// $Id: models.wrm,v 1.121 2007/03/15 10:39:23 edgrif Exp $
// models.wrm - main file defining tree class structures
// This file is read only when starting a new database or when you select 
// "Read Models" or "Add Update File" from the main menu.

//
// Basic Map classes
//

?Map	No_cache // Don't cache segs for this map.
	Display Non_graphic  // Prevents a graphic display!
                Title UNIQUE ?Text
		Flipped // Then coordinates go upwards
                Unit UNIQUE Text 
			// e.g. kb, centiMorgan, MegaParsec
		Centre UNIQUE Float UNIQUE Float  
			// default centre, width - else 0, 10
	    	Extent UNIQUE Float UNIQUE Float  
			// min, max - else min, max gene/locus
		Default_view UNIQUE ?View
		Minimal_view UNIQUE ?View // use this when >1 map displayed
		View ?View                // Columns to display
        Inherits  From_map UNIQUE ?Map 	// To locally edit
		  Author Text	// login name of who created it
 	Main_Marker Main_Locus ?Locus 	// XREF Main_Marker removed to
					// allow tag2 system
		// tag2 system for items shown left of locator
	Map ?Map XREF Map_shown #Map_position
	EMBL_chromosome UNIQUE Text
// Include all objects in these maps (must be mapped and have extents)
	Includes ?Map
	Contains Locus ?Locus XREF Map
        	 Rearrangement ?Rearrangement XREF Map
		 Contig ?Contig XREF Map
		 Clone ?Clone XREF Map
		 Sequence ?Sequence XREF Map
		 Allele ?Allele XREF Map
		 Chrom_Band ?Chrom_Band XREF Map
		 Map_shown ?Map XREF Map
		 // Abstract Phylogenetic tree & Gene Function Mapping
		 Tree_node ?TreeNode XREF Map           // Based upon ?Tree Leaf node order
		 Gene_Function ?Gene_Function XREF Map // for Gene Function grid map
                 Gene_Family ?Gene_Family XREF Map      // for clustering intervals on grid map
		// tag2 system for items shown in main region

?Map_position UNIQUE	Position UNIQUE Float #Map_error
			Ends Left UNIQUE Float #Map_error
			     Right UNIQUE Float #Map_error
			Multi_Position  Float #Map_error
			Multi_Ends Float UNIQUE Float
			With UNIQUE With_locus UNIQUE ?Locus #Map_offset
				    With_clone UNIQUE ?Clone #Map_offset
				// tag2 system for "burying"

?Map_error Error UNIQUE Float

?Map_offset Relative #Map_position

?MultiMap Map ?Map
          Min Int // keep loci appearing on at least min maps. Default = 2 
          Anchor UNIQUE Text UNIQUE Text UNIQUE Text  // Class tag1 tag2
                            // i.e Locus Homeology_group Homelogs
                            // class members on different maps with the
                            // same Anchor tag will be chained

?ManyMap Map ?Map UNIQUE ?View

?ManyPep Protein ?Protein // il  multi pep maps 

//
// Classes for Jo Dicks' comparative stuff
//

?Map_set Map ?Map Int
         Type Species
              List

?Homology_group Type UNIQUE Pairwise ?Locus XREF Pairwise ?Locus XREF Pairwise ?Doc 
                            Fuzzy ?Locus XREF Fuzzy
                Reference ?Paper
                Remark Text
                
?Doc              Reference ?Paper
                  Type    Protein
                          Sequence
                          RFLP
                          Other

//
// Views and Columns
//

?View 	Type 	UNIQUE 	Pepmap
			Fmap
		  	Gmap  Function_Map
			Grid  Grid_map Int #View_tags // Int is priority
			      Grid_exclusive_tags     // if present means view_tags are mutually exclusive
			      Grid_edit_default UNIQUE Text UNIQUE Text 
			      Grid_edit_menu Text UNIQUE Text 
			Pmap  Pmap_probes Pmap_probe_query Text
					  Pmap_probe_height Int
			      Pmap_YAC  Pmap_YAC_query Text
					Pmap_YAC_bold_query Text
					Pmap_YAC_height Int
			      Pmap_cmid Pmap_cmid_query Text
					Pmap_cmid_bold_query Text
					Pmap_cmid_height Int
			      Pmap_locus Pmap_locus_query Text
					 Pmap_locus_height Int
			      Pmap_remark Pmap_remark_query Text
					  Pmap_remark_height Int
				// 1st text tag name, 2nd text optional "Negative"
	Display Submenus	// BOOL for submenus on item boxes
		Cambridge	// Cambridge v. Montpellier behaviour
		No_buttons      // suppress header buttons for WWW 
		Hide_header     // No headers and footers 
	Name 	UNIQUE 	Text
	Columns	Text UNIQUE Int #Column	// Int is BOOL for Hidden/Visible

?Column	UNIQUE	Scale Scale_unit UNIQUE Float	// minimum increment
		      Cursor Cursor_on
			     Cursor_unit UNIQUE Float
		Locator Magnification UNIQUE Float
			Projection_lines_on
		Marker_points
		Marker_intervals
		Contigs
		Reversed_physical
		Physical_genes
		Two_point
		Multi_point
		Likelihood
		Points	Point_query UNIQUE Text
			Point_yellow Text  // To be made redundant.
                        Point_colour Text #Colour // to replace above
			Point_width UNIQUE Int	// max width if not at RHS
                        Point_error_scale UNIQUE Float
			Point_segregate_ordered
                        Point_show_marginal
			Point_pne #Colour // positive, no error
			Point_pe  #Colour // positive, error
			Point_nne #Colour // negative, no error
                	Point_ne  #Colour // negative, error
			Point_symbol Text // can now have more than one of these
		Interval_JTM	#Interval_col_conf
		Interval_RD	#Interval_col_conf
               	Interval_SRK 	#Interval_col_conf
		Derived_tags	DT_query UNIQUE Text
				DT_width UNIQUE Int
				DT_no_duplicates
                                DT_neighbours
                                DT_parents
				DT_follow_parent
                                DT_symbol_query
                                DT_tag Text Int
                                DT_hide
 		Spacer          Spacer_colour #Colour
                                Spacer_width Float
		RH_data		RH_query UNIQUE Text
				RH_spacing UNIQUE Float
				RH_show_all
				RH_positive #Colour
				RH_negative #Colour
				RH_contradictory #Colour
		pepSequence	PS_Highlight_residue   // il all needed for colomn display of peptides
				PS_Residues_per_wrap Int
				PS_Colours Text #Colour
		Hydrophobicity	HP_Show_Zero_bar
				HP_Fixed_Scaling
				HP_Calculation_window Int
				HP_Display_width Int
                Homol           HOM_bump
                pepFeature      FEA_bump
                                FEA_Query Text
                Homol_Name      HOM_NAME_bump
				HOM_NAME_width Int
                pepActiveZone
	        Submaps         Loci_Query UNIQUE Text
				Interval_Query UNIQUE Text
				Show UNIQUE Int
				Tolerance UNIQUE Int
				Pos_By_Loci
	

?View_tags	Colour #Colour
		Surround_colour #Colour	// colour when surround
		Tag Text		// could be many tags

?Interval_col_conf 	Query UNIQUE Text // Query
			Names_on
			No_neighbours
			Show_multiple
			Width UNIQUE Int
			Symbol UNIQUE Text
			Colours Text #Colour // Only for chrom_bands.
			Pne #Colour // positive, no error
			Pe  #Colour // positive, error
			Nne #Colour // negative, no error
                	Ne  #Colour // negative, error
			No_interval_boxes // Only for chrom_bands, to not
				      // show boxes.

//
// WWW display stuff (w6/display.c)
//
// The following is the model supported by wwwDoDisplay()
//
// UNIQUE URL UNIQUE Text
//        Web_location UNIQUE ?<class> // class should have the Build_URL submodel
//
// If neither of these, then it looks in the Class object (i.e. in class Class)
// for Web_location UNIQUE ?WWW_server (model in whooks/sysclass.c) to
// contain a template object in class WWW_server with the Build_URL submodel.
// ?WWW_server can be conveniently used by other users.

