X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=9339b33d5644db3785b74ec41187bc1f4bbb51c7;hb=0d50ab3cdf86523b239e7dcccc551164ed197467;hp=555c839beea214a52586be9bb66d87df48d7d99c;hpb=1734d401110caf8e139973ee2c706f902298a7fd;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 555c839..9339b33 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,19 +47,41 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>27/9/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
         <ul>
-            <li><!-- JAL---></li>
+            <li><!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+            <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+            <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
+            <li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
+            <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+            <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
+            <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+            <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
         </ul> <em>Application</em>
         <ul>
             <li><!-- JAL---></li>
+            <li><!-- JAL---></li>
+            <li><!-- JAL---></li>
+            <li><!-- JAL---></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>
+            <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
             <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 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-2027 -->Support for ENA CDS records with reverse complement operator</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>
+            <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+            <li><!-- JAL-1803 -->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+            <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>
+                    
              
         </ul> <em>Applet</em>
         <ul>
@@ -72,12 +94,20 @@
             <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
             <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
             <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
-            <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
+            <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
             <li><!-- JAL-2067, JAL-  -->Tidied up links in help file table of contents</li>
             <li><!-- JAL-2072  -->Feature based tree calculation not shown for DNA alignments</li>
             <li><!-- JAL-2075  -->Hidden columns ignored during feature based tree calculation</li>
             <li><!-- JAL-2065  -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
             <li><!--  JAL-2086  -->Cannot insert gaps into sequence when set as reference</li>
+            <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as &quot;Sequence position&quot; when mousing over annotation</li>
+            <li><!--  JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
+            <li><!--  JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
+            <li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
+            <li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
+            <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>
             
           </ul>
           <em>Application</em>
@@ -88,11 +118,17 @@
             <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
             <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
             <li><!--  JAL-2085  -->Cannot save project when view has a reference sequence defined</li>
+            <li><!--  JAL-1011  -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
+            <li><!--  JAL-1989  -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
+            <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>                        
             <!--  may exclude, this is an external service stability issue  JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
           </ul>
           <em>Applet</em>
           <ul>
-            <li><!--  --></li>
+            <li><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
           </ul>
         </div>
       </td>
@@ -253,7 +289,7 @@
                 region export in flat file generation</li>
 
               <li>Export alignment views for display with the <a
-                href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+                href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
 
               <li>Export scrollable SVG in HTML page</li>
               <li>Optional embedding of BioJSON data when exporting
@@ -738,7 +774,7 @@
             <a href="https://www.certum.eu">Certum</a> to the Jalview
             open source project).
           </li>
-          <li>Jalview SRS links replaced by Uniprot and EBI-search
+          <li>Jalview SRS links replaced by UniProt and EBI-search
           </li>
           <li>Output in Stockholm format</li>
           <li>Allow import of data from gzipped files</li>
@@ -1093,8 +1129,8 @@
             current built in colourscheme is saved as new scheme</li>
           <li>AlignFrame-&gt;Save in application pops up save
             dialog for valid filename/format</li>
-          <li>Cannot view associated structure for Uniprot sequence</li>
-          <li>PDB file association breaks for Uniprot sequence
+          <li>Cannot view associated structure for UniProt sequence</li>
+          <li>PDB file association breaks for UniProt sequence
             P37173</li>
           <li>Associate PDB from file dialog does not tell you
             which sequence is to be associated with the file</li>
@@ -1669,7 +1705,7 @@
           <li>Save works when Jalview project is default format</li>
           <li>Save as dialog opened if current alignment format is
             not a valid output format</li>
-          <li>Uniprot canonical names introduced for both das and
+          <li>UniProt canonical names introduced for both das and
             vamsas</li>
           <li>Histidine should be midblue (not pink!) in Zappo</li>
           <li>error messages passed up and output when data read
@@ -1698,7 +1734,7 @@
             due to null pointer exceptions</li>
           <li>Secondary structure lines are drawn starting from
             first column of alignment</li>
-          <li>Uniprot XML import updated for new schema release in
+          <li>UniProt XML import updated for new schema release in
             July 2008</li>
           <li>Sequence feature to sequence ID match for Features
             file is case-insensitive</li>
@@ -1842,7 +1878,7 @@
           <li>Re-instated Zoom function for PCA
           <li>Sequence descriptions conserved in web service
             analysis results
-          <li>Uniprot ID discoverer uses any word separated by
+          <li>UniProt ID discoverer uses any word separated by
             &#8739;
           <li>WsDbFetch query/result association resolved
           <li>Tree leaf to sequence mapping improved