From 4fdcc803d2e906c7f21912d8d004b57589a048be Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Oct 2016 20:58:12 +0100
Subject: [PATCH] JAL-2189 tweak ensembl release notes

---
 help/html/features/ensemblsequencefetcher.html |   13 +++----
 help/html/whatsNew.html                        |   48 ++++++++++++------------
 2 files changed, 29 insertions(+), 32 deletions(-)

diff --git a/help/html/features/ensemblsequencefetcher.html b/help/html/features/ensemblsequencefetcher.html
index c842a42..e547c58 100644
--- a/help/html/features/ensemblsequencefetcher.html
+++ b/help/html/features/ensemblsequencefetcher.html
@@ -29,16 +29,13 @@
   retrieve annotated transcripts, peptides and genomic contigs from
   <a href="http://www.ensembl.org">ENSEMBL</a>.
   <br />
-  <img src="selectfetchdb.gif" align="left" width="480" height="204"
-    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+  <img src="selectfetchdb.gif" align="right" width="480" height="204"
+    alt="Database selection dialog with Ensembl sequence source tooltip">
 
-  <p>
-    Two types of ENSEMBL source are provided. ENSEMBL queries the main
-    ENSEMBL warehouse containing data for higher eukaryotes, and
+  <p>Two types of ENSEMBL source are provided. ENSEMBL queries the
+    main ENSEMBL warehouse containing data for higher eukaryotes, and
     EnsemblGenomes, which queries Ensembl Pathogens, and other
-    warehouses.<br /> <em>Ensembl support is new in Jalview, and
-      we expect to merge these sources in a future release.</em>
-  </p>
+    warehouses.</p>
   <p>
     <strong>General Use</strong><br /> If you have a set of Ensembl
     gene or transcript IDs, then you can retrieve them <em>via</em> the
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index f8de1f0..cab871c 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -32,52 +32,52 @@
       2.10 Release Notes</a>, but the highlights are below.
   </p>
   <ul>
-    <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
-      transcripts and proteins can be retrieved via Jalview's new <a
-      href="features/ensemblsequencefetcher.html">Ensembl REST
+    <li><strong>Ensembl sequence fetcher</strong><br />Annotated
+      Genes, transcripts and proteins can be retrieved via Jalview's new
+      <a href="features/ensemblsequencefetcher.html">Ensembl REST
         client</a>. Support for import of Ensembl data allows:
       <ul>
-        <li><strong>Sequence variant data.</strong> Jalview
-          propagates variant annotation on genomic regions onto
-          transcripts and protein products, complete with associated
-          metadata such as clinical significance.</li>
-        <li><strong>Aligned locus view.</strong> Transcripts
+        <li><strong>Aligned locus view</strong><br />Transcripts
           retrieved for a gene identifier via the Ensembl or
           EnsemblGenomes sequence databases are automatically aligned to
           their reference genome, and introns hidden from the view.</li>
+        <li><strong>Sequence variant data</strong><br />Jalview
+          propagates variant annotation on genomic regions onto
+          transcripts and protein products, complete with associated
+          metadata such as clinical significance.</li>
       </ul></li>
-    <li><strong>Working with structures.</strong>
+    <li><strong>Ensembl and ENA 'show cross-references'
+        support</strong><br />The Calculations menu's <strong>'Show
+        cross-references'</strong> now offers Ensembl as well as EMBLCDS and
+      Uniprot when CDS/Protein mapping data is available for download or
+      display. This allows variant annotation to be added directly to an
+      alignment of UniProt sequences.</li>
+    <li><strong>Working with structures</strong>
       <ul>
-        <li><strong>More accurate structure mappings.</strong>
+        <li><strong>More accurate structure mappings</strong><br />
           Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
           to <a href="features/siftsmapping.html">match structures
             to UniProt sequences</a>, even for structures containing
           multiple copies of a sequence.</li>
-        <li><strong>Import structures as mmCIF</strong>. Jalview
+        <li><strong>Import structures as mmCIF</strong><br />Jalview
           now downloads data from the EMBL-EBI's PDBe site as <a
           href="features/mmcif.html">mmCIF</a>. This allows very large
           structures to be imported, such as the HIV virus capsid
           assembly.</li>
         <li><strong>Chimera users will need to upgrade to
-            1.11.1.</strong>If you use Chimera to view structures downloaded by
-          Jalview 2.10, you will need to make sure you are running the
-          latest version of <a href="features/chimera.html">Chimera</a>.</li>
+            1.11.1</strong><br />If you use Chimera to view structures
+          downloaded by Jalview 2.10, you will need to make sure you are
+          running the latest version of <a href="features/chimera.html">Chimera</a>.</li>
       </ul></li>
-    <li><strong>UniProt Free Text Search.</strong> The new search
-      dialog for UniProt allows you to browse and retrieve sequences
-      from UniProt with free-text search and more structured queries</li>
-    <li><strong>Reference sequence alignment view.</strong>.
+    <li><strong>UniProt Free Text Search</strong><br />The new
+      search dialog for UniProt allows you to browse and retrieve
+      sequences with free-text search, or structured queries.</li>
+    <li><strong>Reference sequence alignment view</strong><br />
       Jalview 2.9 introduced support for reference sequences. In 2.10,
       when a reference sequence is defined for the alignment, the
       alignment column ruler is now numbered according to the reference
       sequence. The reference sequence for alignment views can also be
       saved and restored from Jalview projects.</li>
-    <li><strong>Ensembl and ENA 'show cross-references'
-        support.</strong>The Calculations menu's <strong>'Show
-        cross-references'</strong> will now offer Ensembl as well as EMBLCDS and
-      Uniprot when CDS/Protein mapping data is available for download or
-      display.</li>
-
   </ul>
 
 </body>
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