Merge branch 'documentation/JAL-2325_release2101' into develop

diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index ad47dae..8adacc9 100755 (executable)
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -35,11 +35,10 @@ td {
     <strong>Colouring above a percentage identity threshold</strong>
   </p>
   <p>Selecting this option causes the colour scheme to be applied to
-    only those residues that occur in that column more than a certain
+    only those residues that occur in that column at least a certain
     percentage of the time. For instance, selecting the threshold to be
-    100 will only colour those columns with 100% identity.</p>
-   <p>To be coloured, a residue must match the consensus (most commonly occurring) residue for the column (or joint equal consensus).</p>
+    100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column.</p>
    <p>The percentage calculation may include or exclude gaps in the column, depending on the option selected for the <a href="../calculations/consensus.html">consensus calculation</a>.</p>
-   <p>With a threshold of 0, colouring is unchanged (including non-consensus residues).</p>
+   <p>With a threshold of 0, colouring is unchanged.</p>
 </body>
 </html>

diff --git a/help/html/releases.html b/help/html/releases.html
index 3fe08cb..40de3d4 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,6 +47,70 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
+          <strong><a name="Jalview.2.10.1">2.10.1</a><br />
+            <em>22/11/2016</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- --></li>
+          </ul>
+          <em>Application</em>
+          <ul>
+           <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog 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-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
+           <li></li>
+           
+
+          </ul>
+          <em>Applet</em>
+          <ul>
+          </ul>
+          <em>Build and deployment</em>
+          <ul>
+            <li></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>
+          </ul>
+          <em>Application</em>
+          <ul>
+           <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer invalid 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><!-- --></li>
+           <li><!-- --></li>
+           <li><!-- --></li>
+          </ul>
+          <em>Applet</em>
+          <ul>
+          </ul>
+          <em>Build and deployment</em>
+          <ul>
+            <li><!-- JAL-2308, -->Failing/passing unit tests</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>