Magic Tags: Summary
Version: 6/6/96 (Simon Kelley)
This is an annotated version of the models.wrm file for version 4
of ACEDB that contains in principle all and only those tags that
are used in the code somewhere, with brief comments on what they do.
///////////////////////////////////////////////////////////////////////////
// Genetic map
?Map No_cache
// Prevents cacheing if maps as objects in class gMap
// Use if your map chnges frequently and you don't want to
// have to manually rebuild it
Display Non_graphic
// Prevents graphic display
Title UNIQUE ?Text
// displayed on top line
Flipped
// Then coordinates go upwards
Centre UNIQUE Float UNIQUE Float
// First number is default coordinate to centre on
// when displaying the map not from a gene. Second number
// is default display width.
Extent UNIQUE Float UNIQUE Float
// The coordinates of the two ends of the chomosome,
// for drawing the locator image at the left of the display.
View ?View
// list of view objects for controlling display of this map
Default_view UNIQUE ?View
// view use when map first displayed.
Inherits From_map UNIQUE ?Map
Author Text
// Add objects from the inherits_from map to the
// display, if a version of the object doesn't exist
// in this map. Can be used to make different objects
// which display the same map, with different views.
// These have only Default_view, and inherits from.
// Also used by the "Private save" function in gMap.
Minimal_view UNIQUE ?View
// use this when more than 1 map displayed
Main_Marker
// items shown left of locator at full map resolution
Map ?Map Xref Map_shown #Map_position
// Maps may contain maps, or include them.
Includes ?Map
// Put all the objects in the map into this map, positions
// suitably scaled. The map must have a position on this
// map, and an extent.
Contains
// list of all primary items drawable on the map
// each needs a "Map ?Map #Map_position" line
// the following can occur in any class, to make it display on a map
Map ?Map #Map_position
Positive
// object will highlight appropriately when parent does
Negative
// object will highlight appropriately when parent does
Mapping_data 2_point ?2_point_data
Multi_point ?Multi_pt_data
Pos_neg_data ?Pos_neg_data
// these three refer to mapping data objects that can
// be displayed and take part in likelihood calculations
More_data
// look for POositive, Negative and mapping_data in
// too.
// the position to draw the object, and whether it is a point or a line,
// are determined by the #structure in the object to the right of the
// specific map.
?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 UNIQUE #Map_offset
// tag2 system for "burying"
?Map_error Error UNIQUE Float
?Map_offset Relative #Map_position
// multimaps - work via table maker
?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
////////////////////////////////////////////////////////////////////////////
// Views - control Map and Grid displays
// Almost everything in these is meaningful. The data is best set for
// Map displays by the interactive view editor.
?View Type UNIQUE Gmap
// display and columns below belong to this option
Grid Grid_map Int #View_tags
// Int is priority
// View_tags structure gives coloiurs and tags
Grid_edit_default UNIQUE Text
// Text is tag to set/unset on click editing
Grid_edit_menu Text
// List of tags to set/unset from menu
Display Submenus
// if set get submenus on item boxes
Cambridge
// if set get minor variations in drawing style
No_buttons
// if set suppress header buttons for WWW
Name UNIQUE Text
// ??
Columns Text UNIQUE Int #Column
// the key section
// Text is name; Int 0 for Hidden, 1 for Visible
// View_tags structure used for Grid tag->colour specification
?View_tags Colour #Colour
Surround_colour #Colour // colour when surround
Tag Text // could be many tags
// the column structure is a list of different column types, with
// any parameters
?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 UNIQUE Text
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 UNIQUE Text
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_tag Text Int
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
?Interval_col_conf Query UNIQUE Text // Query
Names_on
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
////////////////////////////////////////////////////////////////////////////
// Physical map - PMAP display - will be subsumed in Map
?Contig pMap UNIQUE Int UNIQUE Int
// min, max contained objects, in pMap units
Clone ?Clone XREF Contig
// list of clones
?Clone Remark General_remark ?Text
// show always in the Remark field of PMAP display
Y_remark ?Text
// only show when "Show all remarks"
PCR_remark ?Text
// only show when "Show all remarks"
Position pMap UNIQUE ?Contig XREF Clone UNIQUE Int UNIQUE Int
// endpoints of the clone
Hybridizes_to ?Clone_Grid ?Clone XREF Positive_probe ?Text
// used by GRID display to determine pattern, and by PMAP
// display to generate implicit positions for probes (top
// lines of display).
Positive_probe ?Clone
// reciprocal of Hybridizes_to - see above
Positive_locus ?Locus XREF Positive_clone
// used to attach Loci to the physical map
Sequence ?Sequence XREF Clone
// used to draw yellow sequence boxes on PMAP display
Gridded ?Clone_Grid
// if Clone_Grid == POLY1, makes the clone line thicker!
