format 58
"src" // src
  revision 23
  modified_by 2 "sallet"
  // class settings
  //class diagram settings
  draw_all_relations default hide_attributes default hide_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_multiplicity default show_members_initialization default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
  //use case diagram settings
  package_name_in_tab default show_context default auto_label_position default draw_all_relations default class_drawing_mode default shadow default show_stereotype_properties default
  //sequence diagram settings
  show_full_operations_definition default write_horizontally default class_drawing_mode default drawing_language default draw_all_relations default shadow default show_stereotype_properties default
  //collaboration diagram settings
  show_full_operations_definition default show_hierarchical_rank default write_horizontally default drawing_language default package_name_in_tab default show_context default draw_all_relations default shadow default show_stereotype_properties default
  //object diagram settings
   write_horizontally default package_name_in_tab default show_context default auto_label_position default draw_all_relations default shadow default show_stereotype_properties default
  //component diagram settings
  package_name_in_tab default show_context default auto_label_position default draw_all_relations default shadow default
  draw_component_as_icon default show_component_req_prov default show_component_rea default show_stereotype_properties default
  //deployment diagram settings
  package_name_in_tab default show_context default write_horizontally default auto_label_position default draw_all_relations default shadow default
  draw_component_as_icon default show_component_req_prov default show_component_rea default show_stereotype_properties default
  //state diagram settings
  package_name_in_tab default show_context default auto_label_position default write_trans_label_horizontally default show_trans_definition default draw_all_relations default shadow default
  show_activities default region_horizontally default drawing_language default show_stereotype_properties default
  //activity diagram settings
  package_name_in_tab default show_context default show_opaque_action_definition default auto_label_position default write_flow_label_horizontally default draw_all_relations default shadow default
  show_infonote default drawing_language default show_stereotype_properties default
  
  classview 128002 "src"
    //class diagram settings
    draw_all_relations default hide_attributes default hide_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_multiplicity default show_members_initialization default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
    //collaboration diagram settings
    show_full_operations_definition default show_hierarchical_rank default write_horizontally default drawing_language default package_name_in_tab default show_context default draw_all_relations default shadow default show_stereotype_properties default
    //object diagram settings
     write_horizontally default package_name_in_tab default show_context default auto_label_position default draw_all_relations default shadow default show_stereotype_properties default
    //sequence diagram settings
    show_full_operations_definition default write_horizontally default class_drawing_mode default drawing_language default draw_all_relations default shadow default show_stereotype_properties default
    //state diagram settings
    package_name_in_tab default show_context default auto_label_position default write_trans_label_horizontally default show_trans_definition default draw_all_relations default shadow default
    show_activities default region_horizontally default drawing_language default show_stereotype_properties default
    //class settings
    //activity diagram settings
    package_name_in_tab default show_context default show_opaque_action_definition default auto_label_position default write_flow_label_horizontally default draw_all_relations default shadow default
    show_infonote default drawing_language default show_stereotype_properties default
    class 128002 "OneAltEst"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                      OneAltEst
 ************************************************************"
      classrelation 128002 // <dependency>
	relation 128002 -_->
	  stereotype "friend"
	  a default
	    cpp default "${type}"
	    classrelation_ref 128002 // <dependency>
	  b parent class_ref 128130 // AltEst
      end

      attribute 128002 "id"
	private explicit_type "char"
	multiplicity "[FILENAME_MAX+1]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 128130 "altSplicingEvidence"
	private explicit_type "bool"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 128258 "vi_ExonStart"
	private explicit_type "int"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 128386 "vi_ExonEnd"
	private explicit_type "int"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 128002 "Penalize"
	private explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param inout name "Data" type class_ref 128258 // DATA
	  param in name "altPenalty" explicit_type "double"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 128130 "OneAltEst"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 128258 "OneAltEst"
	public explicit_return_type ""
	nparams 3
	  param inout name "id" explicit_type "char"
	  param in name "i" explicit_type "int"
	  param in name "j" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 128386 "~OneAltEst"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 128514 "Reset"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 128642 "AddExon"
	public explicit_return_type "void"
	nparams 2
	  param in name "" explicit_type "int"
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 128770 "RemoveExon"
	public explicit_return_type "void"
	nparams 1
	  param in name "i" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 128898 "ExtremitiesTrim"
	public explicit_return_type "void"
	nparams 1
	  param in name "exonucleasicLength" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 129026 "IsFiltered"
	public explicit_return_type "int"
	nparams 9
	  param in name "unspliced" explicit_type "bool"
	  param in name "extremelen" explicit_type "bool"
	  param in name "verbose" explicit_type "bool"
	  param in name "minIn" explicit_type "int"
	  param in name "maxIn" explicit_type "int"
	  param in name "maxEx" explicit_type "int"
	  param in name "minEx" explicit_type "int"
	  param in name "minEstLen" explicit_type "int"
	  param in name "maxEstLen" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}, ${t5} ${p5}${v5}, ${t6} ${p6}${v6}, ${t7} ${p7}${v7}, ${t8} ${p8}${v8}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}, ${t6} ${p6}, ${t7} ${p7}, ${t8} ${p8}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 129154 "IsInconsistentWith"
	public explicit_return_type "bool"
	nparams 1
	  param inout name "" type class_ref 128002 // OneAltEst
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 129282 "CompatibleWith"
	public explicit_return_type "bool"
	nparams 1
	  param inout name "pred" type class_ref 128386 // Prediction
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 129410 "Print"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 129538 "UpdateBoundaries"
	cpp_inline public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { start = vi_ExonStart[0]; end = vi_ExonEnd[vi_ExonEnd.size()-1]; };
"
	
	
	
	
      end

      operation 129666 "GetId"
	cpp_inline public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract} { return id;  };
"
	
	
	
	
      end

      operation 129794 "GetEnd"
	cpp_inline public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { return end; };
"
	
	
	
	
      end

      operation 129922 "GetStart"
	cpp_inline public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {return start; };
"
	
	
	
	
      end

      operation 130050 "GetAltSplE"
	cpp_inline public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { return altSplicingEvidence; };
"
	
	
	
	
      end

      operation 130178 "PutAltSplE"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "b" explicit_type "bool"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} { altSplicingEvidence = b;    };
"
	
	
	
	
      end

      operation 130306 "PutIndex"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "i" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} { index = i;};
"
	
	
	
	
      end
    end

    class 128130 "AltEst"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                      AltEst
 ************************************************************"
      attribute 128514 "altPenalty"
	private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 128642 "includedEstFilter"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 128770 "compatibleEstFilter"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 128898 "unsplicedEstFilter"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 129026 "extremeLengthFilter"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 130434 "ReadAltFile"
	private explicit_return_type "int"
	nparams 3
	  param in name "" explicit_type "char"
	  param inout name "nbUnspliced" explicit_type "int"
	  param inout name "nbExtremLen" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}[FILENAME_MAX+1]${v0}, ${t1} & ${p1}${v1}, ${t2} & ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}[FILENAME_MAX+1], ${t1} & ${p1}, ${t2} & ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 130562 "Compare"
	private explicit_return_type "void"
	nparams 3
	  param inout name "nbIncomp" explicit_type "int"
	  param inout name "nbNoevidence" explicit_type "int"
	  param inout name "nbIncluded" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} & ${p0}${v0}, ${t1} & ${p1}${v1}, ${t2} & ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} & ${p0}, ${t1} & ${p1}, ${t2} & ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 129154 "totalAltEstNumber"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 128130 // voae_AltEst (<directional composition>)
	relation 128130 *-->
	  stereotype "std::vector"
	  a role_name "voae_AltEst" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	    classrelation_ref 128130 // voae_AltEst (<directional composition>)
	  b parent class_ref 128002 // OneAltEst
      end

      operation 130690 "AltEst"
	public explicit_return_type ""
	nparams 1
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 130818 "~AltEst"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 130946 "Penalize"
	public explicit_return_type "void"
	nparams 3
	  param in name "i" explicit_type "int"
	  param in name "pos" explicit_type "int"
	  param inout name "Data" type class_ref 128258 // DATA
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} * ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 131074 "convertHitsToAltEst"
	public explicit_return_type "int"
	nparams 4
	  param inout name "AllEST" type class_ref 128642 // Hits
	  param inout name "nbUnspliced" explicit_type "int"
	  param inout name "nbExtremLen" explicit_type "int"
	  param inout name "NumEST" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} & ${p1}${v1}, ${t2} & ${p2}${v2}, ${t3} & ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} & ${p1}, ${t2} & ${p2}, ${t3} & ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end
    end

    class 128258 "DATA"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      class 132354 "SigType"
	visibility package stereotype "enum"
	cpp_decl "${comment}enum ${name} {
${items}
};
"
	java_decl ""
	php_decl ""
	python_2_2 python_decl ""
	idl_decl ""
	explicit_switch_type ""
	
	attribute 153986 "tStart"
	  public type class_ref 132354 // SigType
	  init_value "= 0"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154114 "tStop"
	  public type class_ref 132354 // SigType
	  init_value "= 1"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154242 "Start"
	  public type class_ref 132354 // SigType
	  init_value "= 2"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154370 "Stop"
	  public type class_ref 132354 // SigType
	  init_value "= 3"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154498 "Acc"
	  public type class_ref 132354 // SigType
	  init_value "= 4"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154626 "Don"
	  public type class_ref 132354 // SigType
	  init_value "= 5"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154754 "Ins"
	  public type class_ref 132354 // SigType
	  init_value "= 6"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 154882 "Del"
	  public type class_ref 132354 // SigType
	  init_value "=7"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155010 "LastSigType"
	  public type class_ref 132354 // SigType
	  init_value "= 8"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end
      end

      classrelation 132098 // _sig (sig)
	relation 132098 *--> name "sig"
	  a role_name "_sig" multiplicity "[LastSigType]" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	    classrelation_ref 132098 // _sig (sig)
	  b parent class_ref 129666 // Signal
      end

      class 132738 "ContentsType"
	visibility package stereotype "enum"
	cpp_decl "${comment}enum ${name} {
${items}
};
"
	java_decl ""
	php_decl ""
	python_2_2 python_decl ""
	idl_decl ""
	explicit_switch_type ""
	
	attribute 155138 "ExonF1"
	  public type class_ref 132738 // ContentsType
	  init_value "=0"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155266 "ExonF2"
	  public type class_ref 132738 // ContentsType
	  init_value "=1"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155394 "ExonF3"
	  public type class_ref 132738 // ContentsType
	  init_value "=2"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155522 "ExonR1"
	  public type class_ref 132738 // ContentsType
	  init_value "= 3"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155650 "ExonR2"
	  public type class_ref 132738 // ContentsType
	  init_value "=4"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155778 "ExonR3"
	  public type class_ref 132738 // ContentsType
	  init_value "=5"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 155906 "IntronF"
	  public type class_ref 132738 // ContentsType
	  init_value "= 6"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156034 "IntronR"
	  public type class_ref 132738 // ContentsType
	  init_value "= 7"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156162 "InterG"
	  public type class_ref 132738 // ContentsType
	  init_value "= 8"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156290 "UTR5F"
	  public type class_ref 132738 // ContentsType
	  init_value "= 9"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156418 "UTR5R"
	  public type class_ref 132738 // ContentsType
	  init_value "= 10"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156546 "UTR3F"
	  public type class_ref 132738 // ContentsType
	  init_value "= 11"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156674 "UTR3R"
	  public type class_ref 132738 // ContentsType
	  init_value "=12"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156802 "IntronUTRF"
	  public type class_ref 132738 // ContentsType
	  init_value "= 13"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 156930 "IntronUTRR"
	  public type class_ref 132738 // ContentsType
	  init_value "= 14"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 157058 "LastContentsType"
	  public type class_ref 132738 // ContentsType
	  init_value "= 15"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end
      end

      attribute 157186 "contents"
	public explicit_type "double"
	multiplicity "[LastContentsType]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 157314 "EstMatch"
	public explicit_type "byte"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 128386 "Prediction"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                        Prediction                       **
 ***********************************************************"
      classrelation 131714 // MS (<unidirectional association>)
	relation 131714 --->
	  a role_name "MS" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 131714 // MS (<unidirectional association>)
	  b parent class_ref 131842 // MasterSensor
      end

      classrelation 131842 // X (<unidirectional association>)
	relation 131842 --->
	  a role_name "X" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 131842 // X (<unidirectional association>)
	  b parent class_ref 128514 // DNASeq
      end

      attribute 146050 "ESTMatch"
	private explicit_type "byte"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 157314 "GetESTMatch"
	cpp_inline private explicit_return_type "byte"
	nparams 1
	  param in name "i" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {return (ESTMatch ? ESTMatch[i] : 0);};
"
	
