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Commit 463e2020 authored by rds's avatar rds
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Keep model in step

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......@@ -3,6 +3,9 @@
<!--#set var="author" value="edgrif@sanger.ac.uk" -->
<!-- Start of page. -->
<!-- CVS info: $Id: styles.shtml,v 1.10 2009-05-08 13:08:44 rds Exp $ -->
<style>
pre{ width: 95%; background-color: #DDDDDD; border-style: solid; border-width: 1px; padding: 10px }
.example{ border-color: #000000 }
......@@ -852,199 +855,9 @@ be copied and pasted direct into a models.wrm file.
<h4>The ?ZMap_style Class</h4>
<!-- models included here (see acedb server directory)-->
<pre class="example">
//=========================================================================================
// The New ZMap_style Classes
//
// The new classes all begin with "ZMap_" to separate them from any likely existing
// classes. Acedb tags have scope within classes so we can call our tags what we want.
//
// All classes have a "Remark" field to allow database documentation, this tag is not used by
// ZMap, ZMap uses the "Description" tag in the ?Zmap_style class.
//
//-----------------------------------------------------------------------------------------
//
// Sub classes used in ZMap styles.
//
// Note that ZMap_feature_colour and ZMap_colour are hash included into their parents
// rather than being separate objects for two reasons: 1) the child/parent system for
// ZMap_Style objects largely removes the need for separate colours and 2) we don't
// want to force the DB administrator to have to think up lots of unique names for
// colour objects.
// Specifies a set of colours, colours should be specified in standard X11 colour format,
// e.g. "light pink" or "#ff00de"
//
// There are no default colours.
//
?ZMap_colour Draw UNIQUE Text
Fill UNIQUE Text
Border UNIQUE Text
// Specifies the colours for a feature, the feature will be displayed with "Normal"
// colours initially and then with "Selected" colours when selected in some way.
//
?ZMap_feature_colour Normal UNIQUE #ZMap_colour
Selected UNIQUE #ZMap_colour
// Controls GFF dumping.
?Zmap_GFF Remark Text
Version UNIQUE Int
Source UNIQUE Text
Feature UNIQUE Text
//-----------------------------------------------------------------------------------------
//
// Following "modes" define fields specific to each "type" of feature supported,
// e.g. "transcript", "graph" etc.
//
// Specifies properties unique to a basic feature.
//
?Zmap_mode_basic dummy
// Specifies properties unique to a transcript feature.
//
?Zmap_mode_transcript CDS_colour UNIQUE #ZMap_feature_colour
// Specifies properties unique to an alignment feature.
//
?Zmap_mode_alignment Gapped Internal UNIQUE Int
External UNIQUE Int
// Internal triggers drawing of separate internal blocks/gaps,
// External triggers joining of individual alignments.
// Int gives allowed align errors for a "perfect" match, 0 is default.
Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override.
// Colours for bars joining up intra and inter alignment gaps.
Match_colours Perfect UNIQUE #ZMap_feature_colour
Colinear UNIQUE #ZMap_feature_colour
Non_colinear UNIQUE #ZMap_feature_colour
Pfetchable // If present it means these alignments have pfetch entries.
Blixem UNIQUE Blixem_N // Allow blixem to be run on dna sequences for features in this set.
Blixem_X // Allow blixem to be run on peptide sequences for features in this set.
// Specifies properties unique to a sequence feature.
//
?Zmap_mode_sequence dummy Text
// Specifies properties unique to a peptide feature.
//
?Zmap_mode_peptide dummy Text
// Specifies properties unique to a text feature.
//
?Zmap_mode_text dummy Text
// Specifies properties unique to a graph feature.
//
?Zmap_mode_graph Remark Text
Mode UNIQUE Histogram // Currently we only support histograms.
Baseline UNIQUE Float // baseline value for graph.
// Specifies properties unique to a glyph feature.
