X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6f44b3d43272c66364c669b808e62b48c88aa38a;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=280ea6540dd689732a1d5420dee72dedd0c8fb5b;hpb=8ece51ef041ca6a2761e768a175a90543aa1f943;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 280ea65..6f44b3d 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,31 +47,210 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
+          <strong><a name="Jalview.2.10.1">2.10.1</a><br />
+            <em>29/11/2016</em></strong>
+        </div>
+      </td>
+      <td><div align="left">
+          <em>General</em>
+          <ul>
+            <li>
+              <!-- JAL-98 -->Improved memory usage: sparse arrays used
+              for all consensus calculations
+            </li>
+            <li>
+              <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+            </li>
+            <li>Updated Jalview's Certum code signing certificate
+              for 2016-2017</li>
+          </ul>
+          <em>Application</em>
+          <ul>
+            <li>
+              <!-- JAL-1723 -->Sequence ID tool tip presents abridged
+              set of database cross-references, sorted alphabetically
+            </li>
+            <li>
+              <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
+              from database cross references. Users with custom links
+              will receive a <a href="webServices/urllinks.html#warning">warning
+                dialog</a> asking them to update their preferences.
+            </li>
+            <li>
+              <!-- JAL-2287-->Cancel button and escape listener on
+              dialog warning user about disconnecting Jalview from a
+              Chimera session
+            </li>
+            <li>
+              <!-- JAL-2320-->Jalview's Chimera control window closes if
+              the Chimera it is connected to is shut down
+            </li>
+            <li>
+              <!-- JAL-1738-->New keystroke (B) and Select highlighted
+              columns menu item to mark columns containing
+              highlighted regions (e.g. from structure selections or results
+              of a Find operation)
+            </li>
+            <li>
+              <!-- JAL-2284-->Command line option for batch-generation
+              of HTML pages rendering alignment data with the BioJS
+              MSAviewer
+            </li>
+          </ul>
+        </div></td>
+      <td>
+        <div align="left">
+          <em>General</em>
+          <ul>
+            <li>
+              <!-- JAL-2286 -->Columns with more than one modal residue
+              are not coloured or thresholded according to percent
+              identity (first observed in Jalview 2.8.2)
+            </li>
+            <li>
+              <!-- JAL-2301 -->Threonine incorrectly reported as not
+              hydrophobic
+            </li>
+            <li>
+              <!-- JAL-2318 -->Updates to documentation pages (above PID
+              threshold, amino acid properties)
+            </li>
+            <li>
+              <!-- JAL-2292 -->Lower case residues in sequences are not
+              reported as mapped to residues in a structure file in the
+              View Mapping report
+            </li>
+            <li>
+              <!--JAL-2324 -->Identical features with non-numeric scores
+              could be added multiple times to a sequence
+            </li>
+            <li>
+              <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
+              bond features shown as two highlighted residues rather
+              than a range in linked structure views, and treated
+              correctly when selecting and computing trees from features
+            </li>
+            <li>
+              <!-- JAL-2281-->Custom URL links for database
+              cross-references are matched to database name regardless
+              of case
+            </li>
+
+          </ul>
+          <em>Application</em>
+          <ul>
+            <li>
+              <!-- JAL-2282-->Custom URL links for specific database
+              names without regular expressions also offer links from
+              Sequence ID
+            </li>
+            <li>
+              <!-- JAL-2315-->Removing a single configured link in the
+              URL links pane in Connections preferences doesn't actually
+              update Jalview configuration
+            </li>
+            <li>
+              <!-- JAL-2272-->CTRL-Click on a selected region to open
+              the alignment area popup menu doesn't work on El-Capitan
+            </li>
+            <li>
+              <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
+              files with similarly named sequences if dropped onto the
+              alignment
+            </li>
+            <li>
+              <!-- JAL-2312 -->Additional mappings are shown for PDB
+              entries where more chains exist in the PDB accession than
+              are reported in the SIFTS file
+            </li>
+            <li>
+              <!-- JAL-2317-->Certain structures do not get mapped to
+              the structure view when displayed with Chimera
+            </li>
+            <li>
+              <!-- JAL-2317-->No chains shown in the Chimera view
+              panel's View->Show Chains submenu
+            </li>
+            <li>
+              <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