	
	
	
      end

      operation 157442 "clear"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 157570 "PrintGff"
	private explicit_return_type "void"
	nparams 2
	  param inout name "" explicit_type "FILE"
	  param inout name "" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 157698 "PrintGff3"
	private explicit_return_type "void"
	nparams 3
	  param inout name "" explicit_type "std::ofstream"
	  param inout name "" explicit_type "char"
	  param in name "" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} & ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} & ${p0}, ${t1} * ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "SEB"
      end

      operation 157826 "PrintEgnL"
	private explicit_return_type "void"
	nparams 3
	  param inout name "" explicit_type "FILE"
	  param inout name "" explicit_type "char"
	  param in name "a" explicit_type "int"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "SEB"
      end

      operation 157954 "PrintEgnS"
	private explicit_return_type "void"
	nparams 1
	  param inout name "" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 158082 "PrintEgnD"
	private explicit_return_type "void"
	nparams 1
	  param inout name "" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 158210 "PrintHtml"
	private explicit_return_type "void"
	nparams 2
	  param inout name "" explicit_type "FILE"
	  param inout name "" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 158338 "State2EGNString"
	private explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}const ${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Convert state in string"
      end

      operation 158466 "State2GFFString"
	private explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}const ${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 158594 "CheckConsistency"
	private explicit_return_type "void"
	nparams 5
	  param in name "debut" explicit_type "int"
	  param in name "fin" explicit_type "int"
	  param in name "etat" explicit_type "int"
	  param inout name "cons" explicit_type "int"
	  param inout name "incons" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} * ${p3}${v3}, ${t4} * ${p4}${v4}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} * ${p3}, ${t4} * ${p4}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Verif coherence EST: calcul le nombre de nuc. coherents et
 incoherents avec les match est
 debut/fin/etat: debut et fin de la seq. dont l'etat est etat
 cons/incons: retour des valeurs"
      end

      operation 158722 "ESTScan"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Check and Trim UTR according to EST evidence"
      end

      operation 158850 "UTRCheckAndTrim"
	private explicit_return_type "bool"
	nparams 3
	  param inout name "debut" explicit_type "int"
	  param inout name "fin" explicit_type "int"
	  param in name "etat" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 158978 "UpdateAndDelete"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 159106 "StartHTML"
	private explicit_return_type "void"
	nparams 2
	  param inout name "" explicit_type "char"
	  param inout name "" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " PrintHtml : -ph print the start of the HTML output"
      end

      operation 159234 "EndHTML"
	private explicit_return_type "void"
	nparams 1
	  param inout name "" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " PrintHtml : -ph print the end of the HTML output"
      end

      operation 159362 "fillGff3Line"
	private return_type class_ref 131202 // Gff3Line
	nparams 5
	  param in name "type_sofa" explicit_type "int"
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "strand" explicit_type "char"
	  param in name "framegff" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "SEB"
      end

      operation 159490 "setGff3Attributes"
	private explicit_return_type "void"
	nparams 8
	  param inout name "line" type class_ref 131202 // Gff3Line
	  param in name "type_egn" explicit_type "int"
	  param in name "type_sofa" explicit_type "int"
	  param in name "fea_name" explicit_type "std::string"
	  param in name "j" explicit_type "int"
	  param in name "code" explicit_type "char"
	  param in name "gene_id" explicit_type "std::string"
	  param in name "coding" explicit_type "bool"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}, ${t5} ${p5}${v5}, ${t6} ${p6}${v6}, ${t7} ${p7}${v7}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}, ${t6} ${p6}, ${t7} ${p7}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 159618 "previousExonMustBeUpdated"
	private explicit_return_type "bool"
	nparams 2
	  param inout name "line" type class_ref 131202 // Gff3Line
	  param in name "start" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      classrelation 131970 // vGene (<unidirectional association>)
	relation 131970 --->
	  a role_name "vGene" multiplicity "*" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}*> ${name}${value};
"
	    classrelation_ref 131970 // vGene (<unidirectional association>)
	  b parent class_ref 132226 // Gene
      end

      attribute 146178 "nbGene"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 146306 "seqName"
	public explicit_type "char"
	multiplicity "[FILENAME_MAX+1]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 146434 "optimalPath"
	public explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 159746 "Prediction"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 159874 "Prediction"
	public explicit_return_type ""
	nparams 4
	  param in name "From" explicit_type "int"
	  param in name "To" explicit_type "int"
	  param in name "vPos" explicit_type "std::vector<int>"
	  param in name "vState" explicit_type "std::vector<signed char>"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 160002 "~Prediction"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 160130 "IsOriginal"
	public explicit_return_type "bool"
	nparams 3
	  param inout name "optPred" type class_ref 128386 // Prediction
	  param inout name "altPreds" explicit_type "std::vector<Prediction*>"
	  param in name "seuil" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} & ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} & ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 160258 "TrimAndUpdate"
	public explicit_return_type "void"
	nparams 1
	  param inout name "" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 160386 "SanityCheck"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 160514 "DeleteOutOfRange"
	public explicit_return_type "void"
	nparams 2
	  param in name "s" explicit_type "int"
	  param in name "e" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 160642 "Print"
	public explicit_return_type "void"
	nparams 4
	  param inout name "" type class_ref 128514 // DNASeq
	  param inout name "" type class_ref 131842 // MasterSensor
	  param inout name "OTP_OUT" explicit_type "FILE"
	    defaultvalue "NULL"
	  param in name "append" explicit_type "char"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} * ${p2}${v2}, ${t3} ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}, ${t2} * ${p2}, ${t3} ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 160770 "PrintGeneInfo"
	public explicit_return_type "void"
	nparams 1
	  param inout name "" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 160898 "PlotPred"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 161026 "GetStateForPos"
	public explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 161154 "FindGene"
	public return_type class_ref 132226 // Gene
	nparams 2
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 161282 "IsStart"
	public explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}const ${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Need by Sensor Tester"
      end

      operation 161410 "IsStop"
	public explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}const ${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 161538 "IsDon"
	public explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}const ${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 161666 "IsAcc"
	public explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}const ${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 161794 "IsState"
	public explicit_return_type "bool"
	nparams 3
	  param in name "sig_type" type class_ref 132354 // SigType
	  param in name "pos" explicit_type "int"
	  param in name "strand" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      classrelation 144514 // <association>
	relation 144386 ----
	  a role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 144514 // <association>
	  b role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 144642 // <association>
      end

      classrelation 144770 // <association>
	relation 144514 ----
	  a role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 144770 // <association>
	  b role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 144898 // <association>
      end
    end

    class 128514 "DNASeq"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      attribute 196610 "Size"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196738 "Sequence"
	private explicit_type "short"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196866 "Name"
	public explicit_type "char*"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196994 "Markov0"
	protected explicit_type "double[]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 128642 "Hits"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      operation 148098 "Hits"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 148226 "Hits"
	public explicit_return_type ""
	nparams 12
	  param inout name "name" explicit_type "char"
	  param in name "length" explicit_type "int"
	  param in name "strand" explicit_type "char"
	  param in name "deb" explicit_type "int"
	  param in name "fin" explicit_type "int"
	  param in name "ldeb" explicit_type "int"
	  param in name "lfin" explicit_type "int"
	  param in name "Ph" explicit_type "int"
	  param in name "Scr" explicit_type "int"
	  param in name "prob" explicit_type "double"
	  param in name "level" explicit_type "int"
	  param in name "sup" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}, ${t5} ${p5}${v5}, ${t6} ${p6}${v6}, ${t7} ${p7}${v7}, ${t8} ${p8}${v8}, ${t9} ${p9}${v9}, ${t10} ${p10}${v10}, ${t11} ${p11}${v11}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}, ${t6} ${p6}, ${t7} ${p7}, ${t8} ${p8}, ${t9} ${p9}, ${t10} ${p10}, ${t11} ${p11}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 148354 "ReadFromFile"
	public return_type class_ref 128642 // Hits
	nparams 5
	  param inout name "HitFile" explicit_type "FILE"
	  param inout name "NumHits" explicit_type "int"
	  param in name "level" explicit_type "int"
	  param in name "margin" explicit_type "int"
	  param in name "maxPos" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 148482 "ReadFromGeneFeatureSet"
	public return_type class_ref 128642 // Hits
	nparams 5
	  param inout name "HitSet" type class_ref 130562 // GeneFeatureSet
	  param inout name "NumHits" explicit_type "int"
	  param in name "level" explicit_type "int"
	  param in name "margin" explicit_type "int"
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} & ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} * ${p4}${v4}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} & ${p0}, ${t1} * ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} * ${p4}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 148610 "~Hits"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      attribute 140802 "Name"
	public explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140930 "Strand"
	public explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141058 "Length"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141186 "NGaps"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141314 "Start"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141442 "End"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141570 "Evalue"
	public explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141698 "Rejected"
	public explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 141826 "Level"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " For blastx level 0-9 "
      end

      attribute 141954 "Support"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 130434 // Match (<unidirectional association>)
	relation 130434 --->
	  a role_name "Match" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 130434 // Match (<unidirectional association>)
	  b parent class_ref 131586 // Block
      end

      classrelation 130562 // Next (<unidirectional association>)
	relation 130562 --->
	  a role_name "Next" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 130562 // Next (<unidirectional association>)
	  b parent class_ref 128642 // Hits
      end

      operation 148738 "getName"
	public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end
    end

    class 128770 "Attributes"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
  * class Attributes
  "
      attribute 129282 "id_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 129410 "name_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 129538 "alias_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 129666 "parent_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 128258 // target_ (<unidirectional association>)
	relation 128258 --->
	  a role_name "target_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 128258 // target_ (<unidirectional association>)
	  b parent class_ref 128898 // Target
      end

      attribute 129794 "derivesFrom_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 129922 "note_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 130050 "dbxref_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 130178 "ontologyTerm_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 130306 "database_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 130434 "length_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 130562 "nbExon_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 131202 "Attributes"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors"
      end

      operation 131330 "Attributes"
	public explicit_return_type ""
	nparams 1
	  param in name "line" explicit_type "std::string"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 131458 "Attributes"
	public explicit_return_type ""
	nparams 1
	  param in name "attribut" type class_ref 128770 // Attributes
	cpp_decl "    ${comment}${inline}${name}${(}const ${t0} & ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}const ${t0} & ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 131586 "~Attributes"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 131714 "InitializeDefault"
	public explicit_return_type "void"
	nparams 1
	  param in name "" explicit_type "void"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 131842 "setId"
	public explicit_return_type "void"
	nparams 1
	  param in name "id" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 131970 "setOntologyTerm"
	public explicit_return_type "void"
	nparams 1
	  param in name "term" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132098 "getId"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132226 "getString"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132354 "getParent"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132482 "getOntologyTerm"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132610 "getTarget"
	const public return_type class_ref 128898 // Target
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132738 "hasTarget"
	const public explicit_return_type "bool"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 132866 "operator <<"
	friend cpp_inline public explicit_return_type "std::ostream"
	nparams 2
	  param inout name "o" explicit_type "std::ostream"
	  param in name "attributes" type class_ref 128770 // Attributes
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} & ${p0}${v0}, const ${t1} & ${p1}${v1}${)}${const}${volatile}${throw}${abstract} {
	return o << attributes.getString();
  };
"
	
