputter.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:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (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/JobOutputter.cc
/// @brief  August 2008 job distributor as planned at RosettaCon08 - Base class JobOutputter
/// @author Steven Lewis smlewi@gmail.com

// Unit headers
#include <protocols/jd2/JobOutputter.hh>

// package headers
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobInputter.fwd.hh>
#include <protocols/jd2/util.hh>

// Project headers
#include <protocols/evaluation/EvaluatorFactory.hh>
#include <protocols/evaluation/PoseEvaluator.hh>

// Utility headers
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/string_util.hh>


#include <basic/options/option.hh>
#include <basic/MemTracer.hh>


// option key includes

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

#include <utility/vector1.hh>


///C++ headers
//#include <string> //in the .hh anyway

namespace protocols {
namespace jd2 {

JobOutputter::JobOutputter() : evaluators_(new protocols::evaluation::PoseEvaluators()) {
  evaluation::EvaluatorFactory::get_instance()->add_all_evaluators(*evaluators_);
  basic::mem_tr << "JobOutputter CSTOR" << std::endl;
}

JobOutputter::~JobOutputter() {}

///base implementation does nothing
void JobOutputter::flush() {}

///@details this is copied from protocols/jobdist/Jobs.cc, r24761
/// Checks the current JobInputter input source from the singleton instance of
/// JobDistributor.  If a PDB_FILE, it will deliberately discard any path
/// information in the input tag as well as any file name extension (since
/// input tags are usually file names).  Otherwise, it will keep the entire input
/// tag as-is.
std::string JobOutputter::affixed_numbered_name( JobCOP job ){
  using basic::options::option;
  using namespace basic::options::OptionKeys;

  // Use at least 4 digits in number to match Rosetta++
  core::Size nstruct_width = 0;
  core::Size const nstruct = job->nstruct_max();
  for ( core::Size i = 1; i <= nstruct || nstruct_width < 4; i *= 10 ) {
    nstruct_width += 1;
  }

  // Construct the base name.  For pdb files we need to hack away the paths
  // and extensions.  For all other types of input sources, assume that the
  // string that comes in is exactly the tag we want.  This is important
  // for silent file <-> BOINC usage to avoid problems with duplicate tags
  // caused by path/ext removal.
  std::string base_name = job->input_tag();
  switch ( JobDistributor::get_instance()->job_inputter_input_source() ) {
    case JobInputterInputSource::PDB_FILE : { // remove paths and ext.

      // Treat tags as file names so that we put the number before the extension.
      utility::vector1< std::string > temp_out_names= utility::split( base_name );
      utility::file::FileName out_name = utility::file::combine_names( temp_out_names );
      base_name = out_name.base();

      break;
    }

    default : { // do nothing
      break;
    }
  }

  // now construct the full name
  std::ostringstream oss;
  std::string prefix( option[ out::prefix ].value() );
  if ( job->status_prefix().size() ) {
    prefix = job->status_prefix()+"_";
  }
  oss << prefix << base_name << option[ out::suffix ].value();
  if ( ! option[ out::no_nstruct_label ] || job->nstruct_index() != 1 ) {
    oss << '_' << std::setfill('0') << std::setw(nstruct_width) << job->nstruct_index();
  }
  return oss.str();
}


///@details run the PoseEvaluators on the pose
/// evaluation creates string value pairs which end up in the SilentStruct energy object
/// instead of filling things into a SilentStruct we could provide a different interface...
///  wait until Steven has finished his string/value pair output
void JobOutputter::evaluate(
  core::pose::Pose & pose,
  std::string tag,
  core::io::silent::SilentStruct & pss
) const {
  if ( evaluators()->size() ) {
    evaluators()->apply( pose, tag, pss );
  }
}

///@brief optionally pass a starting (reference) pose to a JobOutputter for comparison purposes and/or as interface for initializing evaluators. (Currently does nothing in this base class.)
void JobOutputter::starting_pose( core::pose::Pose const & ){}

///@details add another PoseEvaluator to the list of evaluations
void JobOutputter::add_evaluation( evaluation::PoseEvaluatorOP ev_in ) {
  evaluators_->add_evaluation( ev_in );
}

///@details set a list of Evaluations
/// ( the list will be copied, the evaluations are OPs )
///
void JobOutputter::set_evaluators( evaluation::PoseEvaluators const& ev_in ) {
  evaluators_ = new protocols::evaluation::PoseEvaluators(ev_in);
}

/// @brief clear the list of evaluators
void JobOutputter::clear_evaluators() {
  evaluators_->clear();
}

/// @details return the list of PoseEvaluators
evaluation::PoseEvaluatorsCOP JobOutputter::evaluators() const {
  return evaluators_;
}


} // jd2
} // protocols