?WWW_server URL Text // Simple hard-wired URL
	    Build_URL Reference_tag Text Text // tag class(optional)
		         // use Text following tag if it exists, restricted to class if specified
			 // search sequentially for first matching class/tag
		      Use_name Text 		   // [class]
		         // applies only if no Reference_tag found, restricted to class is specified
                         // If no simple URL then one of Reference_tag or Use_name must succeed.
		      Rewrite Text UNIQUE Text Text UNIQUE Text  
			     // prefix_to_add [postfix_to_add [prefix_to_remove [postfix_to_remove]]]
		         // Once any removal prefix and postfix are removed, escapes necessary chars
			 // then adds specified prefix and postfix.
			 // If there are multiple rules then the first which matches
			 // prefix_to_remove and postfix_to_remove applies.

//
// Genetic objects
//

// For specifying different triplet encodings.
// Note, you must specify correctly formatted data for all of the tags
//   Translation, Start, Stop, Base1, Base2, Base3
//
?Genetic_code   Other_name ?Text
                Remark Text
                Translation UNIQUE Text
                Start UNIQUE Text
                Stop  UNIQUE Text
                Base1 UNIQUE Text
                Base2 UNIQUE Text
                Base3 UNIQUE Text



?Allele Name	Other_name ?Text
		Qualifier Text	    // sd, sm, ts etc.  Not systematic just now
		Rearrangement ?Rearrangement XREF Allele
	Source	UNIQUE Gene ?Locus XREF Allele
	               Gene_class ?Gene_Class XREF Allele
	Sequence ?Sequence XREF Allele
        Reference_Allele
	Isolation	Author	Text	// Isolator - should be ?Author
			Date	DateType
		        Mutagen UNIQUE Text UNIQUE Text
			Procedure Text
			Transposon_insertion Text  // Text Transposon type
			Derived_from ?Allele XREF Derivative
		// for revertants and deletions from Transposon alleles
			Isolated_for ?Author  
		// person requesting allele -- for transposon insertion
        Location ?Laboratory #Lab_Location
	Derivative ?Allele XREF Derived_from
        Strain ?Strain XREF Allele
        Genetics        Map ?Map #Map_position
                        Mapping_data    2_point ?2_point_data
                                        Multi_point ?Multi_pt_data
	                                Pos_neg_data ?Pos_neg_data
				// above three are for mapping on its own behalf
	                                In_2_point ?2_point_data
                                        In_multi_point ?Multi_pt_data
	                                In_pos_neg_data ?Pos_neg_data
				// these are for when the locus is mapped
			Covers Text // from MRC allele list
	Description     Phenotype       ?Text
			Recessive
                        Dominant
			Semi_dominant
			Weak
                        Temperature_sensitive	Heat_sensitive
						Cold_sensitive
			Amber
                        Maternal	Strictly_Maternal
					With_Maternal_Effect
                        Paternal
			Muscle
	Remark	?Text
        Reference ?Paper XREF Allele               // Mary

?Gene_Class     Phenotype ?Text
                Designating_laboratory UNIQUE ?Laboratory XREF Gene_classes
                Allele ?Allele	XREF Gene_class

?Locus  Name    Other_name ?Text
	Description ?Text
	Symbol  Text //jld
        Species ?Species //jld
        Homology Pairwise ?Homology_group //jld
                 Fuzzy ?Homology_group //jld
        Type	Gene	Reference_Allele ?Allele Text
			Phenotype ?Text
			Complementation_data Text
		Polymorphism    RFLP	Text
				Transposon_insertion  Text
				Detection_method Text
		PCR_product	Primers  Text
				Length   Int	// bp
		Clone_as_locus	UNIQUE ?Clone XREF Clone_as_locus
        Molecular_information	Sequence ?Sequence XREF Locus
                                Product ?Text
				Enzyme ?Enzyme XREF Locus
	Remark ?Text
	Display_map ?Map // Only display these map(s) when drawing
	Map    ?Map XREF Locus #Map_position
	Positive Inside_rearr ?Rearrangement XREF Locus_inside ?Author
		 Positive_clone ?Clone XREF Positive_locus ?Author
	Negative Outside_rearr ?Rearrangement XREF Locus_outside ?Author
		 Negative_clone ?Clone XREF Negative_locus ?Author
	Mapping_data	Well_ordered		// "on the line"
			2_point ?2_point_data
                        Multi_point ?Multi_pt_data
			Pos_neg_data ?Pos_neg_data
        Allele  ?Allele XREF Gene
        Strain  ?Strain XREF Gene
	Laboratory ?Laboratory
        Reference ?Paper XREF Locus
	Expr_pattern ?Expr_pattern XREF Locus
        OMIM ?Text //jld

?Balancer From_left_end
          To_right_end
          Locus ?Locus

?Rearrangement 	Name    Other_name ?Text
			Allele ?Allele XREF Rearrangement
		Type    Deletion
			Duplication	Free_dup
			Translocation
			Compound	Text
                        Phenotype ?Text
		Balances ?Map #Balancer
//	possibility to refer to other Intervals to describe a complex rearrangement
//	for the worm this is not too necessary, but important for fly and mouse
//	or perhaps there should be another class Complex_Rear that refers to
//	several intervals.
	        Reference_strain ?Strain
		Remark ?Text
		Isolation	Author Text	// should be ?Author
				Date DateType
				Mutagen UNIQUE Text UNIQUE Text // Text is dose
        	Display_map ?Map // Only display these map(s) when drawing
		Map     ?Map XREF Rearrangement #Map_position
		Positive Locus_inside ?Locus XREF Inside_rearr ?Author
			 Clone_inside  ?Clone XREF Inside_rearr ?Author
		Negative Locus_outside ?Locus XREF Outside_rearr ?Author
			 Clone_outside ?Clone XREF Outside_rearr ?Author
		Mapping_data	Pos_neg_data ?Pos_neg_data
				2_point ?2_point_data
        	                Multi_point ?Multi_pt_data
		Gridded ?Grid
		Display	Hide_under UNIQUE ?Rearrangement XREF Hides
			Hides ?Rearrangement	// no XREF on purpose
		Location ?Laboratory #Lab_Location
	        Strain   ?Strain XREF Rearrangement
        	Reference ?Paper XREF Rearrangement
      
?Strain  Genotype Text
	 Contains  Gene	 ?Locus XREF Strain
	  	   Allele  ?Allele XREF Strain 
		   Rearrangement	 ?Rearrangement XREF Strain
                   Clone ?Clone XREF In_strain
	 Properties  Males Text
		     Reference_strain Text
		     Outcrossed
		     Mutagen Text
		     CGC_received DateType
         Location ?Laboratory #Lab_Location
	 Made_by Text
	 Remark	?Text
         Reference ?Paper XREF Strain

?Lab_Location	Freezer		Text
		LiquidN2        Text
		Minus70		Text
                Remark		?Text

// Chrom_band just left in to show tags used in code

?Chrom_Band	Display	Dark	// drawn dark grey
			NOR	// Nuclear Organizer - drawn light grey
			Centromere	// special flag for waisted drawing
	                p_Telomere	// special flag for drawing
        	        q_Telomere	// special flag for drawing
                Symbol Text //jld
                Species ?Species //jld
		Map  ?Map XREF Chrom_Band #Map_position
//		Positive Locus ?Locus XREF Chrom_band ?Author
//		Contains ?Chrom_Band XREF Contained_in
//		Contained_in ?Chrom_Band XREF Contains