	
	
	
	comment " Puplic attribute accessor methods
  "
      end

      attribute 130690 "NB_ATTRIBUTES_NAMES_"
	class_attribute const_attribute public explicit_type "int"
	init_value "= 18"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${h_value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 130818 "attributeNames_"
	class_attribute public explicit_type "std::string"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " \"ID=\",\"Note=\",\"Target=\""
      end

      operation 132994 "InitializeAttributeNames"
	cpp_inline public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {
	attributeNames_.push_back(\"ID\");
	attributeNames_.push_back(\"Name\");
	attributeNames_.push_back(\"Alias\");
	attributeNames_.push_back(\"Parent\");
	attributeNames_.push_back(\"Target\");
	attributeNames_.push_back(\"Gap\");
	attributeNames_.push_back(\"Derives_from\");
	attributeNames_.push_back(\"Note\");
	attributeNames_.push_back(\"Dbxref\");
	attributeNames_.push_back(\"Ontology_term\");
	attributeNames_.push_back(\"database\");
	attributeNames_.push_back(\"is_full_length\");
	attributeNames_.push_back(\"target_length\");
	attributeNames_.push_back(\"target_sequence\");
	attributeNames_.push_back(\"nb_exon\");
	attributeNames_.push_back(\"length\");
	attributeNames_.push_back(\"frame_hit\");
	attributeNames_.push_back(\"score_hit\");
  };
"
	
	
	
	
      end
    end

    class 128898 "Target"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
  * class Target
  * define the hit targeted of an alignment
  "
      attribute 158978 "name_"
	private explicit_type "std::string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 132226 // locus_ (<unidirectional association>)
	relation 132226 --->
	  a role_name "locus_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 132226 // locus_ (<unidirectional association>)
	  b parent class_ref 130434 // Locus
      end

      attribute 159106 "sequenceData_"
	private explicit_type "std::string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 159234 "targetLength_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 159362 "isFullLength_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 159490 "frameHit_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 159618 "scoreHit_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      class 132994 "LengthType"
	visibility package stereotype "enum"
	cpp_decl "${comment}enum ${name} {
${items}
};
"
	java_decl ""
	php_decl ""
	python_2_2 python_decl ""
	idl_decl ""
	explicit_switch_type ""
	
	attribute 159746 "UNKNOWN"
	  public type class_ref 132994 // LengthType
	  init_value "= -1"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 159874 "NOT_FULL_LENGTH"
	  public type class_ref 132994 // LengthType
	  init_value "= 0"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 160002 "RIKEN"
	  public type class_ref 132994 // LengthType
	  init_value "= 1"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 160130 "FULL_LENGTH"
	  public type class_ref 132994 // LengthType
	  init_value "=2 "
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end
      end

      operation 167554 "Target"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors"
      end

      operation 167682 "Target"
	public explicit_return_type ""
	nparams 7
	  param in name "name" explicit_type "std::string"
	  param in name "sequenceData" explicit_type "std::string"
	  param in name "targetLength" explicit_type "int"
	  param in name "isFullLength" explicit_type "int"
	  param inout name "locus" type class_ref 130434 // Locus
	  param in name "frameHit" explicit_type "int"
	  param in name "scoreHit" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} * ${p4}${v4}, ${t5} ${p5}${v5}, ${t6} ${p6}${v6}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} * ${p4}, ${t5} ${p5}, ${t6} ${p6}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 167810 "Target"
	public explicit_return_type ""
	nparams 9
	  param in name "name" explicit_type "std::string"
	  param in name "sequenceData" explicit_type "std::string"
	  param in name "targetLength" explicit_type "int"
	  param in name "isFullLength" explicit_type "int"
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "strand" explicit_type "char"
	  param in name "frameHit" explicit_type "int"
	  param in name "scoreHit" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}, ${t5} ${p5}${v5}, ${t6} ${p6}${v6}, ${t7} ${p7}${v7}, ${t8} ${p8}${v8}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}, ${t6} ${p6}, ${t7} ${p7}, ${t8} ${p8}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 167938 "Target"
	public explicit_return_type ""
	nparams 1
	  param inout name "target" type class_ref 128898 // Target
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 168066 "~Target"
	cpp_virtual public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 168194 "setName"
	public explicit_return_type "void"
	nparams 1
	  param in name "name" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Public attribute accessor methods"
      end

      operation 168322 "getName"
	public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 168450 "setLocus"
	public explicit_return_type "void"
	nparams 1
	  param inout name "range" type class_ref 130434 // Locus
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 168578 "getLocus"
	public return_type class_ref 130434 // Locus
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 168706 "setSequenceData"
	public explicit_return_type "void"
	nparams 1
	  param in name "sequenceData" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 168834 "getSequenceData"
	public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 168962 "setGlobalLength"
	public explicit_return_type "void"
	nparams 1
	  param in name "targetLength" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169090 "getGlobalLength"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169218 "setIsFullLength"
	public explicit_return_type "void"
	nparams 1
	  param in name "isFullLength" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169346 "getIsFullLength"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169474 "getFrameHit"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169602 "getScoreHit"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169730 "hasLocus"
	const public explicit_return_type "bool"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169858 "getString"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 169986 "operator <<"
	friend cpp_inline public explicit_return_type "std::ostream"
	nparams 2
	  param inout name "o" explicit_type "std::ostream"
	  param in name "target" type class_ref 128898 // Target
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} & ${p0}${v0}, const ${t1} & ${p1}${v1}${)}${const}${volatile}${throw}${abstract} {
	return o << target.getString();
  };
"
	
	
	
	
      end
    end

    class 129026 "BackPoint"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      classrelation 128386 // <dependency>
	relation 128386 -_->
	  stereotype "friend"
	  a default
	    cpp default "${type}"
	    classrelation_ref 128386 // <dependency>
	  b parent class_ref 129154 // Track
      end

      attribute 130946 "Status"
	private explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 133122 "IsOptimal"
	public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 133250 "SetOptimal"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 133378 "ClearOptimal"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 133506 "IsMarked"
	public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 133634 "SetMark"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 133762 "ClearMark"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 131074 "State"
	public explicit_type "signed char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 131202 "StartPos"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 131330 "Cost"
	public explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 131458 "Additional"
	public explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 128514 // Origin (<unidirectional association>)
	relation 128514 --->
	  a role_name "Origin" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 128514 // Origin (<unidirectional association>)
	  b parent class_ref 129026 // BackPoint
      end

      classrelation 128642 // Next (<unidirectional association>)
	relation 128642 --->
	  a role_name "Next" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 128642 // Next (<unidirectional association>)
	  b parent class_ref 129026 // BackPoint
      end

      classrelation 128770 // Prev (<unidirectional association>)
	relation 128770 --->
	  a role_name "Prev" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 128770 // Prev (<unidirectional association>)
	  b parent class_ref 129026 // BackPoint
      end

      operation 133890 "BackPoint"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 134018 "BackPoint"
	public explicit_return_type ""
	nparams 3
	  param in name "state" explicit_type "char"
	  param in name "pos" explicit_type "int"
	  param in name "cost" explicit_type "double"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 134146 "~BackPoint"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 134274 "InitState"
	cpp_inline public explicit_return_type "void"
	nparams 2
	  param in name "state" explicit_type "int"
	  param in name "start" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract} { State = state; StartPos = start;};
"
	
	
	
	
      end

      operation 134402 "Print"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end
    end

    class 129154 "Track"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      attribute 131586 "NumBPAlloc"
	class_attribute public explicit_type "uint"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 131714 "NumBPCollect"
	class_attribute public explicit_type "uint"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 128898 // Path (<directional composition>)
	relation 128898 *-->
	  a role_name "Path" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	    classrelation_ref 128898 // Path (<directional composition>)
	  b parent class_ref 129026 // BackPoint
      end

      classrelation 129026 // PenD (<unidirectional association>)
	relation 129026 --->
	  a role_name "PenD" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 129026 // PenD (<unidirectional association>)
	  b parent class_ref 129282 // PenaltyDist
	  association_type class_ref 129282 // PenaltyDist
      end

      attribute 131842 "Optimal"
	public explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 131970 "OptPos"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 134530 "LoadPenalty"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param inout name "name" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract} { PenD = new PenaltyDist; PenD->LoadPenaltyDist(name); };
"
	
	
	
	
      end

      operation 134658 "Update"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "cost" explicit_type "double"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  Path.Next->Additional += cost; Optimal += cost;};
"
	
	
	
	
      end

      operation 134786 "PayTheSlope"
	cpp_inline public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {Path.Next->Additional -= PenD->FinalSlope;
                             Optimal  -= PenD->FinalSlope;  };
"
	
	
	
	
      end

      operation 134914 "InsertNew"
	public explicit_return_type "void"
	nparams 4
	  param in name "state" explicit_type "char"
	  param in name "pos" explicit_type "int"
	  param in name "cost" explicit_type "double"
	  param inout name "Or" type class_ref 129026 // BackPoint
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} * ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} * ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135042 "ForceNew"
	public explicit_return_type "void"
	nparams 4
	  param in name "state" explicit_type "char"
	  param in name "pos" explicit_type "int"
	  param in name "cost" explicit_type "double"
	  param inout name "Or" type class_ref 129026 // BackPoint
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} * ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} * ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135170 "BestUsable"
	public return_type class_ref 129026 // BackPoint
	nparams 3
	  param in name "pos" explicit_type "int"
	  param inout name "cost" explicit_type "double"
	  param in name "pen" explicit_type "int"
	    defaultvalue "1"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135298 "BackTrace"
	public return_type class_ref 128386 // Prediction
	nparams 3
	  param in name "From" explicit_type "int"
	  param in name "To" explicit_type "int"
	  param in name "Forward" explicit_type "int"
	    defaultvalue "1"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135426 "Dump"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135554 "Zap"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135682 "ClearMark"
	public explicit_return_type "void"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135810 "Mark"
	public explicit_return_type "void"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 135938 "Sweep"
	public explicit_return_type "void"
	nparams 1
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 136066 "Track"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 136194 "Track"
	public explicit_return_type ""
	nparams 1
	  param inout name "other" type class_ref 129154 // Track
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 136322 "~Track"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end
    end

    class 129282 "PenaltyDist"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      classrelation 131202 // <dependency>
	relation 131202 -_->
	  stereotype "friend"
	  a default
	    cpp default "${type}"
	    classrelation_ref 131202 // <dependency>
	  b parent class_ref 129154 // Track
      end

      classrelation 131330 // <dependency>
	relation 131330 -_->
	  stereotype "friend"
	  a default
	    cpp default "${type}"
	    classrelation_ref 131330 // <dependency>
	  b parent class_ref 129410 // DAG
      end

      attribute 143362 "MinLen"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 143490 "MaxLen"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 143618 "Distribution"
	private explicit_type "double"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 143746 "MinDist"
	private explicit_type "double"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 143874 "Delta"
	private explicit_type "double"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144002 "FinalSlope"
	private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144130 "MaxDelta"
	private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 154114 "PenaltyDist"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 154242 "~PenaltyDist"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 154370 "UpdateMinDist"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 154498 "UpdateMaxDelta"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 154626 "GetDelta"
	cpp_inline public explicit_return_type "double"
	nparams 1
	  param in name "len" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {
    if (len < (int)Delta.size()) return Delta[len];
    return MaxDelta;
  };
"
	
	
	
	
      end

      operation 154754 "MinPen"
	public explicit_return_type "double"
	nparams 1
	  param in name "len" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 154882 "LoadPenaltyDist"
	public explicit_return_type "void"
	nparams 1
	  param inout name "FileName" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 155010 "PlotExp"
	public explicit_return_type "void"
	nparams 3
	  param inout name "h" explicit_type "FILE"
	  param in name "a" explicit_type "int"
	  param in name "b" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 155138 "Dump"
	public explicit_return_type "void"
	nparams 1
	  param inout name "h" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 155266 "Integrate"
	public explicit_return_type "double"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 155394 "Normalize"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 155522 "operator []"
	cpp_inline public explicit_return_type "double"
	nparams 1
	  param in name "len" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {
      if (len < MinLen) return -log(0.0);
      if (len - MinLen < (int)Distribution.size())
	return Distribution[len-MinLen];
      return Distribution.back()+(len-MinLen-Distribution.size()+1)*FinalSlope;
    };
"
	
