Merge branch 'documentation/JAL-3111_release_211' into develop

diff --git a/help/help/html/calculations/pca.html b/help/help/html/calculations/pca.html
index 3529cae..3bf21cb 100755 (executable)
--- a/help/help/html/calculations/pca.html
+++ b/help/help/html/calculations/pca.html
@@ -70,7 +70,7 @@
       nucleotide substitution matrix</a>, or by sequence percentage identity,
       or sequence feature similarity. 
   </p>
-  <img src="pcaviewer.gif">
+  <img src="pcaviewer.png">
   <p>
     <strong>The PCA Viewer</strong>
   </p>
@@ -84,7 +84,9 @@
     towards the front of the view.</p>
   <p>
     The 3d view can be rotated by dragging the mouse with the <strong>left
-      mouse button</strong> pressed. The view can also be zoomed in and out with
+      mouse button</strong> pressed, or with the <strong>arrow
+      keys</strong> when <strong>SHIFT</strong> is pressed. The
+    view can also be zoomed in and out with
     the up and down <strong>arrow keys</strong> (and the roll bar of the
     mouse if present). Labels will be shown for each sequence if the
     entry in the View menu is checked, and the plot background colour
@@ -122,7 +124,7 @@ left-clicking and dragging the mouse over the display. -->
   <p>
     Initially, the display shows the first three components of the
     similarity space, but any eigenvector can be used by changing the
-    selected dimension for the x, y, or z axis through each ones menu
+    selected dimension for the x, y, or z axis through each one's menu
     located below the 3d display. The <strong><em>Reset</em></strong>
     button will reset axis and rotation settings to their defaults.
   </p>
@@ -131,7 +133,7 @@ left-clicking and dragging the mouse over the display. -->
     <em>The output of points and transformed point coordinates was
       added to the Jalview desktop in v2.7.</em> <em>The Reset button
       and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
-      for PAM250 based PCA was added in Jalview 2.8.1.</em>
+      for PAM250 based PCA was added in Jalview 2.8.1.</em><em>In Jalview 2.11, support for saving and restoring PCAs in Project files was added, and the Change parameters menu removed.</em> 
   </p>
   <p>
     <strong>Reproducing PCA calculations performed with older

diff --git a/help/help/html/calculations/pcaviewer.gif b/help/help/html/calculations/pcaviewer.gif
deleted file mode 100644 (file)
index 78c82f2..0000000
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diff --git a/help/help/html/calculations/pcaviewer.png b/help/help/html/calculations/pcaviewer.png
new file mode 100644 (file)
index 0000000..7dc5b80
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diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 8cebf4f..88b0fd7 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -176,10 +176,6 @@ li:before {
                                                                <!-- JAL-3181 -->Consistent ordering of links in sequence id
                                                                popup menu
                                                        </li>
-                                                       <li>
-                                                               <!-- JAL-3021 -->Sequence Details report opens positioned to top
-                                                               of report
-                                                       </li>
                                                </ul></li>
                                        <li><strong>Java 11 Support</strong>
                                                <ul>
@@ -199,6 +195,11 @@ li:before {
             <!-- JAL-3035 -->DAS sequence retrieval and annotation
             capabilities removed from the Jalview Desktop
           </li>
+          <li>
+            <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+            unmarshalling has been replaced by JAXB for Jalview projects
+            and XML based data retrieval clients</li>
+          <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li> 
           <li><!--  -->Jalview Desktop no longer distributed via Java Web Start</li>
         </ul>
         <em>Development and Release Processes</em>
@@ -222,18 +223,14 @@ li:before {
                                                gradle-eclipse
                                        </li>
           <li>
-          Atlassian Bamboo continuous integration server for
+          Atlassian Bamboo continuous integration for
             unattended Test Suite execution</li>
           <li>
             <!-- JAL-2864 -->Memory test suite to detect leaks in common
             operations</li>
           <li>
-            <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
-            implementation) used for Sequence Feature collections</li>
-          <li>
-            <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
-            unmarshalling has been replaced by JAXB for Jalview projects
-            and XML based data retrieval clients</li>
+            <!-- JAL-3140 -->IntervalStoreJ (NCList
+            implementation that alows updates) used for Sequence Feature collections</li>          
         </ul>
       </td>
     <td align="left" valign="top">
@@ -326,6 +323,8 @@ li:before {
           <li>
             <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
           <li>
+            <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
+          <li>
             <!-- JAL-914 -->Help page can be opened twice</li>
         </ul>
         <em>Editing</em>