From 287cf367e3c4a4b2cf27c636caa8a189ba91157f Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 22 Sep 2010 10:08:28 +0000
Subject: [PATCH] Fix and documentation for JAL-657

---
 help/html/features/seqfetch.html |   28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index c4d671a..9dfd283 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -44,23 +44,21 @@ If you are retrieving sequences from the PDB, you can retrieve specific
 chains by appending a colon and the chain id to the PDB id. For example
 :<br>
 <pre> 1GAQ:A</pre>
-<br>
-When retrieving from DAS sequence sources, coordinate range arguments
-can be passed to the server using the standard DAS sequence command
-format (
-<strong>:&lt;start&gt;,&lt;end&gt;</strong>
-)
 </p>
 <p><em>Retrieving parts of large sequence records</em><br>
-Some sequence sources allow a range query to be appended to the sequence
-ID - e.g. 'Mito:1,85779'. If you know a source understands this type of
-query format, then you should untick the checkbox for 'replace commas
-with semi-colons' so the range query can be passed to the server
-(otherwise the query will be split up into two 'Mito:1' and '85779'). In
-some cases, a source that supports range queries usually include a range
-qualification in its example query. In this case, Jalview will
-automatically disable the 'replace commas with semi-colons' option.<br>
-<em>Support for range queries was added in Jalview 2.6</em></p>
+When retrieving from DAS sequence sources, coordinate range arguments
+can be passed to the server using the standard DAS sequence command
+format:<pre>
+  &lt;AccessionId&gt;:&lt;start&gt;,&lt;end&gt;</pre> If you know a source
+understands this type of query format, then you should untick the
+checkbox for 'replace commas with semi-colons' so the range query can be
+passed to the server; otherwise, the query will be split into two (e.g
+'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases,
+however, a source that supports range queries will include a range
+qualification in its example query, and Jalview will then automatically
+disable the 'replace commas with semi-colons' option.<br>
+<em>The option to disable the comma to semi-colon translation was
+added in Jalview 2.6</em></p>
 <p>If you use the WSDBFetch sequence fetcher services (EMBL,
 Uniprot, PDB and PFAM) in work for publication, please cite:</p>
 <p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S.,
-- 
1.7.10.2