	
	
	
      end
    end

    class 129410 "DAG"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      classrelation 129154 // TheSeq (<unidirectional association>)
	relation 129154 --->
	  a role_name "TheSeq" class_relation private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 129154 // TheSeq (<unidirectional association>)
	  b parent class_ref 128514 // DNASeq
      end

      attribute 132098 "SplicedStopPen"
	class_attribute private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 132226 "estuse"
	class_attribute private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 132354 "NormalizingPath"
	class_attribute private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 132482 "PBest"
	class_attribute private explicit_type "double"
	multiplicity "[NbTracks]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 129282 // PrevBP (<unidirectional association>)
	relation 129282 --->
	  a role_name "PrevBP" multiplicity "*" class_relation private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${multiplicity}${value};
"
	    classrelation_ref 129282 // PrevBP (<unidirectional association>)
	  b parent class_ref 129026 // BackPoint
      end

      attribute 132610 "StartPosition"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 132738 "EndPosition"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 129410 // LBP (<directional composition>)
	relation 129410 *-->
	  a role_name "LBP" multiplicity "*" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	    classrelation_ref 129410 // LBP (<directional composition>)
	  b parent class_ref 129154 // Track
      end

      attribute 132866 "EvidenceName"
	public explicit_type "char"
	multiplicity "[FILENAME_MAX+1]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment "   **"
      end

      classrelation 129538 // pred (<unidirectional association>)
	relation 129538 --->
	  a role_name "pred" public
	    comment "   **"
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 129538 // pred (<unidirectional association>)
	  b parent class_ref 128386 // Prediction
      end

      operation 136450 "DAG"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 136578 "DAG"
	public explicit_return_type ""
	nparams 4
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param inout name "PAR" explicit_type "Parameters"
	  param inout name "Seq" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} & ${p2}${v2}, ${t3} * ${p3}${v3}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} & ${p2}, ${t3} * ${p3}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 136706 "DAG"
	public explicit_return_type ""
	nparams 4
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param inout name "RefDag" type class_ref 129410 // DAG
	  param inout name "name" explicit_type "char"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}, ${t3} * ${p3}${v3}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} * ${p2}, ${t3} * ${p3}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 136834 "~DAG"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 136962 "WeightThePrior"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 137090 "LoadDistLength"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 137218 "ShortestPathAlgoForward"
	public explicit_return_type "void"
	nparams 2
	  param in name "position" explicit_type "int"
	  param in name "Data" type class_ref 128258 // DATA
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 137346 "ShortestPathAlgoBackward"
	public explicit_return_type "void"
	nparams 3
	  param in name "position" explicit_type "int"
	  param in name "Data" type class_ref 128258 // DATA
	  param in name "NoContentsUpdate" explicit_type "int"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 137474 "MarkAndSweep"
	public explicit_return_type "void"
	nparams 3
	  param in name "" explicit_type "int"
	  param in name "" explicit_type "int"
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 137602 "BuildPrediction"
	public explicit_return_type "double"
	nparams 3
	  param in name "From" explicit_type "int"
	  param in name "To" explicit_type "int"
	  param in name "Forward" explicit_type "int"
	    defaultvalue "1"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "  int ChooseTheBestTrackIndex (int position, double *bestscore, int sense);
  int ChooseTheBestTrackIndex (int position, double *bestscore, DAG* DagR);
  void InsertLastBestUsableBP (int position, int sense=1);
  void SubstractContents (DATA *data);
  double ConnectDag (DAG *RightDag, int position, DATA * data, int datalength);"
      end

      operation 137730 "Normalize"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "  void CleanPrediction (DAG* dag, DAG* dagrev);"
      end

      operation 137858 "ComputeSigShifts"
	private explicit_return_type "void"
	nparams 3
	  param in name "Strand" type class_ref 129794 // Edge
	  param in name "Data" type class_ref 128258 // DATA
	  param in name "position" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 137986 "ComputeRequired"
	private explicit_return_type "void"
	nparams 3
	  param in name "" type class_ref 129794 // Edge
	  param in name "" type class_ref 128258 // DATA
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 138114 "ApplyScore"
	private explicit_return_type "void"
	nparams 3
	  param in name "position" explicit_type "int"
	  param in name "Data" type class_ref 128258 // DATA
	  param in name "NoContentsUpdate" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 138242 "ApplyLengthPenalty"
	private explicit_return_type "void"
	nparams 3
	  param in name "position" explicit_type "int"
	  param in name "Data" type class_ref 128258 // DATA
	  param in name "NoContentsUpdate" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 138370 "GetStart"
	cpp_inline private explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { return StartPosition; };
"
	
	
	
	
      end

      operation 138498 "Print"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 138626 "StatActive"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 138754 "StatGC"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 195842 "ExPrior"
	class_attribute protected explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 195970 "InPrior"
	class_attribute protected explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196098 "IGPrior"
	class_attribute protected explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196226 "FivePrior"
	class_attribute protected explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196354 "ThreePrior"
	class_attribute protected explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 196482 "IntronFivePrior"
	class_attribute protected explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 129538 "Parameters"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      operation 151938 "UpdateParametersFileName"
	private explicit_return_type "void"
	nparams 2
	  param in name "argc" explicit_type "int"
	  param inout name "argv" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}[]${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}[]${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 152066 "ReadArg"
	private explicit_return_type "void"
	nparams 2
	  param in name "" explicit_type "int"
	  param inout name "" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}[]${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}[]${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 152194 "ReadPar"
	private explicit_return_type "void"
	nparams 1
	  param in name "para_file_name" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 152322 "ShowUsage"
	private explicit_return_type "void"
	nparams 1
	  param in name "" explicit_type "void"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 143234 "fp"
	public explicit_type "FILE"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 152450 "~Parameters"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 152578 "initParam"
	public explicit_return_type "void"
	nparams 2
	  param in name "" explicit_type "int"
	  param inout name "" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}[]${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}[]${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 152706 "count"
	public explicit_return_type "int"
	nparams 1
	  param inout name "key" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 152834 "probeKey"
	public explicit_return_type "bool"
	nparams 2
	  param inout name "key" explicit_type "char"
	  param in name "index" explicit_type "int"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 152962 "getC"
	public explicit_return_type "char"
	nparams 3
	  param in name "key" explicit_type "char"
	  param in name "index" explicit_type "int"
	    defaultvalue "0"
	  param in name "sloppy" explicit_type "int"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}const ${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}const ${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153090 "getD"
	public explicit_return_type "double"
	nparams 3
	  param in name "key" explicit_type "char"
	  param in name "index" explicit_type "int"
	    defaultvalue "0"
	  param in name "sloppy" explicit_type "int"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153218 "getI"
	public explicit_return_type "int"
	nparams 3
	  param in name "key" explicit_type "char"
	  param in name "index" explicit_type "int"
	    defaultvalue "0"
	  param in name "sloppy" explicit_type "int"
	    defaultvalue "0"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153346 "getUseSensor"
	public explicit_return_type "int"
	nparams 2
	  param inout name "" explicit_type "char"
	  param inout name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * * ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153474 "set"
	public explicit_return_type "void"
	nparams 2
	  param in name "key" explicit_type "char"
	  param in name "value" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} * ${p0}${v0}, const ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} * ${p0}, const ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153602 "setD"
	public explicit_return_type "void"
	nparams 2
	  param in name "key" explicit_type "char"
	  param in name "n" explicit_type "double"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} * ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} * ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153730 "setI"
	public explicit_return_type "void"
	nparams 2
	  param in name "key" explicit_type "char"
	  param in name "n" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} * ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} * ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 153858 "WriteParam"
	public explicit_return_type "std::string"
	nparams 2
	  param in name "para_name" explicit_type "std::vector<std::string>"
	  param in name "para_val" explicit_type "std::vector<double>"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      classrelation 142722 // m (<unidirectional association>)
	relation 142722 --->
	  stereotype "map"
	  a role_name "m" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 142722 // m (<unidirectional association>)
	  b parent class_ref 131970 // ltstr
      end
    end

    class 129666 "Signal"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      class 129794 "Edge"
	visibility package stereotype "enum"
	cpp_decl "${comment}enum ${name} {
${items}
};
"
	java_decl ""
	php_decl ""
	python_2_2 python_decl ""
	idl_decl ""
	explicit_switch_type ""
	
	attribute 153218 "Forward"
	  public type class_ref 129794 // Edge
	  init_value "= 0"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 153346 "Reverse"
	  public type class_ref 129794 // Edge
	  init_value "= 1"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 153474 "ForwardNo"
	  public type class_ref 129794 // Edge
	  init_value "= 2"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 153602 "ReverseNo"
	  public type class_ref 129794 // Edge
	  init_value "= 3"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 153730 "LastEdge"
	  public type class_ref 129794 // Edge
	  init_value "= 4"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end
      end

      attribute 153858 "weight"
	public explicit_type "double"
	multiplicity "[LastEdge]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 166146 "Clear"
	cpp_inline public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { for (int i = 0; i < LastEdge; i++) weight[i] = 0.0;};
"
	
	
	
	
      end

      operation 166274 "IsSet"
	cpp_inline public explicit_return_type "bool"
	nparams 1
	  param in name "i" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} { return ((weight[i] != 0.0) || (weight[i+2] != 0.0)); };
"
	
	
	
	
      end

      operation 166402 "SetToDefault"
	cpp_inline public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { 
    if (!IsSet(Forward)) weight[Forward] = NINFINITY;
    if (!IsSet(Reverse)) weight[Reverse] = NINFINITY;
  };
"
	
	
	
	
      end
    end

    class 129922 "SensorLoader"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      attribute 132994 "h"
	protected explicit_type "void"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 133122 "err"
	const_attribute protected explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 133250 "builder_func"
	protected explicit_type "Sensor *(*)(int n, DNASeq *X)"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}  Sensor *(*${name})(int n, DNASeq *X)${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 138882 "SensorLoader"
	public explicit_return_type ""
	nparams 2
	  param in name "fname" explicit_type "char"
	  param in name "func_name" explicit_type "char"
	    defaultvalue "0"
	cpp_decl "    ${comment}${inline}${name}${(}const ${t0} * ${p0}${v0}, const ${t1} * ${p1}${v1}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}const ${t0} * ${p0}, const ${t1} * ${p1}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 139010 "~SensorLoader"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 139138 "MakeSensor"
	public return_type class_ref 130050 // Sensor
	nparams 2
	  param in name "n" explicit_type "int"
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 139266 "LastError"
	cpp_inline public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}const ${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract} { return err; };
"
	
	
	
	
      end
    end

    class 130050 "Sensor"
      abstract visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                        Sensor                           **
 ************************************************************"
      attribute 152834 "instanceNumber"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 163458 "CheckStart"
	protected explicit_return_type "void"
	nparams 3
	  param inout name "" type class_ref 128514 // DNASeq
	  param in name "a" explicit_type "std::vector<int>"
	  param in name "b" explicit_type "std::vector<int>"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163586 "CheckStop"
	protected explicit_return_type "void"
	nparams 3
	  param inout name "" type class_ref 128514 // DNASeq
	  param in name "a" explicit_type "std::vector<int>"
	  param in name "b" explicit_type "std::vector<int>"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163714 "CheckSplices"
	protected explicit_return_type "void"
	nparams 5
	  param inout name "" type class_ref 128514 // DNASeq
	  param in name "a" explicit_type "std::vector<int>"
	  param in name "b" explicit_type "std::vector<int>"
	  param in name "c" explicit_type "std::vector<int>"
	  param in name "d" explicit_type "std::vector<int>"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163842 "PlotStop"
	protected explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param in name "phase" explicit_type "int"
	  param in name "sure" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163970 "PlotStart"
	protected explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param in name "phase" explicit_type "int"
	  param in name "strength" explicit_type "double"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164098 "PlotAcc"
	protected explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param in name "strand" explicit_type "int"
	  param in name "strength" explicit_type "double"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164226 "PlotDon"
	protected explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param in name "strand" explicit_type "int"
	  param in name "strength" explicit_type "double"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164354 "PlotESTHit"
	protected explicit_return_type "void"
	nparams 4
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "strand" explicit_type "int"
	  param in name "filtered" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164482 "PlotESTGap"
	protected explicit_return_type "void"
	nparams 4
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "strand" explicit_type "int"
	  param in name "filtered" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164610 "PlotBlastHit"
	protected explicit_return_type "void"
	nparams 4
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "phase" explicit_type "int"
	  param in name "level" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164738 "PlotBlastGap"
	protected explicit_return_type "void"
	nparams 5
	  param in name "start" explicit_type "int"
	  param in name "phase1" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "phase2" explicit_type "int"
	  param in name "level" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164866 "PlotStartReg"
	protected explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param in name "phase" explicit_type "int"
	  param in name "color" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 164994 "PlotEndReg"
	protected explicit_return_type "void"
	nparams 3
	  param in name "pos" explicit_type "int"
	  param in name "phase" explicit_type "int"
	  param in name "color" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 165122 "PlotRepeat"
	protected explicit_return_type "void"
	nparams 2
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 165250 "GetNumber"
	cpp_inline protected explicit_return_type "int"
	nparams 1
	  param in name "" explicit_type "void"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} { return instanceNumber; };
"
	
