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>
     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>
   <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"
   </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.
     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>
   <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>
   </ol>
   <p>
     <strong>Only retrieving part of a sequence</strong>