ReportToDB.hh

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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/features/ReportToDB.hh
/// @brief  report feature data to sqlite database
/// @author Matthew O'Meara

#ifndef INCLUDED_protocols_features_ReportToDB_hh
#define INCLUDED_protocols_features_ReportToDB_hh

// Unit Headers
#include <protocols/moves/Mover.hh>
#include <protocols/features/ReportToDB.fwd.hh>

// Project Headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <protocols/features/FeaturesReporter.fwd.hh>
#include <protocols/features/FeaturesReporterFactory.fwd.hh>
#include <protocols/features/ProtocolFeatures.fwd.hh>
#include <protocols/features/BatchFeatures.fwd.hh>
#include <protocols/features/StructureFeatures.fwd.hh>


// Utility Headers
#include <utility/sql_database/DatabaseSessionManager.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/vector1.hh>

// Boost Headers
#include <boost/uuid/uuid.hpp>

// C++ Headers
#include <string>


namespace protocols{
namespace features{

class ReportToDB : public protocols::moves::Mover {

public:
  ReportToDB();

  ReportToDB(std::string const & name);

  ReportToDB(
    std::string const & name,
    utility::sql_database::sessionOP db_session,
    std::string const & sample_source,
    bool use_transactions=true,
    core::Size cache_size=2000);

  ReportToDB(ReportToDB const & src);

  virtual ~ReportToDB();

  virtual
  void
  register_options() const;

  virtual moves::MoverOP fresh_instance() const;

  virtual moves::MoverOP clone() const;

  virtual std::string get_name() const { return "ReportToDB"; }

  void
  parse_sample_source_tag_item(
    utility::tag::TagPtr const tag);

  void
  parse_protocol_id_tag_item(
    utility::tag::TagPtr const tag);

  /* Undefined, commenting out to fix PyRosetta build  void
  parse_struct_id_type_tag_item(
    utility::tag::TagPtr const tag);
  */

  /* Undefined, commenting out to fix PyRosetta build  void
  parse_first_struct_id_tag_item(
    utility::tag::TagPtr const tag);
  */

  void
  parse_use_transactions_tag_item(
    utility::tag::TagPtr const tag);

  void
  parse_cache_size_tag_item(
    utility::tag::TagPtr const tag);

  void
  parse_remove_xray_virt_tag_item(
    utility::tag::TagPtr const tag);  
  
  void
  parse_name_tag_item(
    utility::tag::TagPtr const tag);

  void
  parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap & data,
    Filters_map const & /*filters*/,
    protocols::moves::Movers_map const & /*movers*/,
    core::pose::Pose const & pose );

  void
  check_features_reporter_dependencies(
    FeaturesReporterOP test_feature_reporter
  ) const;

  void
  initialize_reporters();

  void
  initialize_database();

  ///@brief initialize the pose and return the relevant residues
  utility::vector1< bool >
  initialize_pose(
    Pose & pose
  ) const;

  ///@brief Add the defined features reporters to the
  ///'features_reporters' table in the database
  void
  write_features_reporters_table() const;

  ///@brief Link the defined features reporters to the batch of
  ///structures extracted with this invocation of the ReportToDB mover
  void
  write_batch_reports_table() const;

  ///@brief write tables linking the batches table with the features
  ///datababase
  void
  write_linking_tables() const;

  void
  apply(
    Pose& pose);

  boost::uuids::uuid
  report_structure_features(
    utility::vector1<bool> const & relevant_residues) const;

  void
  report_features(
    core::pose::Pose const & pose,
    boost::uuids::uuid struct_id,
    utility::vector1<bool> const & relevant_residues) const;

private:
  utility::sql_database::sessionOP db_session_;
  std::string sample_source_;
  std::string name_;

  bool use_transactions_;

  core::Size cache_size_;
  
  bool remove_xray_virt_;

  core::Size protocol_id_;
  core::Size batch_id_;

  // initialized in parse_my_tag
  core::pack::task::TaskFactoryOP task_factory_;

  protocols::features::FeaturesReporterFactory * features_reporter_factory_;
  protocols::features::ProtocolFeaturesOP protocol_features_;
  protocols::features::BatchFeaturesOP batch_features_;
  protocols::features::StructureFeaturesOP structure_features_;
  utility::vector1< protocols::features::FeaturesReporterOP > features_reporters_;
  bool initialized;
};

} // namespace
} // namespace

#endif //include guard