	
	
	
      end

      attribute 152962 "inputFormat_"
	protected explicit_type "std::string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 153090 "type"
	public explicit_type "byte"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 165378 "Sensor"
	public explicit_return_type ""
	nparams 1
	  param in name "n" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 165506 "~Sensor"
	cpp_virtual public explicit_return_type ""
	nparams 1
	  param in name "" explicit_type "void"
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${t0} ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 165634 "Init"
	abstract cpp_virtual public explicit_return_type "void"
	nparams 1
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	
	
	
	
      end

      operation 165762 "GiveInfo"
	abstract cpp_virtual public explicit_return_type "void"
	nparams 3
	  param inout name "" type class_ref 128514 // DNASeq
	  param in name "" explicit_type "int"
	  param inout name "" type class_ref 128258 // DATA
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	
	
	
	
      end

      operation 165890 "Plot"
	abstract cpp_virtual public explicit_return_type "void"
	nparams 1
	  param inout name "" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	
	
	
	
      end

      operation 166018 "PostAnalyse"
	abstract cpp_virtual public explicit_return_type "void"
	nparams 2
	  param inout name "" type class_ref 128386 // Prediction
	  param inout name "" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	
	
	
	
      end
    end

    class 130178 "Gap"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
  * class Gap
  * describe a gap in protein and nucleotide alignment
  "
      attribute 133378 "type_"
	private explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 133506 "length_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 139394 "Gap"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors"
      end

      operation 139522 "Gap"
	public explicit_return_type ""
	nparams 2
	  param in name "type" explicit_type "char"
	  param in name "length" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 139650 "~Gap"
	cpp_virtual public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 139778 "getString"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Public attribute accessor methods"
      end

      operation 139906 "operator <<"
	friend cpp_inline public explicit_return_type "std::ostream"
	nparams 2
	  param inout name "o" explicit_type "std::ostream"
	  param in name "gap" type class_ref 130178 // Gap
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} & ${p0}${v0}, const ${t1} & ${p1}${v1}${)}${const}${volatile}${throw}${abstract} {
	return o << gap.getString();
  };
"
	
	
	
	
      end
    end

    class 130306 "GeneFeature"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
 * class GeneFeature
 "
      attribute 133634 "id_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 133762 "seqid_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 133890 "source_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 134018 "type_"
	private explicit_type "string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 129666 // locus_ (<unidirectional association>)
	relation 129666 --->
	  a role_name "locus_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 129666 // locus_ (<unidirectional association>)
	  b parent class_ref 130434 // Locus
      end

      attribute 134146 "length_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 134274 "score_"
	private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 134402 "phase_"
	private explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 129794 // attributes_ (<unidirectional association>)
	relation 129794 --->
	  a role_name "attributes_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 129794 // attributes_ (<unidirectional association>)
	  b parent class_ref 128770 // Attributes
      end

      attribute 134530 "valid_"
	private explicit_type "bool"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 140034 "ParseLine"
	private explicit_return_type "void"
	nparams 2
	  param inout name "line" explicit_type "char"
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 140162 "GeneFeature"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors"
      end

      operation 140290 "GeneFeature"
	public explicit_return_type ""
	nparams 2
	  param inout name "" explicit_type "char"
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 140418 "GeneFeature"
	public explicit_return_type ""
	nparams 1
	  param in name "gene" type class_ref 130306 // GeneFeature
	cpp_decl "    ${comment}${inline}${name}${(}const ${t0} & ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}const ${t0} & ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 140546 "~GeneFeature"
	cpp_virtual public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment "GeneFeature (string seqId, string source, string type, int start, int end, double score, char strand, char phase, char * attributes);"
      end

      operation 140674 "setValid"
	public explicit_return_type "void"
	nparams 1
	  param in name "valid" explicit_type "bool"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 140802 "setSeqId"
	public explicit_return_type "void"
	nparams 1
	  param in name "id" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 140930 "getValid"
	const public explicit_return_type "bool"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141058 "getSeqId"
	const public explicit_return_type "string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141186 "getString"
	const public explicit_return_type "string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141314 "getPhase"
	const public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141442 "getId"
	const public explicit_return_type "string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141570 "getParent"
	const public explicit_return_type "string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141698 "getType"
	const public explicit_return_type "string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141826 "getLocus"
	const public return_type class_ref 130434 // Locus
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 141954 "getScore"
	const public explicit_return_type "double"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 142082 "getLength"
	const public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 142210 "hasTarget"
	const public explicit_return_type "bool"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 142338 "getAttributes"
	const public return_type class_ref 128770 // Attributes
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 142466 "operator <<"
	friend cpp_inline public explicit_return_type "ostream"
	nparams 2
	  param inout name "o" explicit_type "ostream"
	  param in name "geneFeature" type class_ref 130306 // GeneFeature
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} & ${p0}${v0}, const ${t1} & ${p1}${v1}${)}${const}${volatile}${throw}${abstract} {
      return o <<  geneFeature.getString();
    };
"
	
	
	
	
      end
    end

    class 130434 "Locus"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
  * class Locus
  "
      attribute 142082 "start_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 142210 "end_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 142338 "strand_"
	private explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 148866 "Locus"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors
  "
      end

      operation 148994 "Locus"
	public explicit_return_type ""
	nparams 3
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "strand" explicit_type "char"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 149122 "Locus"
	public explicit_return_type ""
	nparams 1
	  param in name "locus" type class_ref 130434 // Locus
	cpp_decl "    ${comment}${inline}${name}${(}const ${t0} & ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}const ${t0} & ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 149250 "~Locus"
	cpp_virtual public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 149378 "setStart"
	public explicit_return_type "void"
	nparams 1
	  param in name "start" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Puplic attribute accessor methods
  
start"
      end

      operation 149506 "getStart"
	const public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 149634 "setEnd"
	public explicit_return_type "void"
	nparams 1
	  param in name "end" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 149762 "getEnd"
	const public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 149890 "setStrand"
	public explicit_return_type "void"
	nparams 1
	  param in name "strand" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 150018 "getStrand"
	const public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 150146 "getString"
	const public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 150274 "operator <<"
	friend cpp_inline public explicit_return_type "std::ostream"
	nparams 2
	  param inout name "o" explicit_type "std::ostream"
	  param in name "range" type class_ref 130434 // Locus
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} & ${p0}${v0}, const ${t1} & ${p1}${v1}${)}${const}${volatile}${throw}${abstract} {
	return o << range.getString();
  };
"
	
	
	
	
      end
    end

    class 130562 "GeneFeatureSet"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
 * class GeneFeatureSet
 "
      classrelation 129922 // features_ (<unidirectional association>)
	relation 129922 --->
	  stereotype "map"
	  a role_name "features_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<string,${type}*> ${name}${value};
"
	    classrelation_ref 129922 // features_ (<unidirectional association>)
	  b parent class_ref 130306 // GeneFeature
      end

      classrelation 130050 // vRefFeatures_ (<unidirectional association>)
	relation 130050 --->
	  stereotype "vector"
	  a role_name "vRefFeatures_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}*> ${name}${value};
"
	    classrelation_ref 130050 // vRefFeatures_ (<unidirectional association>)
	  b parent class_ref 130306 // GeneFeature
      end

      attribute 134658 "mPosFeatures_"
	private explicit_type "string, int"
	stereotype "map"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 134786 "lastIndex_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 134914 "parentToChildren_"
	private explicit_type "string, vector<GeneFeature *> "
	stereotype "map"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      classrelation 130178 // soTerms_ (<unidirectional association>)
	relation 130178 --->
	  a role_name "soTerms_" class_relation public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 130178 // soTerms_ (<unidirectional association>)
	  b parent class_ref 130690 // SoTerms
      end

      operation 142594 "GeneFeatureSet"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors"
      end

      operation 142722 "GeneFeatureSet"
	public explicit_return_type ""
	nparams 2
	  param inout name "featuresFilename" explicit_type "char"
	  param inout name "soTermsFilename" explicit_type "char"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 142850 "GeneFeatureSet"
	public explicit_return_type ""
	nparams 1
	  param inout name "soTermsFilename" explicit_type "char"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 142978 "~GeneFeatureSet"
	cpp_virtual public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 143106 "existsGeneFeature"
	public explicit_return_type "bool"
	nparams 1
	  param in name "geneFeatureId" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 143234 "printFeature"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 143362 "getIterator"
	public explicit_return_type "vector< GeneFeature *>::iterator"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 143490 "getIteratorParentToChildren"
	public explicit_return_type "map<string, vector<GeneFeature *> >::iterator"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 143618 "getChildren"
	public explicit_return_type "vector< GeneFeature *>"
	nparams 1
	  param in name "id" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} & ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 143746 "getNbFeature"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 143874 "getNbParentFeature"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 144002 "getGeneFeature"
	public return_type class_ref 130306 // GeneFeature
	nparams 1
	  param in name "id" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      classrelation 146178 // <association>
	relation_ref 145666 // <association>
      end
    end

    class 130690 "SoTerms"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
 * class SoTerms
    
    example of enregistrement
    [Term]
    id: SO:0000000
    name: Sequence_Ontology
    subset: SOFA

 "
      attribute 158722 "idToName_"
	private explicit_type "string,string"
	stereotype "map"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 158850 "nameToId_"
	private explicit_type "string,string"
	stereotype "map"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 166530 "SoTerms"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors
SoTerms ( );"
      end

      operation 166658 "~SoTerms"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 166786 "loadFile"
	public explicit_return_type "void"
	nparams 1
	  param inout name "filename" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 166914 "existsId"
	public explicit_return_type "bool"
	nparams 1
	  param in name "name" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 167042 "existsName"
	public explicit_return_type "bool"
	nparams 1
	  param in name "name" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 167170 "size"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 167298 "Print"
	public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 167426 "getIdFromName"
	public explicit_return_type "string"
	nparams 1
	  param in name "name" explicit_type "string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end
    end

    class 130818 "option"
      visibility package stereotype "struct"
      cpp_decl "${comment}${template}struct ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment " Describe the long-named options requested by the application.
   The LONG_OPTIONS argument to getopt_long or getopt_long_only is a vector
   of `struct option' terminated by an element containing a name which is
   zero.

   The field `has_arg' is:
   no_argument		(or 0) if the option does not take an argument,
   required_argument	(or 1) if the option requires an argument,
   optional_argument 	(or 2) if the option takes an optional argument.

   If the field `flag' is not NULL, it points to a variable that is set
   to the value given in the field `val' when the option is found, but
   left unchanged if the option is not found.