?Clone  Remark  General_remark ?Text
		Y_remark ?Text
		PCR_remark ?Text
	Position  Map ?Map XREF Clone #Map_position
        	  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
						// pMap units are bands
		  Clone_as_locus ?Locus XREF Clone_as_locus
		  Clone_left_end ?Sequence	// filled by XREF
		  Clone_right_end ?Sequence	// filled by XREF
		  Pos_neg_data ?Pos_neg_data
	Positive  Inside_rearr ?Rearrangement XREF Clone_inside ?Author
		  Positive_locus ?Locus XREF Positive_clone ?Author
		  Hybridizes_to ?Clone XREF Positive_probe ?Grid
		  Hybridizes_weak ?Clone XREF Pos_probe_weak ?Grid
		  Positive_probe ?Clone XREF Hybridizes_to ?Grid
		  Pos_probe_weak ?Clone XREF Hybridizes_weak ?Grid
	Negative  Negative_locus ?Locus XREF Negative_clone ?Author
		  Outside_rearr ?Rearrangement XREF Clone_outside ?Author
		  Negative_probe ?Clone XREF Does_not_hybridize_to ?Grid
		  Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid
        In_strain ?Strain XREF Clone
	Sequence    ?Sequence XREF Clone
	Length	Seq_length UNIQUE Int 			// bp
		Gel_length UNIQUE Float			// Kb
	Location ?Laboratory #Lab_Location
	Gridded ?Grid
	Grid_data ?Grid_data 
	In_pool ?Pool XREF Clone
        FingerPrint     Gel_Number UNIQUE Int
                        Approximate_Match_to UNIQUE ?Clone XREF Canonical_for
                        Exact_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Funny_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Canonical_for ?Clone UNIQUE Int UNIQUE Int 
				// start and stop offsets from self start
                        Bands   UNIQUE Int UNIQUE Int	// not used
                        Gel ?Motif  #Lane               // Magic tag2 construct
	Contig9	Chromosome UNIQUE ?Map 
                Vaxmap UNIQUE Float
		In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
		Cosmid_grid
                Canon_for_cosmid
	        Flag    UNIQUE Int
		Autopos
	Expression_construct	Pattern ?Text	// archaic
  	Reference ?Paper XREF Clone
        cDNA_group Contains ?Clone XREF Contains Text
                   Contained_in ?Clone XREF Contained_in
                   Best_match UNIQUE ?Text
	Expr_pattern ?Expr_pattern XREF Clone
	Sequence_status	Shotgun	UNIQUE DateType
			Finished UNIQUE DateType
			Accession_number UNIQUE Text

#Lane UNIQUE Bands UNIQUE Float REPEAT // In base pairs: if you prefer to minimise the ace format
             Band_Lengths  UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
             Band Float Text    // if you wish to comment single band value


?Grid	Title	?Text
	Layout	Columns	UNIQUE Int
		Lines_at UNIQUE Int UNIQUE Int	      // x, y spacing for sub-blocks
		Space_at UNIQUE Int UNIQUE Int	      // x, y spacing for main blocks
		No_stagger                            // default is with alternate lines staggered
		//
                // These sizes apply asis to normal and * 0.5 to small grid views.
		Square_size UNIQUE Float UNIQUE Float // Total size of box and surrounding space,
						      // (default = 2.0 1.0)
		Box_size UNIQUE Float UNIQUE Float    // Size of box, cannot be bigger than
                                                      // Square_size dimensions (default 0.9 0.7).
		Label_per_box                         // Do a label per box rather than a label
		                                      // per "Lines_at" sub-block.
		Labels 	UNIQUE	A1_labelling          // label spaced blocks a-h down LHS,
						      // 1-12 across top
				XY_labelling UNIQUE Text UNIQUE Text
						      // X-axis and Y-axis labels in the form of
						      // 01-XX or XX-01, for ascending vs. descending.
						      // Append an 'A', eg. 01-10A, for alphabetic.
	View ?View
	Row Int #Grid_row
	Virtual_row Int UNIQUE ?Grid XREF In_grid REPEAT
	In_grid ?Grid
	// If using lazy_grid, must set XY_labelling to be able to
        // generate object names of the form <prefix><column_label><row_label>
	Lazy_grid	Prefix UNIQUE Text
			Lazy_template Clone UNIQUE ?Clone
				      // PAC   UNIQUE ?Pac  // i comment out undifined classes 
                                      // YAC   UNIQUE ?Yac
                                      // BAC   UNIQUE ?Bac
                                      // Cosmid   UNIQUE ?Cosmid 
                                      // Fosmid   UNIQUE ?Fosmid
                                      // cDNA   UNIQUE ?cDNA
                                      // Hybrid   UNIQUE ?Hybrid
                                      Pool   UNIQUE ?Pool
                                      // Tissue   UNIQUE ?Tissue
                                      Oligo   UNIQUE ?Oligo  // Tag2


?Grid_row UNIQUE Clone UNIQUE ?Clone XREF Gridded REPEAT
		 Rearrangement UNIQUE ?Rearrangement XREF Gridded REPEAT
		 Mixed #Mixed_grid_row

?Mixed_grid_row UNIQUE Clone UNIQUE ?Clone XREF Gridded #Mixed_grid_row
		       Rearr UNIQUE ?Rearrangement XREF Gridded #Mixed_grid_row

?Pool	Contains Clone ?Clone XREF In_pool
		 Subpool ?Pool XREF In_pool
	   // etc. Contains is tag2
	In_pool ?Pool XREF Subpool

?Contig Map ?Map XREF Contig #Map_position
        pMap UNIQUE Int UNIQUE Int         // extremities in pMap units
	Clone ?Clone XREF pMap

//
// Map data classes
//

?2_point_data   Genotype  UNIQUE Text
		Results  UNIQUE Text
		Experiment	Mapper ?Author
				Laboratory ?Laboratory
				Date  UNIQUE DateType
				Temperature UNIQUE Text
		Point_1 UNIQUE Locus_1	UNIQUE ?Locus XREF 2_point UNIQUE ?Allele XREF In_2_point
			       Allele_1 UNIQUE ?Allele XREF 2_point
			       Rearrangement_1 UNIQUE ?Rearrangement XREF 2_point
		Point_2 UNIQUE Locus_2	UNIQUE ?Locus XREF 2_point UNIQUE ?Allele XREF In_2_point
			       Allele_2 UNIQUE ?Allele XREF 2_point
			       Rearrangement_2 UNIQUE ?Rearrangement XREF 2_point
			// Point_1 and Point_2 are tag2 for the mapped loci
			// for now to use this on a map both must be on it with Position type Map info.
		Calculation UNIQUE Full UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // WT X Y XY
				   One_recombinant UNIQUE Int UNIQUE Int // WT X
				   Selected UNIQUE Int UNIQUE Int // X XY
				   One_all UNIQUE Int UNIQUE Int // X ALL
				   Recs_all UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // X Y ALL
				   One_let UNIQUE Int UNIQUE Int // X ALL
				   Tested UNIQUE Int UNIQUE Int // X H
				   Selected_trans UNIQUE Int UNIQUE Int // X XY
				   Backcross UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // WT X Y XY
				   Back_one UNIQUE Int UNIQUE Int // WT X
				   Sex_full UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // WT X Y XY
				   Sex_one UNIQUE Int UNIQUE Int // WT X
				   Sex_cis UNIQUE Int UNIQUE Int // X ALL
				   Dom_one UNIQUE Int UNIQUE Int // WT nonWT
				   Dom_selected UNIQUE Int UNIQUE Int // WT X
				   Dom_semi UNIQUE Int UNIQUE Int // XD ALL
				   Dom_let UNIQUE Int UNIQUE Int // WT ALL
				   Direct UNIQUE Int UNIQUE Int // R T
				   Complex_mixed UNIQUE Int UNIQUE Int // X ALL
				   Lethal_tested UNIQUE Int UNIQUE Int // N WT
			// calculation fields can be used for full likelihood calculations
		Calc  Calc_distance UNIQUE Float
		      Calc_lower_conf UNIQUE Float
		      Calc_upper_conf UNIQUE Float
			// these fields are filled in by software from the Calculation data
	        Simple_distance	Min      UNIQUE Float 
                                Distance UNIQUE Float
                                Max      UNIQUE Float
                                Error    UNIQUE Float
                                Linkage  UNIQUE Text
			// some of these are used for drawing in the absence of Calculation data
		Remark ?Text
	// code uses Point_1, Point_2, Calculation and all its subtags, all the Calc subtags,
	// and most of the Simple_distance subtags.
		