+              work for wrapped alignment views
+            </li>
+            <li>
+              <!--JAL-2197 -->Rename UI components for running JPred
+              predictions from 'JNet' to 'JPred'
+            </li>
+            <li>
+              <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
+              corrupted when annotation panel vertical scroll is not at
+              first annotation row
+            </li>
+            <li>
+              <!--JAL-2332 -->Attempting to view structure for Hen
+              lysozyme results in a PDB Client error dialog box
+            </li>
+          </ul>
+<!--           <em>New Known Issues</em>
+          <ul>
+            <li></li>
+          </ul> -->
+        </div>
+      </td>
+    </tr>
+      <td width="60" nowrap>
+        <div align="center">
           <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
             <em>25/10/2016</em></strong>
         </div>
       </td>
       <td><em>Application</em>
         <ul>
-          <li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
-          <li>Progress bar reports models as they are loaded to structure views</li> 
+          <li>3D Structure chooser opens with 'Cached structures'
+            view if structures already loaded</li>
+          <li>Progress bar reports models as they are loaded to
+            structure views</li>
         </ul></td>
       <td>
         <div align="left">
+          <em>General</em>
+          <ul>
+            <li>Colour by conservation always enabled and no tick
+              shown in menu when BLOSUM or PID shading applied</li>
+            <li>FER1_ARATH and FER2_ARATH labels were switched in
+              example sequences/projects/trees</li>
+          </ul>
           <em>Application</em>
           <ul>
-            <li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
-            <li>Cannot import or associated local PDB files without a PDB ID HEADER line</li>
-            <li>RMSD is not output in Jmol console when superposition is performed</li> 
-            <li>Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan</li>
+            <li>Jalview projects with views of local PDB structure
+              files saved on Windows cannot be opened on OSX</li>
+            <li>Multiple structure views can be opened and
+              superposed without timeout for structures with multiple
+              models or multiple sequences in alignment</li>
+            <li>Cannot import or associated local PDB files without
+              a PDB ID HEADER line</li>
+            <li>RMSD is not output in Jmol console when
+              superposition is performed</li>
+            <li>Drag and drop of URL from Browser fails for Linux
+              and OSX versions earlier than El Capitan</li>
             <li>ENA client ignores invalid content from ENA server</li>
-            <li>Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
-            <li>Exceptions are not raised in console when a new view is created on the alignment</li>
+            <li>Exceptions are not raised in console when ENA
+              client attempts to fetch non-existent IDs via Fetch DB
+              Refs UI option</li>
+            <li>Exceptions are not raised in console when a new
+              view is created on the alignment</li>
+            <li>OSX right-click fixed for group selections:
+              CMD-click to insert/remove gaps in groups and CTRL-click
+              to open group pop-up menu</li>
           </ul>
-          <em>New Known Issues</em>
-          <ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
           <em>Build and deployment</em>
-          <ul><li>URL link checker now copes with multi-line anchor tags</li></ul>
+          <ul>
+            <li>URL link checker now copes with multi-line anchor
+              tags</li>
+          </ul>
+          <em>New Known Issues</em>
+          <ul>
+            <li>Drag and drop from URL links in browsers do not
+              work on Windows</li>
+          </ul>
         </div>
       </td>
     </tr>
@@ -374,6 +553,10 @@
               <!-- JAL-1306 -->Quality and Conservation are now shown on
               load even when Consensus calculation is disabled
             </li>
+            <li>
+              <!-- JAL-1932 -->Remove right on penultimate column of 
+              alignment does nothing
+            </li>
           </ul>
           <em>Application</em>
           <ul>
@@ -520,6 +703,14 @@
               <!-- JAL-1887 -->Incorrect start and end reported for PDB
               to sequence mapping in 'View Mappings' report
             </li>
+            <li>
+              <!-- JAL-2284 -->Unable to read old Jalview projects that
+              contain non-XML data added after Jalvew wrote project.
+            </li>
+            <li><!-- JAL-2118 -->Newly created annotation row reorders
+              after clicking on it to create new annotation for a
+              column.
+            </li>
             <!--  may exclude, this is an external service stability issue  JAL-1941 
             -- > RNA 3D structure not added via DSSR service</li> -->
           </ul>
@@ -588,6 +779,9 @@
         </ul> <em>Applet</em>
         <ul>
           <li>Split frame example added to applet examples page</li>
+        </ul><em>Build and Deployment</em>
+        <ul>
+          <li><!--  JAL-1888 -->New ant target for running Jalview's test suite</li>
         </ul></td>
       <td>
         <div align="left">