   To have a long-named option do something other than set an `int' to
   a compiled-in constant, such as set a value from `optarg', set the
   option's `flag' field to zero and its `val' field to a nonzero
   value (the equivalent single-letter option character, if there is
   one).  For long options that have a zero `flag' field, `getopt'
   returns the contents of the `val' field.  "
      attribute 135042 "name"
	const_attribute public explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 135170 "has_arg"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 135298 "flag"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 135426 "val"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 130946 "anonymous1"
      visibility package stereotype "enum"
      cpp_decl "${comment}enum  {
${items}
};
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "sofa->j'ai pas trouv� de raison de mettre des entiers plutot que des chaines
sauf l'enum
* \\enum
 *  la liste des codes SOFA et des codes SO (moins ceux deja present dans sofa)
 *  \\link http://song.cvs.sourceforge.net/song/ontology/sofa.obo?view=log
 *  \\link http://song.cvs.sourceforge.net/song/ontology/so.obo?view=log
 "
      attribute 135554 "SOFA_GENE"
	public type class_ref 130946 // anonymous1
	init_value "= 704"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 135682 "SOFA_MRNA"
	public type class_ref 130946 // anonymous1
	init_value "= 234"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 135810 "SOFA_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 147"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 135938 "SOFA_INTRON"
	public type class_ref 130946 // anonymous1
	init_value "= 188"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136066 "SOFA_INTERGEN"
	public type class_ref 130946 // anonymous1
	init_value "= 605"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136194 "SOFA_5_UTR"
	public type class_ref 130946 // anonymous1
	init_value "= 204"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136322 "SOFA_3_UTR"
	public type class_ref 130946 // anonymous1
	init_value "= 205"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136450 "SOFA_CDS"
	public type class_ref 130946 // anonymous1
	init_value "= 316"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136578 "SO_5_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 200"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136706 "SO_3_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 202"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136834 "SO_5_CODING_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 196"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 136962 "SO_3_CODING_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 197"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 137090 "SO_5_NONCODING_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 445"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 137218 "SO_3_NONCODING_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 444"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 137346 "SO_SINGLE_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 5845"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 137474 "SO_INTERIOR_EXON"
	public type class_ref 130946 // anonymous1
	init_value "= 4"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 137602 "SO_UTR_INTRON"
	public type class_ref 130946 // anonymous1
	init_value "= 446           ///<  un intron d'UTR
"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 131074 "Sofa"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "/<  un gene
/<  ARNm episse \"does not contain introns\"
/<  un exon de l'ARNm episse
/<  un intron de l'ARNm
/<  region entre 2 genes
/<  5'UTR (de l'ARNm episse)
/<  UTR3' (de l'ARNm episse)
/<  un CDS avec un start ET un stop
/<  un exon contenant CDS/UTR 5'
/<  un exon contenant  CDS/UTR 3'
/<  un exon contenant CDS 5'
/<  un exon contenant  CDS 3'
/<  un exon de 5'UTR (du pre-ARNm)
/<  un exon d'UTR3' (du pre-ARNm)
/<  un exon 'solitaire'
/<  un exon interieur codant (partie d'un CDS)
/<  un intron d'UTR
*  \\class  Sofa
 *  \\brief  Cette classe doit permettre de traiter les codes Sofa
 *  Pour le moment, sont regroupees ici les fonctions qui permettent de gerer
 *  les codes sofa. Du coup elles sont statiques !
 *  \\todo    Faire ça proprement !!!
 "
      operation 144130 "Sofa"
	cpp_inline public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw} {};
"
	
	
	
	
      end

      operation 144258 "~Sofa"
	cpp_inline public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw} {};
"
	
	
	
	
      end

      operation 144386 "getName"
	class_operation public explicit_return_type "std::string"
	nparams 1
	  param in name "code_so" explicit_type "uint"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "/renvoie le nom correspondant au code sofa"
      end

      operation 144514 "codeToString"
	class_operation public explicit_return_type "std::string"
	nparams 1
	  param in name "code_so" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment "/renvoie la chaine \"SO:XXXXXXX\" avec xxx le code sofa"
      end

      classrelation 144898 // <association>
	relation_ref 144514 // <association>
      end

      classrelation 147330 // <association>
	relation 146818 ----
	  a role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 147330 // <association>
	  b role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 147458 // <association>
      end
    end

    class 131202 "Gff3Line"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "* \\class  GFF3Line
 *  \\author  Sebastien Letort
 *  \\date    13 novembre 2006
 *  \\brief  cette classe sert a ecrire une ligne pour le GFF3
 *  \\todo    A terme cette classe doit permettre de lire une ligne gff3
 *  la gestion de la classe interne Attribute est encore en discution
 "
      class 131330 "Attribute"
	visibility package 
	cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
	java_decl ""
	php_decl ""
	python_2_2 python_decl ""
	idl_decl ""
	explicit_switch_type ""
	
	attribute 137730 "liste_"
	  private explicit_type "std::string"
	  cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	operation 144642 "Attribute"
	  cpp_inline public explicit_return_type ""
	  nparams 1
	    param in name "attribut" explicit_type "std::string"
	  cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}${)}${volatile}${throw} {  liste_ = attribut;  };
"
	  
	  
	  
	  
	end

	operation 144770 "~Attribute"
	  cpp_inline public explicit_return_type ""
	  nparams 0
	  cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw} {};
"
	  
	  
	  
	  
	end

	operation 144898 "addAttribute"
	  cpp_inline public explicit_return_type "void"
	  nparams 1
	    param in name "attribut" explicit_type "std::string"
	  cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  liste_ += \";\" + attribut;  };
"
	  
	  
	  
	  
	  comment "/ajoute un attribut a la liste"
	end

	operation 145026 "str"
	  cpp_inline public explicit_return_type "std::string"
	  nparams 0
	  cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {  return liste_;  };
"
	  
	  
	  
	  
	  comment "/renvoie la liste d'attributs sous forme d'une chaine"
	end
      end

      attribute 137858 "seq_id_"
	private explicit_type "std::string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 137986 "source_"
	private explicit_type "std::string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 138114 "type_sofa_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 138242 "score_"
	private explicit_type "float"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 138370 "strand_"
	private explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 138498 "phase_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment "'int' pour gerer le INDEFINI"
      end

      classrelation 130306 // attr_ (<unidirectional association>)
	relation 130306 --->
	  a role_name "attr_" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 130306 // attr_ (<unidirectional association>)
	  b parent class_ref 131330 // Attribute
      end

      class 131458 "elements"
	visibility package stereotype "enum"
	cpp_decl "${comment}enum ${name} {
${items}
};
"
	java_decl ""
	php_decl ""
	python_2_2 python_decl ""
	idl_decl ""
	explicit_switch_type ""
	
	attribute 138626 "SEQ_ID"
	  public type class_ref 131458 // elements
	  init_value "= 0"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 138754 "SOURCE"
	  public type class_ref 131458 // elements
	  init_value "= 1"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 138882 "TYPE"
	  public type class_ref 131458 // elements
	  init_value "= 2"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139010 "START"
	  public type class_ref 131458 // elements
	  init_value "= 3"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139138 "END"
	  public type class_ref 131458 // elements
	  init_value "= 4"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139266 "SCORE"
	  public type class_ref 131458 // elements
	  init_value "= 5"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139394 "STRAND"
	  public type class_ref 131458 // elements
	  init_value "= 6"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139522 "PHASE"
	  public type class_ref 131458 // elements
	  init_value "= 7"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139650 "ATTRIBUTES"
	  public type class_ref 131458 // elements
	  init_value "= 8"
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end

	attribute 139778 "NB_ELEMENTS_GFF3"
	  public type class_ref 131458 // elements
	  init_value "= 9
    "
	  cpp_decl "  ${name}${value},${comment}"
	  java_decl ""
	  php_decl ""
	  python_decl ""
	  idl_decl ""
	end
      end

      operation 145154 "Gff3Line"
	public explicit_return_type ""
	nparams 1
	  param in name "seq_id" explicit_type "std::string"
	    defaultvalue "\"\""
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}${)}${throw}{
${body}}
"
	
	
	
	
	comment "les constructeurs
/constructeur pour une sequence donnee"
      end

      operation 145282 "Gff3Line"
	cpp_inline public explicit_return_type ""
	nparams 1
	  param in name "l" type class_ref 131202 // Gff3Line
	cpp_decl "    ${comment}${inline}${name}${(}const ${t0} & ${p0}${v0}${)}${volatile}${throw} {
      seq_id_ = l.seq_id_;  source_ = l.source_;
      type_sofa_ = l.type_sofa_;
      start_ = l.start_;  end_ = l.end_;
      score_ = l.score_;  strand_ = l.strand_;
      phase_ = l.phase_;
    };
"
	
	
	
	
	comment "ctr par recopie, recopie tous sauf les attributs"
      end

      operation 145410 "~Gff3Line"
	cpp_inline public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw} {
      if(attr_)
        delete attr_;
    };
"
	
	
	
	
	comment "le destructeur"
      end

      operation 145538 "check"
	const cpp_inline public explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {};
"
	
	
	
	
	comment "les methodes
/\\todo  faire une fn de verif permettrait de ne pas initialiser des param
/\\todo  de facon inadequate (type doit etre != de '.')"
      end

      operation 145666 "print"
	const public explicit_return_type "void"
	nparams 2
	  param inout name "out" explicit_type "std::ofstream"
	  param in name "sofa_name" explicit_type "bool"
	    defaultvalue "true"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} & ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} & ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 145794 "getEnd"
	const cpp_inline public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { return end_;  };
"
	
	
	
	
      end

      operation 145922 "getType"
	const cpp_inline public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} { return type_sofa_;  };
"
	
	
	
	
      end

      operation 146050 "header"
	class_operation cpp_inline public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {  return \"##gff-version 3\\n\";  };
"
	
	
	
	
	comment "la premiere ligne obligatoire"
      end

      operation 146178 "header"
	class_operation cpp_inline public explicit_return_type "std::string"
	nparams 3
	  param inout name "seq" explicit_type "char"
	  param in name "start" explicit_type "uint"
	  param in name "end" explicit_type "uint"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract} {
      std::ostringstream buff;
      buff  << \"##gff-version 3\\n\"
            << \"##sequence-region \" << seq
            << \" \" << to_string(start)
            << \" \" << to_string(end)
            << std::endl;
      return buff.str();
    };
"
	
	
	
	
	comment "la premiere ligne obligatoire, suivi de la 2e"
      end

      operation 146306 "endComplexFeature"
	class_operation cpp_inline public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {  return \"###\\n\";  };
"
	
	
	
	
      end

      operation 146434 "setSeqId"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "str" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  seq_id_ = str;  };
"
	
	
	
	
	comment "les methodes inline pour l'initialisation
/affecte seq_id_"
      end

      operation 146562 "setType"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "type" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  type_sofa_ = type;  };
"
	
	
	
	
	comment "/affecte le type_sofa_"
      end

      operation 146690 "setStart"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "start" explicit_type "uint"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  start_ = start;  };
"
	
	
	
	
	comment "/ affecte le champs start"
      end

      operation 146818 "setEnd"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "end" explicit_type "uint"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  end_ = end;  };
"
	
	
	
	
	comment "/ affecte le champs end"
      end

      operation 146946 "setScore"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "score" explicit_type "float"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  score_ = score;  };
"
	
	
	
	
	comment "/ affecte le champs score"
      end

      operation 147074 "setStrand"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "strand" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  strand_ = strand;  };
"
	
	
	
	
	comment "/ affecte le champs strand"
      end

      operation 147202 "setPhase"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "phase" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  phase_ = phase;  };
"
	
	
	
	
	comment "/ affecte le champs phase"
      end

      operation 147330 "setAttribute"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "str" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  attr_ = new Attribute(str);  };
"
	
	
	
	
	comment "/ affecte le champs attributes, provisoire
/ \\todo  faire une fonction plus contrainte avec un objet Attribute ?"
      end

      operation 147458 "addAttribute"
	cpp_inline public explicit_return_type "void"
	nparams 1
	  param in name "str" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract} {  attr_->addAttribute(str);  };
"
	
