sequence.h

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/**
 *  \file RMF/decorator/sequence.h
 *  \brief Helper functions for manipulating RMF files.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */

#ifndef RMF_SEQUENCE_DECORATORS_H
#define RMF_SEQUENCE_DECORATORS_H

#include <RMF/config.h>
#include <RMF/infrastructure_macros.h>
#include <RMF/NodeHandle.h>
#include <RMF/FileHandle.h>
#include <RMF/Decorator.h>
#include <RMF/constants.h>
#include <RMF/Vector.h>
#include <RMF/internal/paths.h>
#include <array>
#include <boost/lexical_cast.hpp>

RMF_ENABLE_WARNINGS
namespace RMF {
namespace decorator {


  /** See also Residue and ResidueFactory.
    */
    class ResidueConst: public Decorator {
    friend class ResidueFactory;
  protected:
    IntKey residue_index_;
StringKey residue_type_;
    ResidueConst(NodeConstHandle nh,
              IntKey residue_index,
StringKey residue_type):
       Decorator(nh),
residue_index_(residue_index),
residue_type_(residue_type) {
    }
  public:
    
  Int get_residue_index() const {
    try {
      return get_node().get_value(residue_index_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_frame_residue_index() const {
    try {
      return get_node().get_frame_value(residue_index_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_static_residue_index() const {
    try {
      return get_node().get_static_value(residue_index_);
    } RMF_DECORATOR_CATCH( );
  }


  String get_residue_type() const {
    try {
      return get_node().get_value(residue_type_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_residue_type() const {
    try {
      return get_node().get_frame_value(residue_type_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_residue_type() const {
    try {
      return get_node().get_static_value(residue_type_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "ResidueConst";
    }
    RMF_SHOWABLE(ResidueConst, "Residue: " << get_node());
  };
   /** See also ResidueFactory.
    */
    class Residue: public ResidueConst {
    friend class ResidueFactory;
    Residue(NodeHandle nh,
              IntKey residue_index,
StringKey residue_type):
       ResidueConst(nh, residue_index,
residue_type) {
    }
  public:
    
  void set_residue_index(Int v) {
    try {
      get_node().set_value(residue_index_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_residue_index(Int v) {
    try {
      get_node().set_frame_value(residue_index_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_residue_index(Int v) {
    try {
      get_node().set_static_value(residue_index_, v);
    } RMF_DECORATOR_CATCH( );
  }


  void set_residue_type(String v) {
    try {
      get_node().set_value(residue_type_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_residue_type(String v) {
    try {
      get_node().set_frame_value(residue_type_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_residue_type(String v) {
    try {
      get_node().set_static_value(residue_type_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "Residue";
    }
  };


  /** Create decorators of type Residue.
    */
  class ResidueFactory: public Factory {
    Category cat_;
IntKey residue_index_;
StringKey residue_type_;


  public:
    ResidueFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    residue_index_(fh.get_key<IntTag>(cat_, "residue index")), residue_type_(fh.get_key<StringTag>(cat_, "residue type")) {
    }
     ResidueFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    residue_index_(fh.get_key<IntTag>(cat_, "residue index")), residue_type_(fh.get_key<StringTag>(cat_, "residue type")) {
    }
    /** Get a ResidueConst for nh.*/
    ResidueConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Residue");
      return ResidueConst(nh, residue_index_,
residue_type_);
    }
    /** Get a Residue for nh.*/
    Residue get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Residue");
      return Residue(nh, residue_index_,
residue_type_);
    }
    /** Check whether nh has all the attributes required to be a
        ResidueConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(residue_index_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(residue_index_).get_is_null()
    && !nh.get_static_value(residue_type_).get_is_null();
    }
    RMF_SHOWABLE(ResidueFactory, "ResidueFactory");
  };
  #ifndef RMF_DOXYGEN
struct ResidueConstFactory: public ResidueFactory {
    ResidueConstFactory(FileConstHandle fh):
    ResidueFactory(fh) {
    }
    ResidueConstFactory(FileHandle fh):
    ResidueFactory(fh) {
    }

