JAL-2189 release notes

diff --git a/help/html/releases.html b/help/html/releases.html
index 0192c70..b8854f3 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,7 +47,7 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>27/9/2016</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
@@ -64,8 +64,7 @@
         <ul>
             <li><!-- JAL---></li>
             <li><!-- JAL---></li>
-            <li><!-- JAL---></li>
-            <li><!-- JAL---></li>
+            <li><!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search dialog</li>
             <li><!--  JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>          
             <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
             <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
@@ -73,6 +72,7 @@
             <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
             <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
             <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
+            <li><!--  JAL-1812 -->Update to groovy-2.4.6-indy - for faster groovy script execution</li>
             <li><!--  JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
             <li><!--  JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
             <li><!--  JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
@@ -81,6 +81,9 @@
             <li><!-- JAL-2183 -->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
             <li><!-- JAL-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
             <li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+            <li><!-- JAL-2028 -->Displayed columns for PDBe and Uniprot querying stored in preferences</li>
+            <li><!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot search results</li>
+            <li><!-- JAL-1977-->Tooltips shown on database chooser</li>
                     
              
         </ul> <em>Applet</em>
@@ -108,7 +111,10 @@
             <li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
             <li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>            
             <li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
-            <li><!-- JAL-2238 -->Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li> 
+            <li><!-- JAL-2238 -->Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li>
+            <li><!-- JAL-1836,1967 -->Cannot import and view PDB structures with chains containing negative resnums (4q4h)</li>
+            <li><!--  JAL-1998 -->ArithmeticExceptions raised when parsing some structures</li>
+            <li><!--  JAL-1991, JAl-1952 -->'Empty' alignment blocks added to Clustal, PIR and PileUp output</li>
             
           </ul>
           <em>Application</em>
@@ -124,7 +130,15 @@
             <li><!--  JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
             <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
             <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
-            <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>                        
+            <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>   
+            <li><!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type</li>
+            <li><!-- JAL-1975 -->Export complete shown after destination file chooser is cancelled during an image export </li>
+            <li><!-- JAL-2025 -->Error when querying PDB Service with sequence name containing special characters</li>
+            <li><!-- JAL-2024 -->Manual PDB structure querying should be case insensitive</li>
+            <li><!-- JAL-2104 -->Large tooltips with broken HTML formatting don't wrap</li>
+            <li><!-- JAL-1128 -->Figures exported from wrapped view are truncated so L looks like I in consensus annotation</li>
+            
+                                                         
             <!--  may exclude, this is an external service stability issue  JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
           </ul>
           <em>Applet</em>

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index e1b00c4..1743f1c 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -37,16 +37,16 @@
     <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
-        client</a>. Support for import of Ensembl data also allows:
+        client</a>. Support for import of Ensembl data allows:
       <ul>
         <li><strong>Sequence variant data.</strong> Jalview
-          propagates variant annotation imported via Ensembl onto
+          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
           retrieved for a gene identifier via the Ensembl or
           EnsemblGenomes sequence databases are automatically aligned to
-          their reference genome.</li>
+          their reference genome, and introns hidden from the view.</li>
       </ul></li>
     <li><strong>Working with structures.</strong>
       <ul>
@@ -59,15 +59,19 @@
           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>
       </ul></li>
-    <li><strong>UniProt Free Text Search</strong>. The new search
+    <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 based alignment
-        visualisation.</strong>. 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></li>
+    <li><strong>Reference sequence alignment view.</strong>.
+      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 'Show cross-references' will now
+      offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
+      mapping data is available for download or display.</li>
   </ul>
 
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