	
	
	
	comment "verifier la chaine ?
/ ajoute un attribut au champ attributes
/ \\todo  faire une fonction plus contrainte ?"
      end

      classrelation 144642 // <association>
	relation_ref 144386 // <association>
      end

      classrelation 147458 // <association>
	relation_ref 146818 // <association>
      end

      attribute 200962 "start_"
	protected explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 201090 "end_"
	protected explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 131586 "Block"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      operation 147586 "Block"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 147714 "Block"
	public explicit_return_type ""
	nparams 6
	  param in name "Start" explicit_type "int"
	  param in name "End" explicit_type "int"
	  param in name "LStart" explicit_type "int"
	  param in name "LEnd" explicit_type "int"
	  param in name "Ph" explicit_type "int"
	  param in name "Scr" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}, ${t5} ${p5}${v5}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 147842 "~Block"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 147970 "AddBlockAfter"
	public explicit_return_type "void"
	nparams 7
	  param in name "Start" explicit_type "int"
	  param in name "End" explicit_type "int"
	  param in name "LStart" explicit_type "int"
	  param in name "LEnd" explicit_type "int"
	  param in name "Ph" explicit_type "int"
	  param in name "Scr" explicit_type "int"
	  param inout name "HSP" explicit_type "char"
	    defaultvalue "NULL"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}, ${t5} ${p5}${v5}, ${t6} * ${p6}${v6}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}, ${t6} * ${p6}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 139906 "Start"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140034 "End"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140162 "Phase"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140290 "Score"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140418 "LStart"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140546 "LEnd"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 140674 "HitSeq"
	public explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 131714 "UseSensor"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                        UseSensor                        **
 ************************************************************"
      attribute 142466 "Priority"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 142594 "Name"
	public explicit_type "char"
	multiplicity "[FILENAME_MAX+1]"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${multiplicity}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 150402 "UseSensor"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 150530 "UseSensor"
	public explicit_return_type ""
	nparams 2
	  param in name "" explicit_type "int"
	  param in name "" explicit_type "char"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}[FILENAME_MAX+1]${v1}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}[FILENAME_MAX+1]${)}${throw}{
${body}}
"
	
	
	
	
      end

      classrelation 144386 // <association>
	relation_ref 144258 // <association>
      end
    end

    class 131970 "ltstr"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
    end

    class 132098 "Feature"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                       Feature Object                    **
 ************************************************************"
      attribute 144258 "number"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144386 "state"
	public explicit_type "signed char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144514 "start"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144642 "end"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144770 "strand"
	public explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 144898 "phase"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 145026 "framegff"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 145154 "frame"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 155650 "Feature"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 155778 "Feature"
	public explicit_return_type ""
	nparams 5
	  param in name "" explicit_type "signed char"
	  param in name "" explicit_type "int"
	  param in name "" explicit_type "int"
	  param in name "" explicit_type "char"
	  param in name "" explicit_type "int"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} ${p3}${v3}, ${t4} ${p4}${v4}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 155906 "~Feature"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 223874 "IsUtr"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224002 "IsIntergenic"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224130 "IsTranscribedAndUnspliced"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224258 "IsCodingExon"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      classrelation 148610 // new_state (<unidirectional association>)
	relation 147970 --->
	  a role_name "new_state" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 148610 // new_state (<unidirectional association>)
	  b parent class_ref 143362 // State
      end
    end

    class 132226 "Gene"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                         Gene Object                     **
 ************************************************************"
      classrelation 131458 // <dependency>
	relation 131458 -_->
	  stereotype "friend"
	  a default
	    cpp default "${type}"
	    classrelation_ref 131458 // <dependency>
	  b parent class_ref 128386 // Prediction
      end

      attribute 145282 "complete"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment "+1:init|sngl +2:term|sngl 3:ALL "
      end

      attribute 145410 "exNumber"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 156034 "Update"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 156162 "clear"
	private explicit_return_type "void"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 145538 "exLength"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 145666 "geneNumber"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 145794 "isvariant"
	public explicit_type "bool"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " true = is a splice variant"
      end

      attribute 145922 "hasvariant"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " has n splice variant (or is number n splice variant if is variant is true)"
      end

      classrelation 131586 // vFea (<unidirectional association>)
	relation 131586 --->
	  a role_name "vFea" multiplicity "*" public
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}*> ${name}${value};
"
	    classrelation_ref 131586 // vFea (<unidirectional association>)
	  b parent class_ref 132098 // Feature
      end

      operation 156290 "Gene"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 156418 "~Gene"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 156546 "isDifferent"
	public explicit_return_type "int"
	nparams 2
	  param in name "o" type class_ref 132226 // Gene
	  param in name "threshold" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} & ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} & ${p0}, ${t1} ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 156674 "operator =="
	public explicit_return_type "bool"
	nparams 1
	  param in name "o" type class_ref 132226 // Gene
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}const ${t0} & ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}const ${t0} & ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 156802 "nbFea"
	cpp_inline public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract} {return vFea.size();};
"
	
	
	
	
      end

      operation 156930 "AddFeature"
	public explicit_return_type "void"
	nparams 3
	  param in name "state" explicit_type "signed char"
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 157058 "PrintInfo"
	public explicit_return_type "void"
	nparams 3
	  param inout name "" explicit_type "FILE"
	  param in name "" explicit_type "int"
	  param inout name "" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} * ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 157186 "GetVariantCode"
	public explicit_return_type "char"
	nparams 1
	  param in name "" explicit_type "void"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      attribute 198530 "inNumber"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 198658 "inLength"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 198786 "utrLength"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 198914 "mrnaLength"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199042 "geneLength"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199170 "cdsStart"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199298 "cdsEnd"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199426 "trStart"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199554 "trEnd"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199682 "tuStart"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 199810 "tuEnd"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 132482 "Tracks"
      visibility package stereotype "enum"
      cpp_decl "${comment}enum ${name} {
${items}
};
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      attribute 146562 "InitF1"
	public type class_ref 132482 // Tracks
	init_value "= 0"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 146690 "InitF2"
	public type class_ref 132482 // Tracks
	init_value "= 1"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 146818 "InitF3"
	public type class_ref 132482 // Tracks
	init_value "= 2"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 146946 "InitR1"
	public type class_ref 132482 // Tracks
	init_value "= 3"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147074 "InitR2"
	public type class_ref 132482 // Tracks
	init_value "= 4"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147202 "InitR3"
	public type class_ref 132482 // Tracks
	init_value "= 5"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147330 "SnglF1"
	public type class_ref 132482 // Tracks
	init_value "= 6"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147458 "SnglF2"
	public type class_ref 132482 // Tracks
	init_value "= 7"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147586 "SnglF3"
	public type class_ref 132482 // Tracks
	init_value "= 8"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147714 "SnglR1"
	public type class_ref 132482 // Tracks
	init_value "= 9"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147842 "SnglR2"
	public type class_ref 132482 // Tracks
	init_value "= 10"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 147970 "SnglR3"
	public type class_ref 132482 // Tracks
	init_value "= 11"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148098 "IntrF1"
	public type class_ref 132482 // Tracks
	init_value "= 12"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148226 "IntrF2"
	public type class_ref 132482 // Tracks
	init_value "= 13"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148354 "IntrF3"
	public type class_ref 132482 // Tracks
	init_value "= 14"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148482 "IntrR1"
	public type class_ref 132482 // Tracks
	init_value "= 15"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148610 "IntrR2"
	public type class_ref 132482 // Tracks
	init_value "= 16"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148738 "IntrR3"
	public type class_ref 132482 // Tracks
	init_value "= 17"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148866 "TermF1"
	public type class_ref 132482 // Tracks
	init_value "= 18"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 148994 "TermF2"
	public type class_ref 132482 // Tracks
	init_value "= 19"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149122 "TermF3"
	public type class_ref 132482 // Tracks
	init_value "= 20"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149250 "TermR1"
	public type class_ref 132482 // Tracks
	init_value "= 21"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149378 "TermR2"
	public type class_ref 132482 // Tracks
	init_value "= 22"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149506 "TermR3"
	public type class_ref 132482 // Tracks
	init_value "= 23"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149634 "IntronF1"
	public type class_ref 132482 // Tracks
	init_value "= 24"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149762 "IntronF2"
	public type class_ref 132482 // Tracks
	init_value "= 25"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 149890 "IntronF3"
	public type class_ref 132482 // Tracks
	init_value "= 26"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150018 "IntronR1"
	public type class_ref 132482 // Tracks
	init_value "= 27"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150146 "IntronR2"
	public type class_ref 132482 // Tracks
	init_value "= 28"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150274 "IntronR3"
	public type class_ref 132482 // Tracks
	init_value "= 29"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150402 "IntronF2T"
	public type class_ref 132482 // Tracks
	init_value "= 30"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150530 "IntronF3TG"
	public type class_ref 132482 // Tracks
	init_value "= 31"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150658 "IntronF3TA"
	public type class_ref 132482 // Tracks
	init_value "= 32"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150786 "IntronR3G"
	public type class_ref 132482 // Tracks
	init_value "= 33"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 150914 "IntronR3A"
	public type class_ref 132482 // Tracks
	init_value "= 34"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151042 "IntronR2AG"
	public type class_ref 132482 // Tracks
	init_value "= 35"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151170 "InterGen"
	public type class_ref 132482 // Tracks
	init_value "= 36"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151298 "UTR5F"
	public type class_ref 132482 // Tracks
	init_value "= 37"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151426 "UTR3F"
	public type class_ref 132482 // Tracks
	init_value "= 38"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151554 "UTR5R"
	public type class_ref 132482 // Tracks
	init_value "= 39"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151682 "UTR3R"
	public type class_ref 132482 // Tracks
	init_value "= 40"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151810 "IntronU5F"
	public type class_ref 132482 // Tracks
	init_value "= 41"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 151938 "IntronU5R"
	public type class_ref 132482 // Tracks
	init_value "= 42"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 152066 "IntronU3F"
	public type class_ref 132482 // Tracks
	init_value "= 43"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 152194 "IntronU3R"
	public type class_ref 132482 // Tracks
	init_value "= 44"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 152322 "NbTracks"
	public type class_ref 132482 // Tracks
	init_value "= 45"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    class 132610 "Range"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "*
  * class Range
  "
      attribute 152450 "start_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 152578 "end_"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 152706 "strand_"
	private explicit_type "char"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      operation 161922 "Range"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
	comment " Constructors/Destructors
  "
      end

      operation 162050 "Range"
	public explicit_return_type ""
	nparams 3
	  param in name "start" explicit_type "int"
	  param in name "end" explicit_type "int"
	  param in name "strand" explicit_type "char"
	cpp_decl "    ${comment}${inline}${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} ${p2}${v2}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} ${p2}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 162178 "Range"
	public explicit_return_type ""
	nparams 1
	  param inout name "range" type class_ref 132610 // Range
	cpp_decl "    ${comment}${inline}${name}${(}${t0} * ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} * ${p0}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 162306 "~Range"
	cpp_virtual public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 162434 "setStart"
	public explicit_return_type "void"
	nparams 1
	  param in name "start" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
	comment " Puplic attribute accessor methods
  
start"
      end

      operation 162562 "getStart"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 162690 "setEnd"
	public explicit_return_type "void"
	nparams 1
	  param in name "end" explicit_type "int"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 162818 "getEnd"
	public explicit_return_type "int"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 162946 "setStrand"
	public explicit_return_type "void"
	nparams 1
	  param in name "strand" explicit_type "char"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163074 "getStrand"
	public explicit_return_type "char"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163202 "getString"
	public explicit_return_type "std::string"
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 163330 "operator <<"
	friend cpp_inline public explicit_return_type "std::ostream"
	nparams 2
	  param inout name "o" explicit_type "std::ostream"
	  param in name "range" type class_ref 132610 // Range
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} & ${name}${(}${t0} & ${p0}${v0}, ${t1} ${p1}${v1}${)}${const}${volatile}${throw}${abstract} {
	return o << range.getString();
  };
"
	
