Skip to content
Snippets Groups Projects
Commit f2c18e77 authored by edgrif's avatar edgrif
Browse files

insert all the missing stuff from the original styles doc.

parent 3d84a192
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
src/zmapServer/acedb/models.wrm
+ 29
− 17
View file @ f2c18e77
......@@ -29,7 +29,7 @@
//
// HISTORY:
// Created: Tue Jun 10 08:15:32 2008 (edgrif)
// CVS info: $Id: models.wrm,v 1.4 2009-05-08 12:47:42 rds Exp $
// CVS info: $Id: models.wrm,v 1.5 2009-05-08 15:05:40 edgrif Exp $
//-------------------------------------------------------------------
//
......@@ -39,7 +39,10 @@
//
// 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 documentation.
// 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.
//
......@@ -99,17 +102,23 @@
// 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.
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
......@@ -148,36 +157,38 @@
//
?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 UNIQUE ?ZMap_Style
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
//
// Column_group allows placement of different sets of features within a single column:
// Controls loading of features, only one tag currently, may need more.
//
// Column_group <style_for_column_group>
//
// Column_group UNIQUE ?ZMap_Style
//
Column_group Col_Parent UNIQUE ?ZMap_Style XREF Col_Child
Col_Child ?ZMap_Style XREF Col_Parent
Feature_loading UNIQUE Immediate // Load at start up (default).
Deferred // Don't load until requested.
//
// 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
Frame_colours Frame_0 UNIQUE #ZMap_feature_colour
......@@ -201,8 +212,12 @@
//
Strand_sensitive Show_up_strand
//
// Is feature read frame dependent ? (optionally only ever show as 3 frames)
Frame_sensitive Show_only_as_3_frame
// 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.
......@@ -211,8 +226,5 @@
//
// Dumping options
Dump GFF #Zmap_GFF
// Deferred loading options
Deferred
//=========================================================================================
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment