X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hb=2b38dcf01ebc4ac100d99fee946a14c4b18f4693;hp=8870550e807e560078abf9ee75575588c767e05f;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 8870550..e726c49 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * 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.
  * 
@@ -26,68 +26,54 @@
   <p>
     <strong>Sequence Fetcher</strong>
   </p>
+	<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
+    when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.</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>).
+    Every time a new fetcher is opened, you will need to <strong>select
+      the database you want to retrieve sequences</strong> from the database
+    chooser.
   </p>
-  <img src="seqfetcher.gif" align="center"
-    alt="The Jalview Sequence Fetcher Dialog Box"
-  >
-  <p>The Sequence Fetcher dialog box 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 when the sequence fetcher is first opened,
-    whilst Jalview compiles the list of available sequence datasources
-    from the currently defined DAS server registry.</p>
+  <img src="selectfetchdb.gif" align="left" width="480" height="204"
+    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
   <p>
-    First, <strong>select the database you want to retrieve
-      sequences from</strong> by clicking the button labeled 'Select database
-    retrieval source'. If a database source is already selected, then
-    the button's label will change to show the currently selected
-    database.
-  </p>
-  <img src="selectfetchdb.gif" align="left"
-    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
-  >
-  <p>Since Jalview 2.8, the available databases are shown as a tree
-    in a popup dialog box. The databases are ordered alphabetically, and
-    if there are many sources for the same type of sequence identifier,
-    they will be grouped together in a sub-branch branch labeled with
-    the identifier.</p>
-  <p>
-    Once you have selected the sequence database using the popup dialog
-    box, <strong>enter one or more accession ids</strong> (as a
-    semi-colon separated list), or press the &quot;Example&quot; button
-    to paste the example accession for the currently selected database
-    into the retrieval box. Finally, press &quot;OK&quot; to initiate
-    the retrieval.
-  </p>
-  <p>
-    <strong>Fetching from The PDB with the EMBL-EBI PDBe Search
-      Interface</strong>
-  </p>
-  <p>
-    Since Jalview 2.9, selecting PDB as the sequence database will open
-    the <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> for
-    discovering and retrieving structures.
-  </p>
-  <p>
-    <strong>Only retrieving part of a sequence</strong>
-  </p>
-  <p>
-    DAS sources (indicated by a &quot;<em>(DAS)</em>&quot;) allow a
-    range to be specified in addition to a sequence ID. 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>
+    The databases are shown as a tree, and ordered alphabetically;
+    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.
   </p>
+  <p>Once you have selected a sequence database, its fetcher dialog
+    will open. Jalview provides two types of dialog:</p>
+  <ol>
+    <li><strong>The Free-text Search Interface</strong> <br />Free-text
+      search clients are provided for PDB (Since 2.9), and UniProt
+      (Since 2.10). They provide access to each database's own query
+      system, enabling you to retrieve data by accession, free text
+      description, or any other type of supported field. For full
+      details, see each client's help page:
+      <ul>
+        <li><a href="pdbsequencefetcher.html">PDB Sequence
+            Fetcher</a></li>
+        <li><a href="uniprotsequencefetcher.html">UniProt
+            Sequence Fetcher</a></li>
+      </ul></li>
+    <li><strong>Accession based sequence retrieval</strong> <br />
+
+      <img src="seqfetcher.gif" align="center"
+      alt="The Jalview Sequence Fetcher Dialog Box"><br /> To
+      retrieve sequences, simply <strong>enter one or more
+        accession ids</strong> (as a semi-colon separated list), or press the
+      &quot;Example&quot; button to paste the example accession for the
+      currently selected database into the retrieval box. Finally, press
+      &quot;OK&quot; to initiate the retrieval.</li>
+  </ol>
 
   <p>If you use the WSDBFetch sequence fetcher services (EMBL,
-    Uniprot, PFAM, and RFAM) in work for publication, please cite:</p>
+    UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
   <p>
     Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
     J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