FingerPrint Canonical_for ?Clone UNIQUE Int UNIQUE Int
// will draw with a (*) indicating buried clones
// and can fetch the buried clones
Bands
// will draw the clone in the "Cosmid" part of the map
Contig9 Vaxmap UNIQUE Float
// used to find contig order in physical chromo map
In_Situ UNIQUE Int UNIQUE Int
// percent of physical chromosome
// used by obscure physical chromo map function
Cosmid_grid
// makes the clone line thicker
Canon_for_cosmid
// makes the clone line thicker
///////////////////////////////////////////////////////////////////////////
///
// grids of objects, traditionally clones gridded for filter hybridisation
?Grid Title ?Text
// used at top of GRID display
Layout Lines_at Int Int // x, y spacing
Space_at Int Int // x, y spacing
No_stagger
// default is with alternate lines staggered
A1_labelling
// label spaced blocks a-h down LHS, 1-12 across top
Row Int #Grid_row
// the items in the grid
Virtual_row Int UNIQUE ?Grid XREF In_grid REPEAT
// alternatively, a set of interleaved component grids
View ?View
// controls the colours and editing process
?Grid_row UNIQUE UNIQUE XREF Gridded REPEAT
// objects of a single class in one row - one tag only
Mixed #Mixed_grid_row
// a row of objects from mixed classes
?Mixed_grid_row UNIQUE UNIQUE XREF Gridded #Mixed_grid_row
// the objects in a mixed row, all with their own tag
?Pool Contains XREF In_pool
Subpool ?Pool XREF In_pool
// etc. Contains is tag2
In_pool ?Pool XREF Subpool
///////////////////////////////////////////////////////////////////////////////
// sequence stuff
?Motif Match_sequence UNIQUE Text
// e.g. restriction site, used by DNA analysis window
?Sequence // displayed in text column at right of fmap
DNA UNIQUE ?DNA UNIQUE Int // Int is the length
// used to get the DNA
Structure From Source UNIQUE ?Sequence
// connects sequences together
Source_Exons Int UNIQUE Int // start at 1
// defines splicing pattern
Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
// connects sequences together
Visible
// object name will be shown with tag2 in the text section
// at right, and will be clickable
Properties Transposon Text
// makes subsequence visible
Coding CDS UNIQUE Int UNIQUE Int
// makes subsequence visible, splicable and translatable
Transcript
// makes subsequence visible and splicable
Assembly_tags Text Int Int Text
// type, start, stop, comment
// all these will be drawn in the Assembly tags column
Allele ?Allele UNIQUE Int UNIQUE Int UNIQUE Text
// allele object, 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 Int Int Text
// tag2 is typically the feature key
// a box is drawn between the Int positions, and the Text
// is shown with the key to the right
Homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// creates the homology boxes.
// the Method determines which column to drawn in and how
// the Float is the score, next two ints are the position
// in the current sequence, and next two the position
// in the target sequence.
Feature ?Method Int Int UNIQUE Float UNIQUE Text
// Method determines column and display style
// Ints are start, end of feature
// Float is score
// Text is shown on select, and same Text are neighbours
Feature ?Method
// all features will be drawn in the same style
?Method Display Colour #Colour
// colour of box
Frame_sensitive
// if set, then three columns, one per frame
Strand_sensitive
// if set, only show positive strand boxes
Score Score_by_offset
// higher score pushes to right (default)
Score_by_width
// higher score boxes are wider
Score_bounds UNIQUE Float UNIQUE Float
// scores for saturation at min width, max width
Percent
// adds '%' in text
Bumpable
// boxes bump right, don't stack (unimplemented)
Width UNIQUE Float
// width of box
Symbol UNIQUE Text
// at top of column; first char only is used
Right_priority UNIQUE Float
// position of column; the greater the more right
Blastn // can calculate percent from score if blastn
Blixem Blixem_X
// can show in Blixem as protein vs DNA
Blixem_N
// can show in Blixem as DNA vs DNA
///////////////////////////////////////////////////////////////////////////////
// bibliographic stuff
?Author Address E_mail Text // used for mailing in treedisp.c, action.c
Paper ?Paper
?Paper Reference Title UNIQUE ?Text
Journal UNIQUE ?Journal XREF Paper
Year UNIQUE Int
Volume UNIQUE Text Text
Page UNIQUE Text UNIQUE Text
Author ?Author XREF Paper
// all the above used by biblio display
///////////////////////////////////////////////////////////////////////////////
// Map data -- all the following fields are used by the genetic map data
// calculation package
?2_point_data Point_1 XREF 2_point
Point_2 XREF 2_point
// the two objects that are mapped
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
Calc Calc_distance UNIQUE Float
Calc_lower_conf UNIQUE Float
Calc_upper_conf UNIQUE Float
?Pos_neg_data Item_1 XREF Pos_neg_data
Item_2 XREF Pos_neg_data
// the two items that are mapped
Calculation UNIQUE Positive
Negative
// the result
?Multi_pt_data Results A_non_B #Multi_counts
B_non_A #Multi_counts
Combined #Multi_counts
?Multi_counts UNIQUE XREF Multi_point UNIQUE Int #Multi_counts
// end of file