JAL-2089 tidied docs for sequence fetcher

diff --git a/help/html/features/selectfetchdb.gif b/help/html/features/selectfetchdb.gif
index 6e1ce10..de0a7e6 100644 (file)
Binary files a/help/html/features/selectfetchdb.gif and b/help/html/features/selectfetchdb.gif differ

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index ff5c1b0..04d3c1d 100755 (executable)
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -32,10 +32,7 @@
     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>
-  <img src="seqfetcher.gif" align="center"
-    alt="The Jalview Sequence Fetcher Dialog Box"
-  >
-  <p>The Sequence Fetcher dialog box can be opened via the
+  <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
@@ -43,47 +40,56 @@
     whilst Jalview compiles the list of available sequence datasources
     from the currently defined DAS server registry.</p>
   <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.
+    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="selectfetchdb.gif" align="left"
+  <img src="selectfetchdb.gif" align="left" width="480" height="204"
     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>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.
+    <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>
+    <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>
     <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>
+    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,