};
  #endif




  /** See also Chain and ChainFactory.
    */
    class ChainConst: public Decorator {
    friend class ChainFactory;
  protected:
    StringKey chain_id_;
StringKey sequence_;
IntKey sequence_offset_;
StringKey uniprot_accession_;
StringKey label_asym_id_;
StringKey chain_type_;
    ChainConst(NodeConstHandle nh,
              StringKey chain_id,
StringKey sequence,
IntKey sequence_offset,
StringKey uniprot_accession,
StringKey label_asym_id,
StringKey chain_type):
       Decorator(nh),
chain_id_(chain_id),
sequence_(sequence),
sequence_offset_(sequence_offset),
uniprot_accession_(uniprot_accession),
label_asym_id_(label_asym_id),
chain_type_(chain_type) {
    }
  public:
    
  String get_chain_id() const {
    try {
      return get_node().get_value(chain_id_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_chain_id() const {
    try {
      return get_node().get_frame_value(chain_id_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_chain_id() const {
    try {
      return get_node().get_static_value(chain_id_);
    } RMF_DECORATOR_CATCH( );
  }


  String get_sequence() const {
    try {
      if (!get_node().get_has_value(sequence_)) return "";
return get_node().get_value(sequence_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_sequence() const {
    try {
      if (!get_node().get_has_value(sequence_)) return "";
return get_node().get_frame_value(sequence_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_sequence() const {
    try {
      if (!get_node().get_has_value(sequence_)) return "";
return get_node().get_static_value(sequence_);
    } RMF_DECORATOR_CATCH( );
  }


  Int get_sequence_offset() const {
    try {
      if (!get_node().get_has_value(sequence_offset_)) return 0;
return get_node().get_value(sequence_offset_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_frame_sequence_offset() const {
    try {
      if (!get_node().get_has_value(sequence_offset_)) return 0;
return get_node().get_frame_value(sequence_offset_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_static_sequence_offset() const {
    try {
      if (!get_node().get_has_value(sequence_offset_)) return 0;
return get_node().get_static_value(sequence_offset_);
    } RMF_DECORATOR_CATCH( );
  }


  String get_uniprot_accession() const {
    try {
      if (!get_node().get_has_value(uniprot_accession_)) return "";
return get_node().get_value(uniprot_accession_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_uniprot_accession() const {
    try {
      if (!get_node().get_has_value(uniprot_accession_)) return "";
return get_node().get_frame_value(uniprot_accession_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_uniprot_accession() const {
    try {
      if (!get_node().get_has_value(uniprot_accession_)) return "";
return get_node().get_static_value(uniprot_accession_);
    } RMF_DECORATOR_CATCH( );
  }


  String get_label_asym_id() const {
    try {
      if (!get_node().get_has_value(label_asym_id_)) return "";
return get_node().get_value(label_asym_id_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_label_asym_id() const {
    try {
      if (!get_node().get_has_value(label_asym_id_)) return "";
return get_node().get_frame_value(label_asym_id_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_label_asym_id() const {
    try {
      if (!get_node().get_has_value(label_asym_id_)) return "";
return get_node().get_static_value(label_asym_id_);
    } RMF_DECORATOR_CATCH( );
  }


  String get_chain_type() const {
    try {
      if (!get_node().get_has_value(chain_type_)) return "UnknownChainType";
return get_node().get_value(chain_type_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_chain_type() const {
    try {
      if (!get_node().get_has_value(chain_type_)) return "UnknownChainType";
return get_node().get_frame_value(chain_type_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_chain_type() const {
    try {
      if (!get_node().get_has_value(chain_type_)) return "UnknownChainType";
return get_node().get_static_value(chain_type_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "ChainConst";
    }
    RMF_SHOWABLE(ChainConst, "Chain: " << get_node());
  };
   /** See also ChainFactory.
    */
    class Chain: public ChainConst {
    friend class ChainFactory;
    Chain(NodeHandle nh,
              StringKey chain_id,
StringKey sequence,
IntKey sequence_offset,
StringKey uniprot_accession,
StringKey label_asym_id,
StringKey chain_type):
       ChainConst(nh, chain_id,
sequence,
sequence_offset,
uniprot_accession,
label_asym_id,
chain_type) {
    }
  public:
    