	
	
	
      end
    end

    class 132866 "TYPE_SENSOR"
      visibility package stereotype "enum"
      cpp_decl "${comment}enum ${name} {
${items}
};
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment " Type de sensor"
      attribute 157442 "Type_Stop"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 1"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 157570 "Type_Start"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 2"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 157698 "Type_Acc"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 4"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 157826 "Type_Don"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 8"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 157954 "Type_TStop"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 16"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 158082 "Type_TStart"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 32"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 158210 "Type_FS"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 64"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 158338 "Type_Content"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 128"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 158466 "Type_Any"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 255"
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 158594 "Type_None"
	public type class_ref 132866 // TYPE_SENSOR
	init_value "= 0     //               : Type indefini
                  "
	cpp_decl "  ${name}${value},${comment}"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end
    end

    classdiagram 128002 "classDiagram_eugene"
      draw_all_relations no hide_attributes default hide_operations default show_members_full_definition yes show_members_visibility default show_members_stereotype default show_members_multiplicity no show_members_initialization yes member_max_width 0 show_parameter_dir no show_parameter_name no package_name_in_tab default class_drawing_mode class drawing_language uml show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
      size A3-Landscape
    end

    classdiagram 129154 "classDiagram_optimization"
      draw_all_relations default hide_attributes default hide_operations default show_members_full_definition yes show_members_visibility default show_members_stereotype default show_members_multiplicity no show_members_initialization no member_max_width 0 show_parameter_dir no show_parameter_name no package_name_in_tab default class_drawing_mode default drawing_language uml show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
      size A4
    end

    classdiagram 132866 "classDiagram_sensors"
      draw_all_relations no hide_attributes yes hide_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_multiplicity default show_members_initialization no member_max_width 29 show_parameter_dir default show_parameter_name no package_name_in_tab default class_drawing_mode default drawing_language uml show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
      size A4
    end

    classdiagram 129282 "classDiagram_hitSensors"
      draw_all_relations no hide_attributes default hide_operations default show_members_full_definition yes show_members_visibility no show_members_stereotype no show_members_multiplicity no show_members_initialization yes member_max_width 0 show_parameter_dir no show_parameter_name no package_name_in_tab default class_drawing_mode default drawing_language uml show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
      size A4
    end

    classdiagram 129410 "classDiagram_gff3"
      draw_all_relations no hide_attributes default hide_operations default show_members_full_definition yes show_members_visibility default show_members_stereotype no show_members_multiplicity no show_members_initialization no member_max_width 0 show_parameter_dir no show_parameter_name no package_name_in_tab default class_drawing_mode default drawing_language uml show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
      size A4
    end

    class 131842 "MasterSensor"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      comment "************************************************************
 **                      MasterSensor                       **
 ************************************************************"
      classrelation 130690 // theSensors (<unidirectional association>)
	relation 130690 --->
	  a role_name "theSensors" multiplicity "*" private
	    comment " list of created instances of sensors"
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}*> ${name}${value};
"
	    classrelation_ref 130690 // theSensors (<unidirectional association>)
	  b parent class_ref 130050 // Sensor
      end

      attribute 142722 "IsInitialized"
	class_attribute private explicit_type "bool"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " when true MSSensorsList is initialized"
      end

      attribute 142850 "PluginsDir"
	class_attribute private explicit_type "std::string"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " path of the plugins dir"
      end

      attribute 142978 "MSSensorsList"
	class_attribute private explicit_type "std::string"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " list of sensors defined at top level"
      end

      attribute 143106 "LoadedSensorsList"
	class_attribute private explicit_type "std::string"
	stereotype "std::vector"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " list of all loaded sensors (included "
      end

      classrelation 130818 // dllList (<unidirectional association>)
	relation 130818 --->
	  stereotype "std::vector"
	  a role_name "dllList" multiplicity "*" class_relation private
	    comment " list of dll (loaded .so)"
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}*> ${name}${value};
"
	    classrelation_ref 130818 // dllList (<unidirectional association>)
	  b parent class_ref 129922 // SensorLoader
      end

      operation 150658 "LoadSensor"
	private explicit_return_type "int"
	nparams 1
	  param in name "name" explicit_type "std::string"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 150786 "~MasterSensor"
	public explicit_return_type ""
	nparams 1
	  param in name "" explicit_type "void"
	cpp_decl "    ${comment}${inline}${virtual}${name}${(}${t0} ${p0}${v0}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${t0} ${p0}${)}${throw}{
${body}}
"
	
	
	
	
	comment " load the .so if it is not yet loaded"
      end

      operation 150914 "InitMaster"
	public explicit_return_type "void"
	nparams 1
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 151042 "InitSensors"
	public explicit_return_type "void"
	nparams 1
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 151170 "GetInfoAt"
	public explicit_return_type "void"
	nparams 3
	  param inout name "X" type class_ref 128514 // DNASeq
	  param in name "pos" explicit_type "int"
	  param inout name "d" type class_ref 128258 // DATA
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} * ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 151298 "PrintDataAt"
	public explicit_return_type "void"
	nparams 4
	  param inout name "X" type class_ref 128514 // DNASeq
	  param in name "pos" explicit_type "int"
	  param inout name "d" type class_ref 128258 // DATA
	  param inout name "OUT" explicit_type "FILE"
	    defaultvalue "stdout"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}, ${t3} * ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} * ${p2}, ${t3} * ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 151426 "GetInfoSpAt"
	public explicit_return_type "int"
	nparams 4
	  param in name "type" explicit_type "byte"
	  param inout name "X" type class_ref 128514 // DNASeq
	  param in name "pos" explicit_type "int"
	  param inout name "d" type class_ref 128258 // DATA
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} ${p0}${v0}, ${t1} * ${p1}${v1}, ${t2} ${p2}${v2}, ${t3} * ${p3}${v3}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} ${p0}, ${t1} * ${p1}, ${t2} ${p2}, ${t3} * ${p3}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 151554 "PostAnalyse"
	public explicit_return_type "void"
	nparams 2
	  param inout name "pred" type class_ref 128386 // Prediction
	  param inout name "MISC_INFO" explicit_type "FILE"
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${t0} * ${p0}${v0}, ${t1} * ${p1}${v1}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 151682 "MakeSensor"
	public return_type class_ref 130050 // Sensor
	nparams 3
	  param in name "name" explicit_type "std::string"
	  param in name "n" explicit_type "int"
	  param inout name "X" type class_ref 128514 // DNASeq
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} * ${name}${(}${t0} ${p0}${v0}, ${t1} ${p1}${v1}, ${t2} * ${p2}${v2}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} * ${class}::${name}${(}${t0} ${p0}, ${t1} ${p1}, ${t2} * ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      classrelation 144258 // <association>
	relation 144258 ----
	  a role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 144258 // <association>
	  b role_name "" protected
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${type} * ${name}${value};
"
	    classrelation_ref 144386 // <association>
      end
    end

    sequencediagram 130562 "seqDiagram_eugene"
      show_full_operations_definition default write_horizontally default class_drawing_mode default drawing_language default draw_all_relations default shadow default show_stereotype_properties default
      overlapping_bars size A4-Landscape
    end

    class 142210 "Main"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
    end

    classinstance 128002 ""
      type class_ref 142210 // Main
      attributes
        end
      relations
        end
    end

    classinstance 128130 ""
      type class_ref 129538 // Parameters
      attributes
        end
      relations
        end
    end

    classinstance 128258 ""
      type class_ref 129410 // DAG
      attributes
        end
      relations
        end
    end

    sequencediagram 131714 "seqDiagram_blastx_gff3"
      show_full_operations_definition default write_horizontally default class_drawing_mode default drawing_language default draw_all_relations default shadow default show_stereotype_properties default
      overlapping_bars size A4-Landscape
    end

    classinstance 129410 ""
      type class_ref 142210 // Main
      attributes
        end
      relations
        end
    end

    classinstance 129538 ""
      type class_ref 131842 // MasterSensor
      attributes
        end
      relations
        end
    end

    classinstance 129666 ""
      type class_ref 129922 // SensorLoader
      attributes
        end
      relations
        end
    end

    classinstance 129794 ""
      type class_ref 136962 // SensorBlastX
      attributes
        end
      relations
        end
    end

    classinstance 129922 ""
      type class_ref 128642 // Hits
      attributes
        end
      relations
        end
    end

    classinstance 131074 ""
      type class_ref 130562 // GeneFeatureSet
      attributes
        end
      relations
        end
    end

    classinstance 131202 ""
      type class_ref 130306 // GeneFeature
      attributes
        end
      relations
        end
    end

    classinstance 131330 ""
      type class_ref 128770 // Attributes
      attributes
        end
      relations
        end
    end

    classdiagram 134018 "state_diag"
      draw_all_relations default hide_attributes default hide_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_multiplicity default show_members_initialization default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_infonote default shadow default show_stereotype_properties default
      size A4
    end

    class 143362 "State"
      visibility package 
      cpp_decl "${comment}${template}class ${name}${inherit} {
${members}};
${inlines}
"
      java_decl ""
      php_decl ""
      python_2_2 python_decl ""
      idl_decl ""
      explicit_switch_type ""
      
      operation 224386 "IsIntergenic"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224514 "IsIntron"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224642 "IsUTR"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224770 "IsUTR3"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 224898 "IsUTR5"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 225026 "IsCodingExon"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 225154 "IsForwardCodingExon"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 225282 "IsReverseCodingExon"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 225410 "IsTranscribedAndUnspliced"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${friend}${static}${inline}${virtual}${type} ${name}${(}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end
    end
  end

  deploymentview 128002 "src"
    //deployment diagram settings
    package_name_in_tab default show_context default write_horizontally default auto_label_position default draw_all_relations default shadow default
    draw_component_as_icon default show_component_req_prov default show_component_rea default show_stereotype_properties default
    artifact 128002 "AltEst"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 128002 // OneAltEst
	class_ref 128130 // AltEst
      end
    end

    artifact 128130 "Attributes"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 128770 // Attributes
      end
    end

    artifact 128258 "BackP"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 129026 // BackPoint
	class_ref 129154 // Track
      end
    end

    artifact 128386 "DAG"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 129410 // DAG
      end
    end

    artifact 128514 "Dll"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 129922 // SensorLoader
      end
    end

    artifact 128642 "Gap"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130178 // Gap
      end
    end

    artifact 128770 "GeneFeature"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130306 // GeneFeature
      end
    end

    artifact 128898 "GeneFeatureSet"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130562 // GeneFeatureSet
      end
    end

    artifact 129026 "getopt"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130818 // option
      end
    end

    artifact 129154 "Gff3Line"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130946 // anonymous1
	class_ref 131074 // Sofa
	class_ref 131202 // Gff3Line
      end
    end

    artifact 129282 "Hits"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 131586 // Block
	class_ref 128642 // Hits
      end
    end

    artifact 129410 "Locus"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130434 // Locus
      end
    end

    artifact 129538 "MSensor"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 131714 // UseSensor
	class_ref 131842 // MasterSensor
      end
    end

    artifact 129666 "Param"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
      end
    end

    artifact 129794 "PenaltyDist"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 129282 // PenaltyDist
      end
    end

    artifact 129922 "Prediction"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 132098 // Feature
	class_ref 132226 // Gene
	class_ref 128386 // Prediction
      end
    end

    artifact 130050 "Prediction_cte"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 132482 // Tracks
      end
    end

    artifact 130178 "Range"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 132610 // Range
      end
    end

    artifact 130306 "Sensor"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130050 // Sensor
      end
    end

    artifact 130434 "SensorIF"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 129666 // Signal
	class_ref 128258 // DATA
	class_ref 132866 // TYPE_SENSOR
      end
    end

    artifact 130562 "SoTerms"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 130690 // SoTerms
      end
    end

    artifact 130690 "Target"
      stereotype "source"
      cpp_h "#ifndef ${NAMESPACE}_${NAME}_H
#define ${NAMESPACE}_${NAME}_H

${comment}
${includes}
${declarations}
${namespace_start}
${definition}
${namespace_end}
#endif
"
      cpp_src "${comment}
${includes}
${namespace_start}
${members}
${namespace_end}"
      associated_classes
	class_ref 128898 // Target
      end
    end
  end

  package_ref 128130 // Parametrization

  package_ref 128258 // SensorPlugins
end
