format 58
"Riken" // src::SensorPlugins::Riken
  revision 1
  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 131074 "Riken"
    //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 139522 "RAFLgene"
      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 " ************
 * RAFLgene *     // RAFL: Riken Arabidopsis Full Length cDNA 
 ************"
      attribute 187266 "deb"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 187394 "fin"
	public explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 187522 "sens"
	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 187650 "ID"
	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 213634 "RAFLgene"
	public explicit_return_type ""
	nparams 0
	cpp_decl "    ${comment}${inline}${name}${(}${)}${volatile}${throw};
"
	cpp_def "${comment}${inline}${class}::${name}${(}${)}${throw}{
${body}}
"
	
	
	
	
      end

      operation 213762 "~RAFLgene"
	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 139650 "SensorRiken"
      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 "************************************************************
 **                     SensorRiken                         **
 ************************************************************"
      classrelation 139266 // <generalisation>
	relation 139266 ---|>
	  a public
	    cpp default "${type}"
	    classrelation_ref 139266 // <generalisation>
	  b parent class_ref 130050 // Sensor
      end

      classrelation 139394 // RAFL (<directional composition>)
	relation 139394 *-->
	  stereotype "std::vector"
	  a role_name "RAFL" private
	    cpp default "    ${comment}${static}${mutable}${volatile}${const}${stereotype}<${type}> ${name}${value};
"
	    classrelation_ref 139394 // RAFL (<directional composition>)
	  b parent class_ref 139522 // RAFLgene
      end

      attribute 187778 "RAFLpos"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " Position par rapport a un gene RAFL"
      end

      attribute 187906 "RAFLindex"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " Index du RIKEN en cours"
      end

      attribute 188034 "StrandRespect"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
      end

      attribute 188162 "MIN_EST_DIFF"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default = 100;"
      end

      attribute 188290 "MAX_OVERLAP"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default = 60;"
      end

      attribute 188418 "MAX_RIKEN_LENGTH"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default = 60000;"
      end

      attribute 188546 "MAX_RIKEN_EST_LENGTH"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default  = 3000;"
      end

      attribute 188674 "MIN_RIKEN_LENGTH"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default  = 120; // 2* riken overlap (60)"
      end

      attribute 188802 "MIN_RIKEN_EST_LENGTH"
	private explicit_type "int"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default  = 10;"
      end

      attribute 188930 "RAFLPenalty"
	private explicit_type "double"
	cpp_decl "    ${comment}${static}${mutable}${volatile}${const}${type} ${name}${value};
"
	java_decl ""
	php_decl ""
	python_decl ""
	idl_decl ""
	comment " default  = -120;"
      end

      operation 213890 "checkRAFL"
	private explicit_return_type "int"
	nparams 6
	  param inout name "tmp" type class_ref 139522 // RAFLgene
	  param in name "beg5" explicit_type "int"
	  param in name "end5" explicit_type "int"
	  param in name "beg3" explicit_type "int"
	  param in name "end3" explicit_type "int"
	  param in name "len" 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}${)}${const}${volatile}${throw}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} & ${p0}, ${t1} ${p1}, ${t2} ${p2}, ${t3} ${p3}, ${t4} ${p4}, ${t5} ${p5}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 214018 "SensorRiken"
	public explicit_return_type ""
	nparams 2
	  param in name "n" explicit_type "int"
	  param inout name "X" type class_ref 128514 // DNASeq
	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 214146 "readRiken"
	public explicit_return_type "void"
	nparams 3
	  param in name "name" explicit_type "char"
	  param inout name "X" type class_ref 128514 // DNASeq
	  param inout name "RAFLtmp" explicit_type "std::vector<RAFLgene>"
	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 214274 "readRikenGff3"
	public explicit_return_type "void"
	nparams 3
	  param inout name "geneFeatureSet" type class_ref 130562 // GeneFeatureSet
	  param inout name "X" type class_ref 128514 // DNASeq
	  param inout name "RAFLtmp" explicit_type "std::vector<RAFLgene>"
	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 214402 "~SensorRiken"
	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 214530 "Init"
	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}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 214658 "GiveInfo"
	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}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} ${p1}, ${t2} * ${p2}${)}${const}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 214786 "Plot"
	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}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end

      operation 214914 "PostAnalyse"
	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}${abstract};
"
	cpp_def "${comment}${inline}${type} ${class}::${name}${(}${t0} * ${p0}, ${t1} * ${p1}${)}${const}${volatile}${throw}${staticnl}{
  ${body}}
"
	
	
	
	
      end
    end
  end

  deploymentview 131074 "Riken"
    //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 135426 "Sensor.Riken"
      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 139522 // RAFLgene
	class_ref 139650 // SensorRiken
      end
    end
  end
end