  void set_chain_id(String v) {
    try {
      get_node().set_value(chain_id_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_chain_id(String v) {
    try {
      get_node().set_frame_value(chain_id_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_chain_id(String v) {
    try {
      get_node().set_static_value(chain_id_, v);
    } RMF_DECORATOR_CATCH( );
  }


  void set_sequence(String v) {
    try {
      get_node().set_value(sequence_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_sequence(String v) {
    try {
      get_node().set_frame_value(sequence_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_sequence(String v) {
    try {
      get_node().set_static_value(sequence_, v);
    } RMF_DECORATOR_CATCH( );
  }


  void set_sequence_offset(Int v) {
    try {
      get_node().set_value(sequence_offset_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_sequence_offset(Int v) {
    try {
      get_node().set_frame_value(sequence_offset_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_sequence_offset(Int v) {
    try {
      get_node().set_static_value(sequence_offset_, v);
    } RMF_DECORATOR_CATCH( );
  }


  void set_uniprot_accession(String v) {
    try {
      get_node().set_value(uniprot_accession_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_uniprot_accession(String v) {
    try {
      get_node().set_frame_value(uniprot_accession_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_uniprot_accession(String v) {
    try {
      get_node().set_static_value(uniprot_accession_, v);
    } RMF_DECORATOR_CATCH( );
  }


  void set_label_asym_id(String v) {
    try {
      get_node().set_value(label_asym_id_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_label_asym_id(String v) {
    try {
      get_node().set_frame_value(label_asym_id_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_label_asym_id(String v) {
    try {
      get_node().set_static_value(label_asym_id_, v);
    } RMF_DECORATOR_CATCH( );
  }


  void set_chain_type(String v) {
    try {
      get_node().set_value(chain_type_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_chain_type(String v) {
    try {
      get_node().set_frame_value(chain_type_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_chain_type(String v) {
    try {
      get_node().set_static_value(chain_type_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "Chain";
    }
  };


  /** Create decorators of type Chain.
    */
  class ChainFactory: public Factory {
    Category cat_;
StringKey chain_id_;
StringKey sequence_;
IntKey sequence_offset_;
StringKey uniprot_accession_;
StringKey label_asym_id_;
StringKey chain_type_;






  public:
    ChainFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    chain_id_(fh.get_key<StringTag>(cat_, "chain id")), sequence_(fh.get_key<StringTag>(cat_, "sequence")), sequence_offset_(fh.get_key<IntTag>(cat_, "sequence offset")), uniprot_accession_(fh.get_key<StringTag>(cat_, "uniprot accession")), label_asym_id_(fh.get_key<StringTag>(cat_, "label asym id")), chain_type_(fh.get_key<StringTag>(cat_, "chain type")) {
    }
     ChainFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    chain_id_(fh.get_key<StringTag>(cat_, "chain id")), sequence_(fh.get_key<StringTag>(cat_, "sequence")), sequence_offset_(fh.get_key<IntTag>(cat_, "sequence offset")), uniprot_accession_(fh.get_key<StringTag>(cat_, "uniprot accession")), label_asym_id_(fh.get_key<StringTag>(cat_, "label asym id")), chain_type_(fh.get_key<StringTag>(cat_, "chain type")) {
    }
    /** Get a ChainConst for nh.*/
    ChainConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Chain");
      return ChainConst(nh, chain_id_,
sequence_,
sequence_offset_,
uniprot_accession_,
label_asym_id_,
chain_type_);
    }
    /** Get a Chain for nh.*/
    Chain get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Chain");
      return Chain(nh, chain_id_,
sequence_,
sequence_offset_,
uniprot_accession_,
label_asym_id_,
chain_type_);
    }
    /** Check whether nh has all the attributes required to be a
        ChainConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(chain_id_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(chain_id_).get_is_null();
    }
    RMF_SHOWABLE(ChainFactory, "ChainFactory");
  };
  #ifndef RMF_DOXYGEN
struct ChainConstFactory: public ChainFactory {
    ChainConstFactory(FileConstHandle fh):
    ChainFactory(fh) {
    }
    ChainConstFactory(FileHandle fh):
    ChainFactory(fh) {
    }

