JAL-3032 just the changes pulled already

[jalview.git] / help / html / features / seqfetch.html

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 44aa1c2..e726c49 100755 (executable)
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -26,19 +26,13 @@
   <p>
     <strong>Sequence Fetcher</strong>
   </p>
   <p>
     <strong>Sequence Fetcher</strong>
   </p>

-  <p>
-    Jalview can retrieve sequences from certain databases using either
-    the DBFetch service provided by the EMBL European Bioinformatics
-    Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
-    command (configured in <a href="dassettings.html">DAS settings</a>).
-  </p>
-  <p>The Sequence Fetcher can be opened via the &quot;File&quot;
+       <p>Jalview can retrieve sequences from a range of sequence, 3D
+               structure, genomic and domain family databases provided by EMBL-EBI.</p>
+       <p>The Sequence Fetcher can be opened via the &quot;File&quot;

     menu on the main desktop in order to retrieve sequences as a new
     alignment, or opened via the &quot;File&quot; menu of an existing
     alignment to import additional sequences. There may be a short delay
     menu on the main desktop in order to retrieve sequences as a new
     alignment, or opened via the &quot;File&quot; menu of an existing
     alignment to import additional sequences. There may be a short delay

-    when the sequence fetcher is first opened, whilst Jalview compiles
-    the list of available sequence datasources from the currently
-    defined DAS server registry.</p>
+    when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.</p>

   <p>
     Every time a new fetcher is opened, you will need to <strong>select
       the database you want to retrieve sequences</strong> from the database
   <p>
     Every time a new fetcher is opened, you will need to <strong>select
       the database you want to retrieve sequences</strong> from the database

@@ -51,11 +45,6 @@
     tooltips are shown if you mouse over some sources, explaining what
     the database will retrieve. You can select one by using the up/down
     arrow keys and hitting return, or by double clicking with the mouse.
     tooltips are shown if you mouse over some sources, explaining what
     the database will retrieve. You can select one by using the up/down
     arrow keys and hitting return, or by double clicking with the mouse.

-    <br />
-    <em>If you have DAS sources enabled, then you may have several
-      sources for the same type of sequence identifier, and these will
-      be grouped together in a sub-branch branch labeled with the
-      identifier.</em>

   </p>
   <p>Once you have selected a sequence database, its fetcher dialog
     will open. Jalview provides two types of dialog:</p>
   </p>
   <p>Once you have selected a sequence database, its fetcher dialog
     will open. Jalview provides two types of dialog:</p>

@@ -82,17 +71,6 @@
       currently selected database into the retrieval box. Finally, press
       &quot;OK&quot; to initiate the retrieval.</li>
   </ol>
       currently selected database into the retrieval box. Finally, press
       &quot;OK&quot; to initiate the retrieval.</li>
   </ol>

-  <p>
-    <strong>Only retrieving part of a sequence</strong>
-  </p>
-  <p>
-    When using DAS sources (indicated by a &quot;<em>(DAS)</em>&quot;),
-    you can append a range in addition to a sequence ID. For example, to
-    retrieve 50 residues starting at position 35 in UNIPROT sequence
-    P73137 using the UNIPROT DAS server, you would enter
-    &quot;'P73137:35,84'.<br /> <em>Full support for DAS range
-      queries was introduced in Jalview 2.8</em>
-  </p>

 
   <p>If you use the WSDBFetch sequence fetcher services (EMBL,
     UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
 
   <p>If you use the WSDBFetch sequence fetcher services (EMBL,
     UniProt, PFAM, and RFAM) in work for publication, please cite:</p>