From 0bb18e76033e7b8f4f76b23747793302ed4d9881 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 4 Dec 2008 10:46:43 +0000
Subject: [PATCH] added local das sequence source CLI and documentation

---
 help/html/features/clarguments.html     |    4 +++-
 help/html/releases.html                 |    3 +++
 help/html/webServices/dbreffetcher.html |   10 ++++++++--
 src/jalview/bin/Jalview.java            |   16 +++++++++-------
 4 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 8d6a4d8..2a1e0b8 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -93,7 +93,9 @@
 		<td>
 		<div align="left">Add and enable a das server with given
 		nickname (alphanumeric or underscores only) for retrieval of features
-		for all alignments</div>
+		for all alignments<br>
+		Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
+		<em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
 		</td>
 	</tr>
 	<tr>
diff --git a/help/html/releases.html b/help/html/releases.html
index 20504cb..3286434 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -24,6 +24,8 @@
 		</td>
 		<td>
 		<ul>
+		<li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li> 
+		<li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
 		<li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
 		</li>
 		<li>URL links generated from description line for regular-expression based URL links (applet and application)
@@ -43,6 +45,7 @@
 		</td>
 		<td>
 		<ul>
+		<li>Better handling of exceptions during sequence retrieval</li>
 		<li>URL links generated for all feature links (bugfix)</li>
 		<li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
 		<li>Added URL embedding instructions to features file documentation.</li>
diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html
index 98300aa..516f106 100644
--- a/help/html/webServices/dbreffetcher.html
+++ b/help/html/webServices/dbreffetcher.html
@@ -12,9 +12,15 @@ uses references for the retrieval of <a
 	href="../features/dasfeatures.html">DAS features</a>, and for
 retrieving sequence cross-references such as the protein products of a
 DNA sequence.</p>
+<p><strong>Initiating reference retrieval</strong><br>
+The application provides three ways to access the retrieval function. Either:
+<ul><li>select the <strong>Discover PDB IDs</strong> option from the structure submenu of the sequence's popup menu</li>
+<li>Select one of the options from the alignment window's <strong>Web Services</strong> menu to fetch references from either the EBI databases plus currently selected DAS sources, or an individual database source</li>
+<li>Answer 'Yes' when asked if you wish to retrieve database references for your sequences after initiating a DAS Sequence Feature fetch.</li>
+</ul> 
 <p>Jalview discovers references for a sequence by generating a set
 of ID queries from the ID string of each sequence in the alignment. It
-then tries to query all the databases it can access in order to match
+then tries to query a subset of all the databases it can access in order to match
 the alignment sequence to any records retrieved from the database. If a
 match is found, then the sequence is annotated with that database's
 reference, and any cross-references that it's records contain.</p>
@@ -23,7 +29,7 @@ The method of accession id discovery is derived from the method which
 earlier Jalview versions used for Uniprot sequence feature retrieval,
 and was originally restricted to the identifaction of valid Uniprot
 accessions.<br>
-Essentially, Jalview will try to retrieve records from all the databases
+Essentially, Jalview will try to retrieve records from a subset of the databases
 accessible by the <a href="../features/seqfetch.html">sequence
 fetcher</a> using each sequence's ID string (or each string in the ID
 separated by the '&#8739;' symbol).</p>
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bb1b7f2..8205374 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -80,13 +80,15 @@ public class Jalview
                       + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                       + "-png FILE\tCreate PNG image FILE from alignment.\n"
                       + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
-                      + "-eps FILE\tCreate EPS file FILE from alignment."
-                      + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
-                      + "-noquestionnaire\tTurn off questionnaire check."
-                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
-                      + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
-                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)"
-                      + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+                      + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+                      + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+                      + "-noquestionnaire\tTurn off questionnaire check.\n"
+                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+                      +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+                      +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+                      + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+                      + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
     }
 
-- 
1.7.10.2