?Pos_neg_data	Genotype  UNIQUE Text
		Results  UNIQUE Text
		Experiment Mapper ?Author
			   Laboratory ?Laboratory
			   Date  UNIQUE DateType
		Item_1	UNIQUE	Locus_1	UNIQUE ?Locus XREF Pos_neg_data UNIQUE ?Allele XREF In_pos_neg_data
			     	Rearrangement_1 UNIQUE ?Rearrangement XREF Pos_neg_data
				Allele_1 UNIQUE ?Allele XREF Pos_neg_data
				Clone_1 UNIQUE ?Clone XREF Pos_neg_data
		Item_2	UNIQUE	Locus_2	UNIQUE ?Locus XREF Pos_neg_data UNIQUE ?Allele XREF In_pos_neg_data
			     	Rearrangement_2 UNIQUE ?Rearrangement XREF Pos_neg_data
				Allele_2 UNIQUE ?Allele XREF Pos_neg_data
				Clone_2 UNIQUE ?Clone XREF Pos_neg_data
		Calculation UNIQUE Positive
				   Negative
		Remark ?Text
	// code uses Item_1, Item_2, Positive and Negative

?Multi_pt_data	Genotype  UNIQUE Text
		Experiment  Mapper ?Author
			    Laboratory ?Laboratory
			    Date  UNIQUE DateType
		Selected A UNIQUE Locus_A UNIQUE ?Locus UNIQUE ?Allele XREF In_multi_point
				  Allele_A UNIQUE ?Allele
				  Rearrangement_A UNIQUE ?Rearrangement
			 B UNIQUE Locus_B UNIQUE ?Locus UNIQUE ?Allele XREF In_multi_point
				  Allele_B UNIQUE ?Allele
				  Rearrangement_B UNIQUE ?Rearrangement
		Locus ?Locus UNIQUE ?Allele XREF In_multi_point	    // just to pair up alleles
		Results A_non_B #Multi_counts
			B_non_A	#Multi_counts
			Combined #Multi_counts
		Old_CGC_results Text
		Remark ?Text
	// code uses all the Results subtags, and the #Multi_counts structure

?Multi_counts	UNIQUE Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
		       Allele UNIQUE ?Allele XREF Multi_point UNIQUE Int #Multi_counts
		       Rearrangement UNIQUE ?Rearrangement XREF Multi_point UNIQUE Int #Multi_counts

?Grid_data	Experiment  Mapper ?Author
			    Laboratory ?Laboratory
			    Date  UNIQUE DateType
		Positive Hybridizes_to ?Clone
			 Positive_product ?Clone
		Grid_data Grid UNIQUE ?Grid
			  Probe	UNIQUE	STS UNIQUE ?STS XREF Grid_data
					Clone UNIQUE ?Clone XREF Grid_data
		// tag 2 for probe - REQUIRED
			  Default_negative
		// if set then all non-explicit elements on Grid score -ve

//
// Laboratory/Bibliography
//

?Laboratory     Address Mail Text
                        Phone Text
                        E_mail Text
			Fax Text
                CGC     Representative UNIQUE ?Author XREF Laboratory 
                        Strain_designation Text
                        Allele_designation Text
                        Gene_classes ?Gene_Class XREF Designating_laboratory
		Staff   ?Author XREF Laboratory

?Author Full_name Text
	EMBL_name UNIQUE Text	// embl.c uses instead of emblified object name if exists
	Laboratory UNIQUE ?Laboratory XREF Staff
	Old_lab ?Laboratory
        Address Mail Text
                E_mail Text
                Phone Text
		Fax   Text
        Paper ?Paper
	Sequence ?Sequence XREF From_author
        Keyword ?Keyword

?Journal Paper ?Paper XREF Journal

?Paper  Reference       Title UNIQUE ?Text 
                        Journal UNIQUE ?Journal XREF Paper
			Publisher UNIQUE Text
			Editor ?Text
                        Page  UNIQUE  Text UNIQUE Text
                        Volume UNIQUE Text Text
                        Year UNIQUE Int
			In_book #Paper
			Contained_in ?Paper XREF Contains	// old form
			Medline_acc UNIQUE Int
        Author ?Author XREF Paper
	Affiliation Text	// Authors' affiliation if available
        Abstract ?LongText
	Type UNIQUE Text
	Contains ?Paper XREF Contained_in
        Refers_to Locus ?Locus XREF Reference
                  Allele ?Allele XREF Reference
		  Rearrangement ?Rearrangement XREF Reference
		  Sequence ?Sequence XREF Reference
		  Strain ?Strain XREF Reference
		  Clone ?Clone XREF Reference
		  Protein ?Protein XREF Reference
		  Expr_pattern ?Expr_pattern XREF Reference
                  Cell ?Cell XREF Reference
                  Cell_group ?Cell_group XREF Reference
                  Tree ?Tree XREF Reference
                  Gene_Function ?Gene_Function XREF Reference
                  Gene_Family   ?Gene_Family   XREF Reference
        Keyword ?Keyword

//
// Cell models
//

?Cell   Fate    ?Text
        Embryo_division_time Text
        Remark        ?Text
        Lineage Parent  UNIQUE  ?Cell XREF Daughter
                Daughter      ?Cell XREF Parent
                Lineage_name    Text
                Equivalence_fate ?Cell XREF Equivalence_origin
                Equivalence_origin ?Cell XREF Equivalence_fate
        Group   In_group ?Cell XREF Group_member	// archaic
                Group_member    ?Cell XREF In_group	// archaic
	Cell_group ?Cell_group XREF Cell
	Life_stage ?Life_stage XREF Cell
        Tree_node ?TreeNode XREF Cell
        Reference ?Paper XREF Cell
	Data	Expr_pattern ?Expr_pattern XREF Cell
		Reconstruction ?Reconstruction XREF Cell #ReconCellInfo
	        Neurodata ?Cell #Neurodata

?Neurodata      Send    Text    UNIQUE Int              // series count
                Send_joint      Text    UNIQUE Int      // ditto for the rest
                Receive Text    UNIQUE Int
                Receive_joint   Text    UNIQUE Int
                Gap_junction    Text    UNIQUE Int
                Contact Text    UNIQUE Int

?Reconstruction Cell ?Cell
		Author ?Author
		Date UNIQUE DateType
		Remark ?Text
		Description ?LongText

