2.2 documentation

diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index 3f7b599..b119b91 100644 (file)
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -23,13 +23,22 @@ performed on the visible group representative will be propogated to all
 the sequences in that group. <br>
 The hidden representative sequences will not be used in any calculations
 or web service alignments (<em>nb. this may change in the future</em>).
-<br>
-<blockquote><em><strong>Warning:</strong>hidden
-representative sequence groups are only partly implemented in the
-jalview 2.2 release. When a hidden representative group is created in
-one alignment view, it will be propagated to all other views. Similarly,
-revealing the represented sequences in one view will reveal them in all
-other views. This will be resolved in a future Jalview release. </em></blockquote>
+<p><strong><em>Hidden Sequence Representatives and
+Multiple</em> Views</strong><br>
+<em>A word of warning: hidden representative sequence groups are
+only partly implemented in the jalview 2.2 release, and the following
+issues will be resolved in the future.</em><br>
+Currently, represented hidden groups are only made correctly if there is
+just one alignment view. When multiple views on an alignment exist, then
+the represented group will be displayed correctly in the view in which
+it was made, but in other views, both representative and hidden
+sequences will be visible, but will behave as if they are grouped. <br>
+Hidden representatives are propagated correctly to a new view if they
+exist in the current view. However, if the represented sequences are
+revealed in any one view, then in all other views they will simply be
+marked as hidden, and their association with the representative sequence
+will be lost.<br>
+</blockquote>
 </p>
 <p><strong><em>Hiding Columns</em></strong><br>
 To hide selected columns in an alignment, use the <strong>&quot;View

diff --git a/help/html/features/newkeystrokes.html b/help/html/features/newkeystrokes.html
index 8fd671e..12ea967 100644 (file)
--- a/help/html/features/newkeystrokes.html
+++ b/help/html/features/newkeystrokes.html
@@ -8,16 +8,25 @@ alignment even easier. The selection commands in the <strong>Edit</strong>
 menu, and the alignment formatting controls within the <strong>View</strong>
 menu have also been moved into their own respective <strong>Select</strong>
 and <strong>Format</strong> menus.</p>
-<p>Some of the most important new keystrokes are shown below :
+<p>Some of the more important new keystrokes are shown below :
 <ul>
        <li><strong>Page Up</strong> and <strong>Page Down</strong>
        scrolls through the alignment view.</li>
        <li><strong>Control I</strong> inverts the currently selected
        sequence set, and <strong>Control Alt I</strong> will invert the
        currently selected set of columns.
-       <li><strong>Control+V</strong> will paste the contents of the
+       <li><strong>Control V</strong> will paste the contents of the
        clipboard to the current alignment window, and <strong>Control
        Shift V</strong> pastes the data to a new window.</li>
+       <li><strong>Control O</strong> opens the file browser for loading
+       a new alignment or Jalview archive.</li>
+       <li><strong>Control S</strong> saves the alignment with the
+       current filename and format, and <strong>Control Shift S</strong> opens
+       the <strong>Save As...</strong> dialog box.</li>
+       <li><strong>Control T</strong> creates a new alignment view, and <strong>Control
+       W</strong> closes the current view, or if none remain, then the whole alignment.</li>
+       <li><strong>Control E</strong> will remove gapped columns in the alignment.</li>
+       <li><strong>Control D</strong> opens the <strong>Remove Redundancy</strong> dialog box.</li>
 </ul>
 </p>
 </body>