From 47d3be6418801ac6a88fa44e808f853bfea3a336 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Tue, 27 Apr 2010 13:43:06 +0000
Subject: [PATCH] proposed zmap config
---
doc/Design_notes/notes/featureset_col.html | 25 ++++++++++++++++++++--
1 file changed, 23 insertions(+), 2 deletions(-)
diff --git a/doc/Design_notes/notes/featureset_col.html b/doc/Design_notes/notes/featureset_col.html
index f9cab41a5..8e5d0decc 100644
--- a/doc/Design_notes/notes/featureset_col.html
+++ b/doc/Design_notes/notes/featureset_col.html
@@ -1,4 +1,4 @@
-<!-- $Id: featureset_col.html,v 1.2 2010-04-27 13:11:47 mh17 Exp $ -->
+<!-- $Id: featureset_col.html,v 1.3 2010-04-27 13:43:06 mh17 Exp $ -->
<h2>Columns Featuresets and Data Sources</h2>
<fieldset><legend>Definitions</legend>
<p><a href="Design_notes/modules/zmapFeature.shtml#terminology">zmapFeature.shtml</a> has some notes about the words used for various data items in the ZMap code (which cannot be changed without a lot of work) and this section aims to define terms to be used to describe things that can be configured by the user/ otterlace or presented to the user/ annotators, or used in an external interface eg data servers and X-remote. This may seem pedantic, but there is some confusion caused by the re-use of words to refer to different objects.</p>
@@ -88,9 +88,9 @@ We can default a style to be the same name as the featureset without breaking mo
[columns]
mRNA = vertebrate_mRNA ; polyA_tail:glyph_A_tail ; polyA_signal:basic
</pre>
-
</p>
+
<h4>Request timing</h4>
<p>We wish to define some data as 'requested on startup' or 'requested on demand'. Currently (April 2010) this is done via server config ('delayed=true/false') and this applies to all featuresets supplied by that server.</p>
<p>It would be possible to specify startup and delayed featuresets per server, but perhaps this is overkill: it is just as easy to configure two servers. </p>
@@ -117,3 +117,24 @@ featuresets = featureset1_name:GFF_source1 ; featureset2_name:GFF_source2 ; etc
</fieldset>
+<fieldset><legend>Alternative Configuration format</legend>
+<p>The config options described above look slightly unwieldy and it is possible to split this up into seperate stanzas where options are defined as 'xxx = yyy:zzz'. Specifically this would mean defining a featureset's optional style in a new stanza:
+<pre>
+[featureset_styles]
+EST_rat = EST_rat_style
+</pre>
+and by analogy the GFF source for a featureset could be defined as:
+<pre>
+[GFF_source]
+vertebrate_mRNA = vertrna
+</pre>
+</p>
+
+<p>For neatness, it would be desirable to have each config stanza using a similar format, in which case the columns option in [ZMap] would need to be modified and another stanza for column styles created:
+<pre>
+[column_styles]
+EST_rat = align_col_style
+</pre>
+
+</fieldset>
+
--
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