?ReconCellInfo	Birth UNIQUE Float
	 	Timepoint Float #Timepoint

?Timepoint XYZ UNIQUE Float UNIQUE Float UNIQUE Float


//
// Sequence models 
//

?Sequence DNA UNIQUE ?DNA UNIQUE Int		// Int is the length
		// if you want to register a length without a DNA sequence, then use
		// a dummy sequence object, say "-".  This ensures that when a real
		// sequence appears, its length dominates.
	  Wormpep
	  Structure  From	Source UNIQUE ?Sequence
				Source_Exons Int UNIQUE Int // start at 1
		     Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
		     Overlap_right UNIQUE ?Sequence XREF Overlap_left UNIQUE Int
			// potentially use Overlap_right integer for auto-linking
		     Overlap_left UNIQUE ?Sequence XREF Overlap_right
		     Clone_left_end ?Clone XREF Clone_left_end UNIQUE Int
		     Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int
	  DB_info	Database ?Database UNIQUE Text UNIQUE Text // ID  Accession_number
                        AC_number UNIQUE Text // alternative place to store/find accession number
			Secondary_accession Text // used by embl.c to avoid primary/secondary confusion
			NI_number UNIQUE Text
		  	DB_remark ?Text		// EMBL/Genbank
			Keyword ?Keyword	// EMBL/Genbank
			Protein_id ?Sequence UNIQUE Text // Sequence is entry being dumped.  Must 
							 // specify because genes in overlap regions have
							 // different Protein_ids in each EMBL entry!
			DB_annotation ?Database UNIQUE ?LongText
			EMBL_dump_info #EMBL_dump_info
	  Origin  From_database UNIQUE ?Database UNIQUE Int	// release number
		  From_author ?Author XREF Sequence
		  From_laboratory ?Laboratory
		  Production_group Text
		  Finishing_group Text
		  Date DateType Text			// Text for comments on operation
		  Date_directory UNIQUE Int 	// date of this version for cosmids
		  Species ?Species
                  Genetic_code  UNIQUE ?Genetic_code    // specify a different genetic coding.
		  Method UNIQUE ?Method UNIQUE Float	// score
	  Map ?Map XREF Sequence #Map_position		// use in particular for Genomic_canonical
	  Visible	Title UNIQUE ?Text
	  		Other_name ?Text	// for repeats
			Matching_Genomic ?Sequence XREF Matching_cDNA
		 	Matching_cDNA ?Sequence XREF Matching_Genomic
			Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA
		  	Clone ?Clone XREF Sequence 
          	        Locus ?Locus XREF Sequence
			Enzyme ?Enzyme XREF DNA
		        Related_DNA ?Sequence XREF Related_DNA
		        Related_protein ?Protein XREF Related_DNA
			Remark ?Text
			Confidential_remark ?Text
			Brief_identification UNIQUE ?Text
	  		Reference ?Paper XREF Sequence
			Expression_construct ?Clone	// archaic
			Expr_pattern ?Expr_pattern XREF Sequence
		// tag2 system: names of all objects following next tag are shown in the 
		//   general annotation display column as "tag:objname"
	  Properties    Pseudogene Text		// explanation
			Transposon Text		// transposon type
			Genomic_canonical
			Link            
			cDNA cDNA_EST
			RNA	// if set then use U in place of T
			Coding	CDS UNIQUE Int UNIQUE Int // start, end in spliced DNA coords,
                                                          // default:  1, end-of-CDS
				CDS_predicted_by ?Method Float // score of method
				Precursor
			End_not_found
			Start_not_found UNIQUE  Int // Gives position of start frame for protein
                                                    // translation when start of CDS is before first
                                                    // exon in this object (should be in range 1 -> 3).
			Transcript	UNIQUE	mRNA	UNIQUE  Processed_mRNA
								Unprocessed_mRNA
						tRNA UNIQUE Text
						rRNA UNIQUE Text
						snRNA UNIQUE Text
						scRNA UNIQUE Text
						misc_RNA UNIQUE Text
			Status	Received UNIQUE DateType
				Library_construction UNIQUE DateType
				Shotgun	UNIQUE DateType
				Shotgun_complete UNIQUE DateType
				Contiguous UNIQUE DateType
				Finished UNIQUE DateType
				Submitted UNIQUE DateType
				Annotated UNIQUE DateType
				Archived UNIQUE DateType UNIQUE Text // Date Disk
			Match_type  UNIQUE Match_with_function
					   Match_without_function
				// These are designed specifically for measuring 
				// statistics.  What you match should be listed in 
				// Brief_id, Remark etc.  The aim now is to use Brief_id
				// exactly for what you would like a half-line summary to
				// contain, for making tables etc.
	  Quality UNIQUE ?BaseQuality UNIQUE Int
	  SCF_Position UNIQUE ?BasePosition UNIQUE Int
	  Assembly  Total_contig_length Int
		    Nbr_gel_readings Int
		    Nbr_contigs Int			// total number
		    Nbr_large_contigs Int		// number > 750bp
		    Large_contig_length Int		// lengths > 750bp
		    Pads_in_large_contigs Int
		    Ns_in_large_contigs Int
		    Double_strand Int	// amount of sequence left to double strand
		// Should most of these be UNIQUE, giving the current status, or is
		// the idea that they will show the time progression?
	  Splices	Confirmed_intron  Int Int #Splice_confirmation
			Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
			Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
	  Oligo ?Oligo XREF In_sequence Int UNIQUE Int	// for OSP and human mapping mostly
	  Assembly_tags	Text Int Int Text // type, start, stop, comment
	  Allele ?Allele XREF Sequence UNIQUE Int UNIQUE Int UNIQUE Text
		// start, stop, replacement sequence
		// if an insertion point Text is transposon name (distinguished
		// by containing non ACTG letters), and (n, n+1) = T A, so indicates 
		// direction (if known).
		// if a deletion, put '-' as the replacement sequence
	  EMBL_feature  CAAT_signal	Int Int Text #EMBL_info
			GC_signal	Int Int Text #EMBL_info
			TATA_signal	Int Int Text #EMBL_info
			allele_seq	Int Int Text #EMBL_info
			conflict	Int Int Text #EMBL_info
			mat_peptide	Int Int Text #EMBL_info
			misc_binding	Int Int Text #EMBL_info
			misc_feature	Int Int Text #EMBL_info
			misc_signal	Int Int Text #EMBL_info
			misc_recomb	Int Int Text #EMBL_info
			modified_base	Int Int Text #EMBL_info
			mutation	Int Int Text #EMBL_info
			old_sequence	Int Int Text #EMBL_info
			polyA_signal	Int Int Text #EMBL_info
			polyA_site	Int Int Text #EMBL_info
			prim_binding	Int Int Text #EMBL_info
			prim_transcript Int Int Text #EMBL_info
			promoter	Int Int Text #EMBL_info
			repeat_region	Int Int Text #EMBL_info
			repeat_unit	Int Int Text #EMBL_info
			satellite	Int Int Text #EMBL_info
			sig_peptide	Int Int Text #EMBL_info
			variation	Int Int Text #EMBL_info
			enhancer	Int Int Text #EMBL_info
			protein_bind	Int Int Text #EMBL_info
			stem_loop	Int Int Text #EMBL_info
			primer_bind	Int Int Text #EMBL_info
			transit_peptide Int Int Text #EMBL_info
			misc_structure  Int Int Text #EMBL_info
			precursor_RNA   Int Int Text #EMBL_info
			LTR             Int Int Text #EMBL_info
			terminator      Int Int Text #EMBL_info
		// EMBL_features are for legitimate EMBL feature table entries only
	  Match_table UNIQUE ?MatchTable
	  Homol	DNA_homol ?Sequence XREF DNA_homol ?Method Float Int Int Int Int #Homol_info
		Pep_homol ?Protein XREF DNA_homol ?Method Float Int Int Int Int #Homol_info
		Motif_homol ?Motif XREF DNA_homol ?Method Float Int Int Int Int #Homol_info
		// We will generate a column for each distinct ?Method.  So for
		// distinct Worm_EST and Worm_genomic columns, use ?Method objects
		// Worm_EST_Blastn and Worm_genomic_Blastn.
	  Feature ?Method Int Int UNIQUE Float UNIQUE Text #Feature_info
		// Float is score, Text is note
		// note is shown on select, and same notes are neighbours
		// again, each method has a column double-click shows the method.
		// Absorb Assembly_tags?
	  In_alignment ?Alignment XREF Sequence Int UNIQUE Int
          Tree_node ?TreeNode XREF Sequence // Phylogenetic trees

#EMBL_info	Location UNIQUE Text	// full location if non-trivial
		Qualifier Note Text	// all qualifiers correctly
			  Product Text
	// We could have in #EMBL_info a more complete representation of
	// feature table qualifiers/syntax.  I doubt this is worth it.

