JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 04d3c1d..44aa1c2 100755 (executable)
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -32,53 +32,55 @@
     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; 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>
+  <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 compiles
+    the list of available sequence datasources from the currently
+    defined DAS server registry.</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 chooser.
+    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" width="480" height="204"
-    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
-  >
-  <p>The databases are shown as a tree, and ordered alphabetically;
+    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+  <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>
+    <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/>
+  <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>
+      <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>