};
  #endif




  /** See also Fragment and FragmentFactory.
    */
    class FragmentConst: public Decorator {
    friend class FragmentFactory;
  protected:
    IntsKey residue_indexes_;
    FragmentConst(NodeConstHandle nh,
              IntsKey residue_indexes):
       Decorator(nh),
residue_indexes_(residue_indexes) {
    }
  public:
    
  Ints get_residue_indexes() const {
    try {
      return get_node().get_value(residue_indexes_);
    } RMF_DECORATOR_CATCH( );
  }
  Ints get_frame_residue_indexes() const {
    try {
      return get_node().get_frame_value(residue_indexes_);
    } RMF_DECORATOR_CATCH( );
  }
  Ints get_static_residue_indexes() const {
    try {
      return get_node().get_static_value(residue_indexes_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "FragmentConst";
    }
    RMF_SHOWABLE(FragmentConst, "Fragment: " << get_node());
  };
   /** See also FragmentFactory.
    */
    class Fragment: public FragmentConst {
    friend class FragmentFactory;
    Fragment(NodeHandle nh,
              IntsKey residue_indexes):
       FragmentConst(nh, residue_indexes) {
    }
  public:
    
  void set_residue_indexes(Ints v) {
    try {
      get_node().set_value(residue_indexes_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_residue_indexes(Ints v) {
    try {
      get_node().set_frame_value(residue_indexes_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_residue_indexes(Ints v) {
    try {
      get_node().set_static_value(residue_indexes_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "Fragment";
    }
  };


  /** Create decorators of type Fragment.
    */
  class FragmentFactory: public Factory {
    Category cat_;
IntsKey residue_indexes_;

  public:
    FragmentFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    residue_indexes_(fh.get_key<IntsTag>(cat_, "residue indexes")) {
    }
     FragmentFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    residue_indexes_(fh.get_key<IntsTag>(cat_, "residue indexes")) {
    }
    /** Get a FragmentConst for nh.*/
    FragmentConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Fragment");
      return FragmentConst(nh, residue_indexes_);
    }
    /** Get a Fragment for nh.*/
    Fragment get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Fragment");
      return Fragment(nh, residue_indexes_);
    }
    /** Check whether nh has all the attributes required to be a
        FragmentConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(residue_indexes_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(residue_indexes_).get_is_null();
    }
    RMF_SHOWABLE(FragmentFactory, "FragmentFactory");
  };
  #ifndef RMF_DOXYGEN
struct FragmentConstFactory: public FragmentFactory {
    FragmentConstFactory(FileConstHandle fh):
    FragmentFactory(fh) {
    }
    FragmentConstFactory(FileHandle fh):
    FragmentFactory(fh) {
    }

};
  #endif




  /** See also BackwardsCompatibilityFragment and BackwardsCompatibilityFragmentFactory.
    */
    class BackwardsCompatibilityFragmentConst: public Decorator {
    friend class BackwardsCompatibilityFragmentFactory;
  protected:
    IntsKey indexes_;
    BackwardsCompatibilityFragmentConst(NodeConstHandle nh,
              IntsKey indexes):
       Decorator(nh),
indexes_(indexes) {
    }
  public:
    
  Ints get_indexes() const {
    try {
      return get_node().get_value(indexes_);
    } RMF_DECORATOR_CATCH( );
  }
  Ints get_frame_indexes() const {
    try {
      return get_node().get_frame_value(indexes_);
    } RMF_DECORATOR_CATCH( );
  }
  Ints get_static_indexes() const {
    try {
      return get_node().get_static_value(indexes_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "BackwardsCompatibilityFragmentConst";
    }
    RMF_SHOWABLE(BackwardsCompatibilityFragmentConst, "BackwardsCompatibilityFragment: " << get_node());
  };
   /** See also BackwardsCompatibilityFragmentFactory.
    */
    class BackwardsCompatibilityFragment: public BackwardsCompatibilityFragmentConst {
    friend class BackwardsCompatibilityFragmentFactory;
    BackwardsCompatibilityFragment(NodeHandle nh,
              IntsKey indexes):
       BackwardsCompatibilityFragmentConst(nh, indexes) {
    }
  public:
    
  void set_indexes(Ints v) {
    try {
      get_node().set_value(indexes_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_indexes(Ints v) {
    try {
      get_node().set_frame_value(indexes_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_indexes(Ints v) {
    try {
      get_node().set_static_value(indexes_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "BackwardsCompatibilityFragment";
    }
  };