#Feature_info	EMBL_dump UNIQUE EMBL_dump_YES
				 EMBL_dump_NO
			// overrides for embl dump based on method
	        EMBL_qualifier Text
			// additional to those in the method, includes '/'
		Frame UNIQUE	Frame_0 /* in frame */
				Frame_1	/* 1 base then codon */
				Frame_2 /* 2 bases then codon */
//		Bury

#Homol_info Segs #Match_seg	// old way to give gapped alignment -  used in pephomolcol for Belvu call
	    Align Int UNIQUE Int UNIQUE Int	// correct way to give gapped alignments for FMAP
	     // for each ungapped block, self_start target_start [length]
	     // if no length then until next block (so no double gap) 
	     // if no Align assume ungapped
	    AlignDNAPep Int UNIQUE Int UNIQUE Int 
	    // DNA self  versus Peptide target
	    AlignPepDNA Int UNIQUE Int UNIQUE Int 
	    // Peptide self versus DNA target
	    EMBL_dump UNIQUE EMBL_dump_YES
			     EMBL_dump_NO
			// overrides for embl dump based on method
	    EMBL_qualifier Text
			// additional to those in the method, includes '/'
//	    Bury		// do not show on the standard display

?Splice_confirmation cDNA
		     EST
		     Homology
		     UTR
		     False

?Repeat_info	Percent_Identity UNIQUE Int
		Score ?Method UNIQUE Float
		N_gaps UNIQUE Int
		Loop UNIQUE Int UNIQUE Int	// rel start, stop
		Unit_Length UNIQUE Int

?Protein  Title UNIQUE ?Text
	  Other_name ?Text	// for repeats
	  Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Length + checksum
	  View ?View
	  Default_view UNIQUE ?View
	  DB_info	Database ?Database Text Text // ID  Accession_number
		  	DB_remark ?Text		// Swissprot CC entries
			Keyword ?Keyword	// Swissprot
	  		DB_searched ?Database Text // Version
	  Origin  From_Database ?Database UNIQUE Int	// release number
		  Date DateType Text			// Text for comments on operation
		  Species ?Species
		  Wormpep Replaces ?Protein XREF Replaced_by
			  Inactive Replaced_by ?Protein XREF Replaces
		// inactive wormpep entries won't be output in standard wormpep dumps
	  Visible	Corresponding_DNA ?Sequence XREF Corresponding_protein
		        Related_DNA ?Sequence XREF Related_protein
		        Related_protein ?Protein XREF Related_protein
			Enzyme ?Enzyme XREF Protein
			Reference ?Paper XREF Protein
			Expr_pattern ?Expr_pattern XREF Protein
		// tag2 system.  For now I have not populated this column.  For C. elegans
		// wormpep we want to get the information from the ?Corresponding_DNA 
		// object.  Because those objects have long term continuity, while wormpep
		// objects are one per protein sequence.  At least that is the current 
		// plan.
	  Swiss_feature	Text Int Int Text // feature name, start, stop, note
	  Match_table UNIQUE ?MatchTable
	  Homol	DNA_homol ?Sequence XREF Pep_homol ?Method Float Int Int Int Int #Homol_info
		Pep_homol ?Protein XREF Pep_homol ?Method Float Int Int Int Int #Homol_info
		Motif_homol ?Motif XREF Pep_homol ?Method Float Int Int Int Int #Homol_info
		Align_homol ?Alignment XREF Pep_homol ?Method Float Int Int Int Int #Homol_info
	  Feature ?Method Int Int UNIQUE Float	// display according to method
					// double-click shows the method
	  In_alignment ?Alignment XREF Protein Int UNIQUE Int
          Tree_node ?TreeNode XREF Protein // Phylogenetic trees

?Motif	Match_sequence  UNIQUE Text	// Text is the DNA or protein sequence
	Num_mismatch UNIQUE Int		// Allowed number of mismatches when matching
					// (default 0)
	Restriction     Isoschizomer ?Motif XREF Isoschizomer
		        Offset UNIQUE Int   
			Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
		        Overhang UNIQUE Int
		        Company UNIQUE Text
			Redundant
        Remark ?Text
	Title ?Text
	DB_info	Database ?Database Text Text // ID  Accession_number
	  	DB_remark ?Text
		DB_text ?LongText
	Substrate UNIQUE DNA
			 Peptide
	Match_table UNIQUE ?MatchTable
	Homol	DNA_homol ?Sequence XREF Motif_homol ?Method Float Int Int Int Int #Homol_info
		Pep_homol ?Protein XREF Motif_homol ?Method Float Int Int Int Int #Homol_info
		Motif_homol ?Motif XREF Motif_homol ?Method Float Int Int Int Int #Homol_info

?Accession_number  Entry Sequence ?Sequence
                         Protein ?Protein
                         Motif ?Motif
                   Web_location ?Database // use for WWW display


?Database     Name ?Text // Full name
              Contents ?Text // Description of material included
              WWW Reference_tag Text Text // tag class(optional)
                  Use_name Text // class(optional)
                  Rewrite Text UNIQUE Text Text UNIQUE Text

?Method	Remark ?Text
        // the Display information controls how the column looks.
	Display No_display                                      // column is not displayed at all.
                Colour #Colour
                CDS_colour #Colour                              // CDS outlined in this colour.
		Frame_sensitive
		Strand_sensitive Show_up_strand #Colour
		Score	Score_by_offset	// has priority over width, for Jean
			Score_by_width
			Score_by_histogram UNIQUE Float	// baseline value
			Score_bounds UNIQUE Float UNIQUE Float 
				// limits for squashing
			Percent // Score will be displayed as a '%' in fmap reportline + bounds default to 25 & 100.
		Overlap_mode UNIQUE	Overlap		  // draw on top - default
					Bumpable	  // bump to avoid overlap
			     		Cluster		  // one column per homol target
		Width UNIQUE Float
		Symbol UNIQUE Text	// first char only is used
		Right_priority UNIQUE Float // the greater the more right
		Max_mag UNIQUE Float	// don't show if more bases per line
		Min_mag UNIQUE Float	// don't show if fewer bases per line
		Show_text      // only put text in right-hand column if set
                Gapped         // draw sequences or homols with gaps
                Join_blocks    // link up all blocks of a single feature with lines
	Blastn		// can calculate percent from score if blastn
	Blixem  Blixem_X
		Blixem_N
		Blixem_P
	Belvu
	EMBL_dump EMBL_feature UNIQUE Text		// require this
		  EMBL_threshold UNIQUE Float		// apply to score unless overridden
		  EMBL_qualifier Text UNIQUE Text
	  // if 1 Text, it is the entire qualifier including '/'
	  // if 2 Texts, 1st is an sprintf format and 2nd is
	  //   an argument.  If this is "score", "note", "y1", "y2" or "target"
	  //   then use the corresponding field of the Feature or Homol line.
	  // multiple formats will be concatenated until one starts with '/'.
	Gene_assemble	Gene_assemble_method ?Method UNIQUE Float
				// Float factor to multiply score by
			Intron_min UNIQUE Int
			Exon_min UNIQUE Int
			Intron_cost UNIQUE Float UNIQUE Float UNIQUE Int
				// base cost, cost per log bp beyond min
				// Int is min for this if not Intron_min
			Inter_gene_cost UNIQUE Float
	GF_parameters	GF_range UNIQUE Int
				// +- range for genefinder feature calculation
			GF_ATG_cutoff UNIQUE Float
			GF_5_cutoff UNIQUE Float
			GF_3_cutoff UNIQUE Float
	GFF	GFF_source UNIQUE Text
		GFF_feature UNIQUE Text
	EMBL_dump_info #EMBL_dump_info // when used for controlling dump

#EMBL_dump_info	EMBL_dump_method UNIQUE ?Method
		ID_template UNIQUE Text
		ID_division UNIQUE Text
		DE_format UNIQUE Text  
		OS_line UNIQUE Text    
		OC_line Text           
		RL_submission Text     
		EMBL_reference ?Paper  
		CC_line Text           
		source_organism UNIQUE Text   
		gene_from_name

