JAL-1445 updated documentation and added link in whatsNew

diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 9335d93..9526ed5 100755 (executable)
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -37,15 +37,30 @@ they are currently being displayed (only the ticked features and groups
 are displayed). <strong><em>You can change the colour or
 shading style used for a feature in the associated alignment by clicking
 on its colour box.</em></strong></p>
-  <p>
-    <strong><em>Selecting alignment columns by feature</em></strong><br>
-    <strong>Double-click</strong> a feature to add all the columns where
-    that feature is found to the current column selection. <strong>Shift+Double-click</strong>
-    will add all the columns where that feature is <strong>not</strong>
-    found. You can also find these options in the feature's pop-up menu
-    (see below). <br />
-    <em>Select columns by feature was added in Jalview 2.8.1</em>
-  </p>
+       <p>
+               <a name="selectbyfeature"><strong><em>Selecting
+                                       alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+                       a feature type</strong> allows you to select columns in the alignment that
+               contain (or do not contain) features of that type. If a region of the
+               alignment is currently selected, then only features in the current
+               selection will be searched. The following keys affect the way in which
+               selections are made:
+       
+       <ul>
+               <li>Hold down <strong>Alt</strong> to select columns not
+                       containing features of a particular type.
+               </li>
+               <li>Hold down <strong>Shift</strong> to add columns to the
+                       current selection.
+               </li>
+               <li>Press <strong>Command/Windows key</strong> to toggle column
+                       selection state (XOR)
+               </li>
+       </ul>
+       Options are also provided in the feature's pop-up menu (see below).
+       <br />
+       <em>Select columns by feature was added in Jalview 2.8.1</em>
+       </p>
   <p><strong><em>Feature settings pop-up menu</em></strong><br>
 <strong>Right-click</strong> on a feature to open a pop-up menu that
 allows you to sort the alignment or current selection using that feature

diff --git a/help/html/releases.html b/help/html/releases.html
index c709a5f..b6fb83c 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -41,13 +41,42 @@
   </td>
       <td> <!--  New features -->
       <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
-        <ul>
+      <ul>
+      <li>i18n Internationalisation of user interface and translation for Spanish locale</li>
+      </ul>
+      <em>Application</em><ul>
+        <li>Define/Undefine group on current selection with Ctrl-G</li>
+ <li>Select columns containing particular features from Feature Settings dialog</li>
+<li>View all 'representative' PDB structures for selected sequences</li>
+<li>Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service</li>
+<li></li>
+      <li>Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows) </li>
+        </ul>
+      <em>Applet</em><ul>
+      
         </ul> <em>Other improvements</em>
         <ul>
         </ul>
       </td>
       <td><!--  issues resolved -->
-        <ul>
+        <em>Application</em><ul>
+                                       <li>Newly created RNA secondary structure line doesn't have
+                                               'display all symbols' flag set</li>
+                                 <li>T-COFFEE alignment score shading scheme not saved in
+                                               jalview project</li>
+                                       <li>Local file cannot be loaded in freshly downloaded Jalview</li>
+                                       <li>??? unresolved ??? Jalview icon not shown on dock in
+                                               Mountain Lion/Webstart</li>
+                                       <li>Load file from desktop file browser fails</li>
+                                       <li>Occasional NPE thrown when calculating large trees</li>
+                               </ul>
+        <em>Applet</em>
+                       <ul>
+                                       <li>Apply to all groups ticked but colourscheme changes don't
+                                               affect groups</li>
+                               </ul> 
+                               <em>Other</em><ul>
+        <li></li>
         </ul>
       </td>
     </tr>

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 7a786d5..a016a35 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -43,7 +43,7 @@
        <strong>Enhancements and new features</strong>
        <ul>
        <li>
-  <li>Extended the <a href="features/featuresettings.html">feature settings dialog</a> to allow columns to be selected containing particular sequence features.</li>
+  <li>Extended the feature settings dialog to <a href="features/featuresettings.html#selectbyfeature">select columns containing particular sequence features.</a></li>
        </ul>
        <strong>Bug fixes</strong>
        <ul>