  /** Create decorators of type BackwardsCompatibilityFragment.
    */
  class BackwardsCompatibilityFragmentFactory: public Factory {
    Category cat_;
IntsKey indexes_;

  public:
    BackwardsCompatibilityFragmentFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    indexes_(fh.get_key<IntsTag>(cat_, "indexes")) {
    }
     BackwardsCompatibilityFragmentFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    indexes_(fh.get_key<IntsTag>(cat_, "indexes")) {
    }
    /** Get a BackwardsCompatibilityFragmentConst for nh.*/
    BackwardsCompatibilityFragmentConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  BackwardsCompatibilityFragment");
      return BackwardsCompatibilityFragmentConst(nh, indexes_);
    }
    /** Get a BackwardsCompatibilityFragment for nh.*/
    BackwardsCompatibilityFragment get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  BackwardsCompatibilityFragment");
      return BackwardsCompatibilityFragment(nh, indexes_);
    }
    /** Check whether nh has all the attributes required to be a
        BackwardsCompatibilityFragmentConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(indexes_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(indexes_).get_is_null();
    }
    RMF_SHOWABLE(BackwardsCompatibilityFragmentFactory, "BackwardsCompatibilityFragmentFactory");
  };
  #ifndef RMF_DOXYGEN
struct BackwardsCompatibilityFragmentConstFactory: public BackwardsCompatibilityFragmentFactory {
    BackwardsCompatibilityFragmentConstFactory(FileConstHandle fh):
    BackwardsCompatibilityFragmentFactory(fh) {
    }
    BackwardsCompatibilityFragmentConstFactory(FileHandle fh):
    BackwardsCompatibilityFragmentFactory(fh) {
    }

};
  #endif




  /** See also Domain and DomainFactory.
    */
    class DomainConst: public Decorator {
    friend class DomainFactory;
  protected:
    std::array<IntKey, 2> residue_indexes_;
    DomainConst(NodeConstHandle nh,
              std::array<IntKey, 2> residue_indexes):
       Decorator(nh),
residue_indexes_(residue_indexes) {
    }
  public:
    
  IntRange get_residue_indexes() const {
    try {
      IntRange ret;
      ret[0] = get_node().get_value(residue_indexes_[0]);
      ret[1] = get_node().get_value(residue_indexes_[1]);
      return ret;
    } RMF_DECORATOR_CATCH( );
  }
  IntRange get_static_residue_indexes() const {
    try {
      IntRange ret;
      ret[0] = get_node().get_static_value(residue_indexes_[0]);
      ret[1] = get_node().get_static_value(residue_indexes_[1]);
      return ret;
    } RMF_DECORATOR_CATCH( );
  }
  IntRange get_frame_residue_indexes() const {
    try {
    IntRange ret;
      ret[0] = get_node().get_frame_value(residue_indexes_[0]);
      ret[1] = get_node().get_frame_value(residue_indexes_[1]);
      return ret;
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "DomainConst";
    }
    RMF_SHOWABLE(DomainConst, "Domain: " << get_node());
  };
   /** See also DomainFactory.
    */
    class Domain: public DomainConst {
    friend class DomainFactory;
    Domain(NodeHandle nh,
              std::array<IntKey, 2> residue_indexes):
       DomainConst(nh, residue_indexes) {
    }
  public:
    
  void set_residue_indexes(Int v0, Int v1) {
    try {
      get_node().set_value(residue_indexes_[0], v0);
      get_node().set_value(residue_indexes_[1], v1);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_residue_indexes(Int v0, Int v1) {
    try {
      get_node().set_frame_value(residue_indexes_[0], v0);
      get_node().set_frame_value(residue_indexes_[1], v1);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_residue_indexes(Int v0, Int v1) {
    try {
      get_node().set_static_value(residue_indexes_[0], v0);
      get_node().set_static_value(residue_indexes_[1], v1);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "Domain";
    }
  };