?Oligo	Sequence UNIQUE Text  // verbatim sequence 
	Length UNIQUE Int
	GC UNIQUE Float
	STS STS1 UNIQUE ?STS XREF Oligo1
	    STS2 UNIQUE ?STS XREF Oligo2
        OSP  Score UNIQUE Float
             Tm UNIQUE Float
             Pairwise_scores ?Oligo XREF Pairwise_scores UNIQUE Float Float // score and Tm
        In_sequence ?Sequence XREF Oligo
        Status Temporary
               Ordered UNIQUE DateType
               Received UNIQUE DateType
               Location ?Laboratory #Lab_Location

?STS	Oligo1 UNIQUE ?Oligo
	Oligo2 UNIQUE ?Oligo
	Map ?Map #Map_position
	Grid_data ?Grid_data 

//
// METABOLIC SECTION - from Stan Letovsky and the Soybase project
//

?Pathway	Structure Components ?Pathway XREF In_Pathway
			  In_Pathway ?Pathway XREF Components
			  Diagram UNIQUE ?PathwayDiagram XREF Pathway
		Enzyme ?Enzyme XREF Catalyzes #Reference
		Metabolites 	Major_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
				Minor_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
				Major_Product ?Metabolite XREF Produced_by #ReactantInfo
				Minor_Product ?Metabolite XREF Produced_by #ReactantInfo
				Cofactor_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
				Cofactor_Product ?Metabolite XREF Produced_by #ReactantInfo
				Additional_Cofactor_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
				Additional_Cofactor_Product ?Metabolite XREF Produced_by #ReactantInfo
		Ancillary	Anc_reactants ?Metabolite #ReactantInfo
				Anc_products ?Metabolite #ReactantInfo // e.g. for transport. 
				Anc_Enzyme ?Enzyme #Reference
		Activator ?Metabolite XREF Activates #RegulatorInfo
		Inhibitor ?Metabolite XREF Inhibits #RegulatorInfo
		Remark ?Text

?RegulatorInfo	Type UNIQUE Active_site
		Ki Text  //for inhibitor
		Remark ?Text
		Reference ?Paper

?ReactantInfo	Major_Role
		Minor_Role
		Cofactor
		N Int // etc.
		Km Text #Reference
		Vmax Text #Reference
		Substrate_specificity ?Text #Reference
		Remark ?Text
		Reference ?Paper
	
?Enzyme		Other_name ?Text
		EC_Number ?Text #Reference  // probably should be under reaction
		Corresponds_to	Locus ?Locus XREF Enzyme
				DNA ?Sequence XREF Enzyme
				Protein ?Protein XREF Enzyme
		Catalyzes ?Pathway
		Remark ?Text
		Reference ?Paper

?Metabolite	Consumed_by	?Pathway
		Produced_by	?Pathway
		Activates	?Pathway
		Inhibits ?Pathway XREF Inhibitor
		Remark ?Text

?PathwayDiagram	Name ?Text
		Pathway ?Pathway		
		Node Int Float Float Int ?Metabolite // ID X Y LabelID Metabolite
		Arc  Int Int Int  Int Int Float  ?Pathway
		   // ID  Label From To  Curvature Radius Step
		TangentArc Int Int
		   // Arc Tangent
		Label Int Float Float Text // ID X Y Label

?Reference	Reference ?Paper
		Remark ?Text
		Species ?Species
		Description ?Text //For trait information

?Expr_pattern	Experiment	Laboratory ?Laboratory
				Author ?Author 
				Date UNIQUE DateType
				Strain UNIQUE ?Strain
		Reference ?Paper XREF Expr_pattern
		Expression_of	Sequence ?Sequence XREF Expr_pattern
				Clone ?Clone XREF Expr_pattern
				Locus ?Locus XREF Expr_pattern
				Protein ?Protein XREF Expr_pattern
		Expressed_in	Cell ?Cell XREF Expr_pattern
				Cell_group ?Cell_group XREF Expr_pattern
				Life_stage ?Life_stage XREF Expr_pattern
		Type	Reporter_gene ?Text
			In_situ ?Text
			Antibody ?Text
		Pattern ?Text
		Remark ?Text
		Picture ?Picture XREF Expr_pattern		

?Picture Description ?Text
	 Pick_me_to_call Text Text
	 Expr_pattern ?Expr_pattern XREF Picture

?Cell_group	Fate ?Text	
		Remark	?Text
		Contains	Cell ?Cell XREF Cell_group
				Sub_group ?Cell_group XREF Contained_in
		Contained_in ?Cell_group XREF Sub_group
		Type	UNIQUE  Tissue
				Organ
				Region
		Expr_pattern ?Expr_pattern XREF Cell_group	
		Life_stage ?Life_stage XREF Cell_group
                Reference ?Paper XREF Cell_group

?Life_stage	Contains Cell ?Cell XREF Life_stage
			 Cell_group ?Cell_group XREF Life_stage
		Expr_pattern ?Expr_pattern XREF Life_stage
		Remark	?Text

//
// Alignment models
//

?Alignment Description ?Text
	   Consensus UNIQUE Verbatim UNIQUE Text
	   Alignment	Sequence ?Sequence XREF In_alignment Int UNIQUE Int #Align_component  // Member_Alignment
			Protein ?Protein XREF In_alignment Int UNIQUE Int #Align_component
			Include_alignment ?Alignment XREF In_alignment UNIQUE Int UNIQUE Int #Align_component
	   In_alignment #Alignment
	   Parent ?Alignment XREF Child
	   Child ?Alignment XREF Parent Int UNIQUE Int #Align_component
	   Is_subalign
	   Homol Pep_homol ?Protein XREF Align_homol ?Method Float Int Int Int Int #Homol_info

?Align_component  Verbatim UNIQUE Text				// use this not extracted seq if present
		  Extract UNIQUE DNA #Extract_info
				 Peptide #Extract_info
				 Translate #Extract_info
				 Alignment #Extract_info
		  Partial UNIQUE Int UNIQUE Int			// start, end of self
		  Properties  Is_frame_shifted
			      Has_introns
			      Checked
			      Core
				 
?Extract_info UNIQUE Gap UNIQUE Int #Extract_info
		     Seg UNIQUE Int UNIQUE Int #Extract_info
		     Insert UNIQUE Int #Extract_info		// add X's, not .'s

?Match_seg UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int #Match_seg  // Start, End of Aligment;  Start, End of Subject

////////////////////////////////////////////////////////////////////////////
// models for Drawing display - not used yet
// do not use - they may well change, but I leave them here because
// they form the basis for what is in the code - no, comment them out
//
//?Image   File #Image_file
//	 Drawing Centre UNIQUE Float UNIQUE Float
//         	 Scale UNIQUE Float		 // units -> pixels
//		 Bounds UNIQUE Float UNIQUE Float UNIQUE Float UNIQUE Float
//         Display  Default_view UNIQUE ?View
//  		  View ?View
//  	 Contains  Cell ?Cell #DrawInfo
//  		 // Contains is tag2 for objects - where is under Drawing
//
//#Image_file File_name UNIQUE Text
//  	    File_type UNIQUE GIF	// could add JPEG, TIFF etc
//  	    Colormap UNIQUE Greyscale
//                            Color
////
//#DrawInfo Shape UNIQUE Point UNIQUE Float UNIQUE Float
//				// x y
//	               Rectangle UNIQUE Float UNIQUE Float UNIQUE Float UNIQUE Float
//				// x1 y1 x2 y2
//		       Polygon Float UNIQUE Float
//				// column of x y pairs
//          Colour  Foreground UNIQUE #Colour   // default BLACK
//                  Background UNIQUE #Colour   // default TRANSPARENT
// 
// Example
//
// Image image1
// file file_name "mm.gif"
// file file_type GIF
// Contains Cell cell.1 Rectangle 1 1 50 50
// Contains Cell cell.1 FOREGROUND RED
// Contains Cell cell.2 Rectangle 100 100 250 250
// Contains Cell cell.2 FOREGROUND GREEN
// Bounds -300 -300 300 300
// scale 1
// centre 0 0 
// 
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////              

