Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / help / html / webServices / dbreffetcher.html

diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html
index fdf48a1..1f61dea 100644 (file)
--- a/help/html/webServices/dbreffetcher.html
+++ b/help/html/webServices/dbreffetcher.html
@@ -1,6 +1,6 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,34 +25,32 @@
 <p>
 <p>
   <strong>Discovering Database References for Sequences</strong><br>
-  Database references are associated with a sequence are displayed as a
-  list in the tooltip shown when mousing over its sequence ID. Jalview
-  uses references for the retrieval of <a
-    href="../features/viewingpdbs.html"
-  >PDB structures</a> and <a href="../features/dasfeatures.html">DAS
-    features</a>, and for retrieving sequence cross-references such as the
-  protein products of a DNA sequence.
+  Database references associated with a sequence are displayed as an
+  abbreviated list in the tooltip shown when mousing over its sequence
+  ID, and can be viewed in full via the
+  <a href="../io/exportseqreport.html">Sequence Details</a> window. .
+  Jalview also uses references for the retrieval of
+  <a href="../features/viewingpdbs.html">PDB structures</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>Choose one of the options from the 'Fetch DB Refs' submenu in
+       <li>select the <strong>Structure Chooser...</strong> option from
+               the Sequence ID popup menu.
+       </li>
+       <li>Choose one of the options from the 'Fetch DB Refs' submenu in
     the alignment window's <strong>Web Services</strong> menu:
     <ul>
-      <li><em>Standard Databases</em> will fetch references from
-        the EBI databases plus currently selected DAS sources</li>
-      <li>The other entries submenus leading to lists of individual
+                       <li><em>Standard Databases</em> will fetch references from EBI
+                               databases appropriate for the sequence type (Nucleotide or Protein)</li>
+                       <li>The other entries submenus leading to lists of individual
         database sources that Jalview can access.</li>
     </ul>
   </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
@@ -64,13 +62,13 @@
 <p>
   <strong>The Sequence Identification Process</strong><br> 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 identification of valid Uniprot
+  earlier Jalview versions used for UniProt sequence feature retrieval,
+  and was originally restricted to the identification of valid UniProt
   accessions.<br> 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).
+    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>
 <p>If a record (or set of records) is retrieved by any query derived
   from the ID string of a sequence, then the sequence is aligned to the