  /** Create decorators of type Domain.
    */
  class DomainFactory: public Factory {
    Category cat_;
std::array<IntKey, 2> residue_indexes_;
  template <class H> std::array<IntKey, 2> get_residue_indexes_keys(H fh) const {
     std::array<IntKey, 2> ret;
     ret[0] = fh.template get_key<IntTag>(cat_, "first residue index");
     ret[1] = fh.template get_key<IntTag>(cat_, "last residue index");
     return ret;
    }

  public:
    DomainFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    residue_indexes_(get_residue_indexes_keys(fh)) {
    }
     DomainFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    residue_indexes_(get_residue_indexes_keys(fh)) {
    }
    /** Get a DomainConst for nh.*/
    DomainConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Domain");
      return DomainConst(nh, residue_indexes_);
    }
    /** Get a Domain for nh.*/
    Domain get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Domain");
      return Domain(nh, residue_indexes_);
    }
    /** Check whether nh has all the attributes required to be a
        DomainConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(residue_indexes_[0]).get_is_null() && !nh.get_value(residue_indexes_[1]).get_is_null() && nh.get_value(residue_indexes_[0]) < nh.get_value(residue_indexes_[1]);
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(residue_indexes_[0]).get_is_null() && !nh.get_static_value(residue_indexes_[1]).get_is_null() && nh.get_value(residue_indexes_[0]) < nh.get_value(residue_indexes_[1]);
    }
    RMF_SHOWABLE(DomainFactory, "DomainFactory");
  };
  #ifndef RMF_DOXYGEN
struct DomainConstFactory: public DomainFactory {
    DomainConstFactory(FileConstHandle fh):
    DomainFactory(fh) {
    }
    DomainConstFactory(FileHandle fh):
    DomainFactory(fh) {
    }

};
  #endif




  /** See also Typed and TypedFactory.
    */
    class TypedConst: public Decorator {
    friend class TypedFactory;
  protected:
    StringKey type_name_;
    TypedConst(NodeConstHandle nh,
              StringKey type_name):
       Decorator(nh),
type_name_(type_name) {
    }
  public:
    
  String get_type_name() const {
    try {
      return get_node().get_value(type_name_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_frame_type_name() const {
    try {
      return get_node().get_frame_value(type_name_);
    } RMF_DECORATOR_CATCH( );
  }
  String get_static_type_name() const {
    try {
      return get_node().get_static_value(type_name_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "TypedConst";
    }
    RMF_SHOWABLE(TypedConst, "Typed: " << get_node());
  };
   /** See also TypedFactory.
    */
    class Typed: public TypedConst {
    friend class TypedFactory;
    Typed(NodeHandle nh,
              StringKey type_name):
       TypedConst(nh, type_name) {
    }
  public:
    
  void set_type_name(String v) {
    try {
      get_node().set_value(type_name_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_type_name(String v) {
    try {
      get_node().set_frame_value(type_name_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_type_name(String v) {
    try {
      get_node().set_static_value(type_name_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "Typed";
    }
  };


  /** Create decorators of type Typed.
    */
  class TypedFactory: public Factory {
    Category cat_;
StringKey type_name_;

  public:
    TypedFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    type_name_(fh.get_key<StringTag>(cat_, "type name")) {
    }
     TypedFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    type_name_(fh.get_key<StringTag>(cat_, "type name")) {
    }
    /** Get a TypedConst for nh.*/
    TypedConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Typed");
      return TypedConst(nh, type_name_);
    }
    /** Get a Typed for nh.*/
    Typed get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Typed");
      return Typed(nh, type_name_);
    }
    /** Check whether nh has all the attributes required to be a
        TypedConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(type_name_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(type_name_).get_is_null();
    }
    RMF_SHOWABLE(TypedFactory, "TypedFactory");
  };
  #ifndef RMF_DOXYGEN
struct TypedConstFactory: public TypedFactory {
    TypedConstFactory(FileConstHandle fh):
    TypedFactory(fh) {
    }
    TypedConstFactory(FileHandle fh):
    TypedFactory(fh) {
    }

};
  #endif




  /** See also Copy and CopyFactory.
    */
    class CopyConst: public Decorator {
    friend class CopyFactory;
  protected:
    IntKey copy_index_;
    CopyConst(NodeConstHandle nh,
              IntKey copy_index):
       Decorator(nh),
copy_index_(copy_index) {
    }
  public:
    