// ?Script class complements Pick_me_to_call
// (WIN32 code implementation only at present (rbrusk Jul '98)
?Script	Program     Text					// Name of program (i.e. perl) as opposed to script name
        Options     Text					// Switches to program itself (i.e. -d for perl debug mode)
        Directory   Text					// Working Directory (for data only)
        Script      Text					// Name of perl script (located in wperl)
        Args        Switches Text				// Commandline switches understood by the script 
		    Input    Prompt_User_Input			// Prompt user for input source filename
                             Input_File          Text		// Input file name, of data in form "Input_Format"
                             Input_Format UNIQUE TextIn		// Text only input
                                                 FastaIn	// Fasta Sequence formatted input
                                                 AceIn		// Ace file input
                    Output   Prompt_User_Output			// Prompt user for output target filename
                             Output_File          Text		// Output file name
                             Output_Format UNIQUE TextOut	// Text only output
                                                  FastaOut	// FastaOutput
                                                  AceOut	// If Output is "AceOut", display single objects
								// in their default display; multiple "type B" objects
								// are displayed in a "Forest" display? 
        Display     Text					// User specified completion dialog message 

//	Evolutionary Tree Construction 
//	and Comparative Genomics ACEDB Models
//
//      Richard Bruskiewich (rbrusk@octogene.medgen.ubc.ca)
//	Last Modified: August 31, 1998
//
// ***  Need to add DtDendrogram to displays.wrm somewhat as follows:
//
//	_DDtDendrogram -g TEXT_FULL_SCROLL -x 0.1 -y 0.01 -w 0.8 -height 0.5 -help dendrogram
//
// ***  Suggest that users also add/modify options.wrm to make DtDendrogram the defaults for the following:
//
//	_VCell             -V -D DtDendrogram
//	_VTree             -V -D DtDendrogram
//	_VTreeNode	   -V -D DtDendrogram
//	_VTaxon	           -V -D DtDendrogram
//	_VSpecies          -V -D DtDendrogram
//
// ***  Users should (must?) add Tree_node ?TreeNode XREF's to the following classes in order to
//      fully benefit from DtDendrogram functionality (this excerpt from "Contains" tag in ?TreeNode) 
//
//		           Sequence UNIQUE ?Sequence XREF Tree_node
//		           Protein  UNIQUE ?Protein  XREF Tree_node
//                         Cell     UNIQUE ?Cell     XREF Tree_node
//                         URL      UNIQUE ?Url      XREF Tree_node
//
//
///////////////////////////////////////////////////////////////////////////////
//
//      Taxonomy Classes
//
?Taxon   Common_name  UNIQUE ?Text
         Other_names  Text
         Rank  UNIQUE Superkingdom
                      Kingdom
                      Phylum
                      Subphylum
                      Superclass
                      Class
                      Subclass
                      Superorder
                      Order
                      Suborder
                      Superfamily
                      Family
                      Subfamily
                      Genus
                      Species UNIQUE ?Species XREF Taxon
                      No_Rank
         Description  ?Text
	 Taxonomy     UNIQUE ?TreeNode	// Unique taxonomy tree 
         // Note: ?Taxon objects can be associated with more than one tree
         Tree_node    ?TreeNode XREF Taxon 
	 // Optional colour code (i.e. on Phylogenetic trees)
	 Display      Foreground_Colour   #Colour  
	              Background_Colour   #Colour  

?Species Common_name  ?Text
         Taxon UNIQUE ?Taxon XREF Species
         Loci         ?Locus
         Sequences    ?Sequence
         Proteins     ?Protein
         Reference    ?Paper

//
///////////////////////////////////////////////////////////////////////////////
//
//      The Tree Classes
//
?Tree    Description UNIQUE ?Text		// Used as graph display title if present
         Type UNIQUE Taxonomy			// Controls semantics of tree display
                     DNA
                     Protein
                     Cell_Lineage
         Root UNIQUE ?TreeNode                  // "Root" node of the current tree
         Tree_node   ?TreeNode                  // Nodes in other ?Trees within which this ?Tree is embedded
         Display     No_Header			// Suppresses display "header"
                     Descriptive_Labels		// Show descriptive labels
                     Colour			// Taxon_colouring if present
                     Normalization    UNIQUE Float	// Normalization factor for display (defaults to 1.0)
                     Bootstrap_Factor UNIQUE Float	// Normalization factor for bootstrap values (defaults to 1.0)
                     Hide_Bootstraps
                     Alignment UNIQUE Top	// How the dendrogram is to be drawn
                                      Middle
                                      Bottom
                                      Unrooted  // Unrooted "star" tree
         Reference   ?Paper XREF Tree

?TreeNode       Label UNIQUE ?Text		// Tree vertex label, e.g. sequence name or taxon   
                Id    UNIQUE Int		// Node numbering...
                Description  ?Text
		Type UNIQUE  Root		// Root ?TreeNode should be so designated!
                             Interior
		             Leaf
                Distance UNIQUE	Float		// "Evolutionary distance" or branch length
                Bootstrap UNIQUE	Float		// Node subtree "bootstrap" values
                Tree   UNIQUE   ?Tree
		Parent UNIQUE   ?TreeNode XREF  Child
		Child           ?TreeNode XREF  Parent
                Display  Hide			// Hide the subtree (children) of this node
                         Colour   UNIQUE #Colour // Fixes the colour of the subtree; 
                                                 // overridden by child node settings
                         Hide_Bootstraps         // Hide all bootstraps in subtree...
                         Show_Bootstrap          // ... except those with the "Show_Bootstrap" tag set
                Contains Embedded_Tree UNIQUE ?Tree XREF Tree_node 
                         Taxon    UNIQUE ?Taxon     XREF Tree_node
		         Sequence UNIQUE ?Sequence  XREF Tree_node
		         Protein  UNIQUE ?Protein   XREF Tree_node
                         Cell     UNIQUE ?Cell      XREF Tree_node
//                         URL      UNIQUE ?Url       XREF Tree_node // RD 010801 don't understand
                Pick_me_to_call   Text   Text
                Positive Has_Gene_Function           ?Gene_Function XREF PosTreeNode
                         Family_Member               ?Gene_Family XREF PosTreeNode
                Negative Does_NOT_Have_Gene_Function ?Gene_Function XREF NegTreeNode
                         NOT_Family_Member           ?Gene_Family XREF NegTreeNode
                Map ?Map XREF      Tree_node #Map_position  // Leaf node ordinate

//
///////////////////////////////////////////////////////////////////////////////
//
// Function_Map (gmap) related classes
//
// Keeps track of gene functional attributes
?Gene_Function  Description Text
		Positive PosTreeNode        ?TreeNode    XREF Has_Gene_Function
		         In_Gene_Family     ?Gene_Family XREF Has_Gene_Function
		Negative NegTreeNode        ?TreeNode    XREF Does_NOT_Have_Gene_Function
		         NOT_In_Gene_Family ?Gene_Family XREF Does_NOT_Have_Gene_Function
                Map ?Map XREF Gene_Function #Map_position // For a feature map of genes
		Reference ?Paper XREF Gene_Function

?Gene_Family    Description Text
                Type SuperFamily
		     Family
		     Subfamily
                Positive PosTreeNode                 ?TreeNode      XREF Family_Member
		         Has_Gene_Function           ?Gene_Function XREF In_Gene_Family
		Negative NegTreeNode                 ?TreeNode      XREF NOT_Family_Member
                         Does_NOT_Have_Gene_Function ?Gene_Function XREF NOT_In_Gene_Family
                Map ?Map XREF Gene_Family #Map_position // For a feature map of genes
                Reference ?Paper XREF Gene_Family 


// end of file
