From f2c18e7718af9d58fcf613f9d82ab12148a887ad Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Fri, 8 May 2009 15:05:40 +0000
Subject: [PATCH] insert all the missing stuff from the original styles doc.
---
src/zmapServer/acedb/models.wrm | 46 +++++++++++++++++++++------------
1 file changed, 29 insertions(+), 17 deletions(-)
diff --git a/src/zmapServer/acedb/models.wrm b/src/zmapServer/acedb/models.wrm
index baede848d..42484c7c1 100755
--- a/src/zmapServer/acedb/models.wrm
+++ b/src/zmapServer/acedb/models.wrm
@@ -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
-
//=========================================================================================
--
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