// $Id: models.wrm,v 1.120 2003/09/01 14:06:08 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 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 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 // '%' in text, + default bounds 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