  Int get_copy_index() const {
    try {
      return get_node().get_value(copy_index_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_frame_copy_index() const {
    try {
      return get_node().get_frame_value(copy_index_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_static_copy_index() const {
    try {
      return get_node().get_static_value(copy_index_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "CopyConst";
    }
    RMF_SHOWABLE(CopyConst, "Copy: " << get_node());
  };
   /** See also CopyFactory.
    */
    class Copy: public CopyConst {
    friend class CopyFactory;
    Copy(NodeHandle nh,
              IntKey copy_index):
       CopyConst(nh, copy_index) {
    }
  public:
    
  void set_copy_index(Int v) {
    try {
      get_node().set_value(copy_index_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_copy_index(Int v) {
    try {
      get_node().set_frame_value(copy_index_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_copy_index(Int v) {
    try {
      get_node().set_static_value(copy_index_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "Copy";
    }
  };


  /** Create decorators of type Copy.
    */
  class CopyFactory: public Factory {
    Category cat_;
IntKey copy_index_;

  public:
    CopyFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    copy_index_(fh.get_key<IntTag>(cat_, "copy index")) {
    }
     CopyFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    copy_index_(fh.get_key<IntTag>(cat_, "copy index")) {
    }
    /** Get a CopyConst for nh.*/
    CopyConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Copy");
      return CopyConst(nh, copy_index_);
    }
    /** Get a Copy for nh.*/
    Copy get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  Copy");
      return Copy(nh, copy_index_);
    }
    /** Check whether nh has all the attributes required to be a
        CopyConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(copy_index_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(copy_index_).get_is_null();
    }
    RMF_SHOWABLE(CopyFactory, "CopyFactory");
  };
  #ifndef RMF_DOXYGEN
struct CopyConstFactory: public CopyFactory {
    CopyConstFactory(FileConstHandle fh):
    CopyFactory(fh) {
    }
    CopyConstFactory(FileHandle fh):
    CopyFactory(fh) {
    }

};
  #endif




  /** See also State and StateFactory.
    */
    class StateConst: public Decorator {
    friend class StateFactory;
  protected:
    IntKey state_index_;
    StateConst(NodeConstHandle nh,
              IntKey state_index):
       Decorator(nh),
state_index_(state_index) {
    }
  public:
    
  Int get_state_index() const {
    try {
      return get_node().get_value(state_index_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_frame_state_index() const {
    try {
      return get_node().get_frame_value(state_index_);
    } RMF_DECORATOR_CATCH( );
  }
  Int get_static_state_index() const {
    try {
      return get_node().get_static_value(state_index_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "StateConst";
    }
    RMF_SHOWABLE(StateConst, "State: " << get_node());
  };
   /** See also StateFactory.
    */
    class State: public StateConst {
    friend class StateFactory;
    State(NodeHandle nh,
              IntKey state_index):
       StateConst(nh, state_index) {
    }
  public:
    
  void set_state_index(Int v) {
    try {
      get_node().set_value(state_index_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_state_index(Int v) {
    try {
      get_node().set_frame_value(state_index_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_state_index(Int v) {
    try {
      get_node().set_static_value(state_index_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "State";
    }
  };


  /** Create decorators of type State.
    */
  class StateFactory: public Factory {
    Category cat_;
IntKey state_index_;

  public:
    StateFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    state_index_(fh.get_key<IntTag>(cat_, "state index")) {
    }
     StateFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    state_index_(fh.get_key<IntTag>(cat_, "state index")) {
    }
    /** Get a StateConst for nh.*/
    StateConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  State");
      return StateConst(nh, state_index_);
    }
    /** Get a State for nh.*/
    State get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  State");
      return State(nh, state_index_);
    }
    /** Check whether nh has all the attributes required to be a
        StateConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(state_index_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(state_index_).get_is_null();
    }
    RMF_SHOWABLE(StateFactory, "StateFactory");
  };
  #ifndef RMF_DOXYGEN
struct StateConstFactory: public StateFactory {
    StateConstFactory(FileConstHandle fh):
    StateFactory(fh) {
    }
    StateConstFactory(FileHandle fh):
    StateFactory(fh) {
    }