//
?Zmap_mode_glyph Remark Text
Mode UNIQUE Splice
// Specifies how columns should be displayed when bumped.
?Zmap_bump Remark Text
Bump_mode UNIQUE Unbump // No bumping (default)
Overlap // Bump any features overlapping each other.
Start_position // Bump if features have same start coord.
Alternating // Alternate features between two sub_columns, e.g. to display assemblies.
All // A sub-column for every feature.
Name // A sub-column for features with the same name.
Name_interleave // All features with same name in a single sub-column
// but several names interleaved in each sub-column, the most compact display.
Name_no_interleave // Display as for Interleave but no interleaving of different names.
Name_colinear // As for No Interleave but for alignments only colinear shown.
Name_best_Ends // As for No Interleave but for alignments sorted by 5' and 3' best/biggest matches, one sub_column per match.
//-----------------------------------------------------------------------------------------
//
// ZMap style, secifies display and processing options for features.
//
?ZMap_Style Remark Text
// Text displayed in zmap to describe features.
Description UNIQUE Text
//
// Parent points to a parent style from which attributes can be inherited,
// there can be an arbitrary depth of parents/children but they must form
// a DAG, cycles are _not_ permitted.
Parent Style_parent UNIQUE ?ZMap_Style XREF Style_child
Style_child ?ZMap_Style XREF Style_parent
//
// The mode of the features, i.e. transcript, text or what.....
Mode UNIQUE Basic #Zmap_mode_basic
Transcript #Zmap_mode_transcript
Alignment #Zmap_mode_alignment
Sequence #Zmap_mode_sequence
Peptide #Zmap_mode_peptide
Plain_Text #Zmap_mode_text
Graph #ZMap_mode_graph
Glyph #ZMap_mode_glyph
//
// Controls loading of features, only one tag currently, may need more.
//
Feature_loading Deferred_load // Don't load features initially.
//
// Controls all aspects of feature display.
//
Display Col_display UNIQUE Not_displayable // never display this column (for meta columns)
Displayable Col_state UNIQUE Hide // hide column always (can be unset by user)
Show_hide // hide column according to zoom/mark etc. (can be unset by user)
Show // show column always (can be unset by user)
Show_when_empty // Show set even if empty (default FALSE)
// No_Compress // Always show, even in "compressed" display.
//
Colours UNIQUE #ZMap_feature_colour
//
Width UNIQUE Float // default is 0.0
//
// Don't show below/above these magnifications, default is always show.
Min_mag UNIQUE Float
Max_mag UNIQUE Float
//
// Should boxes have pointy ends to show features direction ? (default = FALSE)
Directional_ends
//
// Bumping controls display of features when there are so many in a column that they overlap.
Bump_mode #Zmap_bump // sets current mode.
Bump_default #ZMap_bump // sets normal bumping mode for column.
Bump_fixed // Cannot be changed from initial mode.
Bump_spacing UNIQUE Float // default is 0.0, i.e. no gap between bumped features.
//
Strand_sensitive Show_up_strand
//
// Read frame sensitive features, in 3 frame mode shown in separate reading frame cols.
Frame_sensitive Frame_display Show_only_as_3_frame // show only in 3 frame mode.
Show_only_as_1_column // show only in 3 frame mode but as single col.
Frame_colours Frame_0 UNIQUE #ZMap_feature_colour
Frame_1 UNIQUE #ZMap_feature_colour
Frame_2 UNIQUE #ZMap_feature_colour
//
// Score_bounds controls feature width when related to score, specifies min/max.
Score Score_style UNIQUE Score_by_width // only visual display supported for now.
Score_bounds UNIQUE Float UNIQUE Float // limits for squashing
Score_type UNIQUE Score_percent // score is a '%' (use in display ?)
//
// Dumping options
Dump GFF #Zmap_GFF
//=========================================================================================
<!--#include virtual="models.wrm.shtml"-->
</pre>
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