};
  #endif




  /** See also ExplicitResolution and ExplicitResolutionFactory.
    */
    class ExplicitResolutionConst: public Decorator {
    friend class ExplicitResolutionFactory;
  protected:
    FloatKey explicit_resolution_;
    ExplicitResolutionConst(NodeConstHandle nh,
              FloatKey explicit_resolution):
       Decorator(nh),
explicit_resolution_(explicit_resolution) {
    }
  public:
    
  Float get_explicit_resolution() const {
    try {
      return get_node().get_value(explicit_resolution_);
    } RMF_DECORATOR_CATCH( );
  }
  Float get_frame_explicit_resolution() const {
    try {
      return get_node().get_frame_value(explicit_resolution_);
    } RMF_DECORATOR_CATCH( );
  }
  Float get_static_explicit_resolution() const {
    try {
      return get_node().get_static_value(explicit_resolution_);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "ExplicitResolutionConst";
    }
    RMF_SHOWABLE(ExplicitResolutionConst, "ExplicitResolution: " << get_node());
  };
   /** See also ExplicitResolutionFactory.
    */
    class ExplicitResolution: public ExplicitResolutionConst {
    friend class ExplicitResolutionFactory;
    ExplicitResolution(NodeHandle nh,
              FloatKey explicit_resolution):
       ExplicitResolutionConst(nh, explicit_resolution) {
    }
  public:
    
  void set_explicit_resolution(Float v) {
    try {
      get_node().set_value(explicit_resolution_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_frame_explicit_resolution(Float v) {
    try {
      get_node().set_frame_value(explicit_resolution_, v);
    } RMF_DECORATOR_CATCH( );
  }
  void set_static_explicit_resolution(Float v) {
    try {
      get_node().set_static_value(explicit_resolution_, v);
    } RMF_DECORATOR_CATCH( );
  }

    static std::string get_decorator_type_name() {
         return "ExplicitResolution";
    }
  };


  /** Create decorators of type ExplicitResolution.
    */
  class ExplicitResolutionFactory: public Factory {
    Category cat_;
FloatKey explicit_resolution_;

  public:
    ExplicitResolutionFactory(FileConstHandle fh):
    cat_(fh.get_category("sequence")),
    explicit_resolution_(fh.get_key<FloatTag>(cat_, "explicit resolution")) {
    }
     ExplicitResolutionFactory(FileHandle fh):
    cat_(fh.get_category("sequence")),
    explicit_resolution_(fh.get_key<FloatTag>(cat_, "explicit resolution")) {
    }
    /** Get a ExplicitResolutionConst for nh.*/
    ExplicitResolutionConst get(NodeConstHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  ExplicitResolution");
      return ExplicitResolutionConst(nh, explicit_resolution_);
    }
    /** Get a ExplicitResolution for nh.*/
    ExplicitResolution get(NodeHandle nh) const {
      RMF_USAGE_CHECK((nh.get_type() == RMF::REPRESENTATION), std::string("Bad node type. Got \"")
                                      + boost::lexical_cast<std::string>(nh.get_type())
                                      + "\" in decorator type  ExplicitResolution");
      return ExplicitResolution(nh, explicit_resolution_);
    }
    /** Check whether nh has all the attributes required to be a
        ExplicitResolutionConst.*/
    bool get_is(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_value(explicit_resolution_).get_is_null();
    }
    bool get_is_static(NodeConstHandle nh) const {
      return (nh.get_type() == RMF::REPRESENTATION)
    && !nh.get_static_value(explicit_resolution_).get_is_null();
    }
    RMF_SHOWABLE(ExplicitResolutionFactory, "ExplicitResolutionFactory");
  };
  #ifndef RMF_DOXYGEN
struct ExplicitResolutionConstFactory: public ExplicitResolutionFactory {
    ExplicitResolutionConstFactory(FileConstHandle fh):
    ExplicitResolutionFactory(fh) {
    }
    ExplicitResolutionConstFactory(FileHandle fh):
    ExplicitResolutionFactory(fh) {
    }

};
  #endif



} /* namespace decorator */
} /* namespace RMF */
RMF_DISABLE_WARNINGS

#endif /* RMF_SEQUENCE_DECORATORS_H */