added annotationColouring to whats new and updated IO and cursorMode

(mac os and backspace==delete)

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 62cba6b..316b63d 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -11,6 +11,7 @@
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
           <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>\r
           <tocitem text="Annotations File" target="annotations.fileformat"/>\r
+          <tocitem text="Colour by Annotation Value" target="colours.annotation"/>\r
         </tocitem>\r
        <tocitem text="Release History" target="release"/>\r
        <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r

diff --git a/help/html/features/cursorMode.html b/help/html/features/cursorMode.html
index 5172cfa..579d886 100755 (executable)
--- a/help/html/features/cursorMode.html
+++ b/help/html/features/cursorMode.html
@@ -44,9 +44,11 @@ unavailable in cursor mode).</p>
     To group insert, hold control or shift together with space.</li>
 </ul>
 <ul>
-  <li>Delete - Delete a gap at the cursor position.<br>
-    To delete 12 spaces at the current cursor, type 12 before pressing Delete.<br>
-    To group delete, hold down control or shift together with Delete.</li>
+  <li>Delete (or backspace) - Delete a gap at the cursor position.<br>
+    To delete 12 spaces at the current cursor, type 12 before pressing
+    Delete (or backspace).<br>
+    To group delete, hold down control or shift together with Delete
+    (or backspace).</li>
 </ul>
 </p>
 </body>

diff --git a/help/html/io/index.html b/help/html/io/index.html
index 063f329..79e7576 100755 (executable)
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -24,15 +24,20 @@ alignment file then you will be given an error message. If you think
 Jalview really should be able to read your file, then send an email\r
 containing the problem file to jalview@jalview.org.\r
 </p>\r
+<p>Jalview can also read jalview specific files for <a href="../features/featuresFormat.html">sequence features</a>\r
+and <a href="../features/annotationsFormat.html">alignment annotation</a>.</p>\r
 <p><strong>Output</strong> </p>\r
 <p>Each alignment, whether it is the original or an edited version may be saved\r
   in the standard formats using <strong>File&#8594;Save As</strong></p>\r
 <p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
 Jalview will by default append the sequence start and end to each sequence name, \r
 in the format /start-end. If you do not want this behaviour for a particular file \r
-output, open the &quot;Output&quot; tab on the Preferences window where you can \r
+output, open the &quot;Output&quot; tab on the <a href="../features/preferences.html">Preferences</a> window where you can \r
 select which file formats you want to append the start and end sequence positions \r
-for. \r
+for.\r
+<p>Quantitative and symbolic <a href="../features/annotation.html">alignment annotation</a> can be exported as a\r
+comma separated value file by right clicking on an annotation row\r
+under the alignment.</p>\r
 <p>You can also save the current set of alignments and their colours, annotations and\r
 trees in a Jalview archive file using <strong>Desktop&#8594;Save project</strong>. </p>\r
 <p>&nbsp;</p>\r

diff --git a/help/html/keys.html b/help/html/keys.html
index 085c343..6db5df4 100755 (executable)
--- a/help/html/keys.html
+++ b/help/html/keys.html
@@ -69,18 +69,22 @@ parameters (prefixing the command key and separated by commas).</p>
 <table border=1><tr><td><strong>Compound\r
 Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>\r
 <tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a\r
-numeric parameter (<strong>[p]</strong>) or repetition number for a cursor movement or edit\r
+numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit\r
 command.</td></tr>\r
-<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or more numeric parameters ([p1],[p2]) for a command.</td></tr>\r
-<tr><td><strong>[p1],[p2]<br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (p1) and row (p2) in the alignment.<br><em>e.g. '5,6&lt;Return&gt;' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
-<tr><td><strong>[p1]S</strong></td><td>Cursor</td><td>Jump to the p1'th sequence in the alignment.</td></tr>\r
-<tr><td><strong>[p1]P</strong></td><td>Cursor</td><td>Jump to p1'th amino acid in current sequence.</td></tr>\r
-<tr><td><strong>[p1]C</strong></td><td>Cursor</td><td>Jump to p1'th column in the alignment.</td></tr>\r
+<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or\r
+more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>\r
+<tr><td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (<strong><em>p1</em></strong>) and row (<strong><em>p2</em></strong>) in the alignment.<br><em>e.g. '5,6&lt;Return&gt;' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
+<tr><td><strong><em>p</em>S</strong></td><td>Cursor</td><td>Jump to the <strong><em>p</em></strong>'th sequence in the alignment.</td></tr>\r
+<tr><td><strong><em>p</em>P</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th amino acid in current sequence.</td></tr>\r
+<tr><td><strong><em>p</em>C</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th column in the alignment.</td></tr>\r
 <tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>\r
 <tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>\r
-<tr><td><strong>[p1]<br>Space</strong></td><td>Cursor</td><td>Inserts p1 gaps at the current position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-<tr><td><strong>[p1]<br>Delete</strong></td><td>Cursor</td><td>Remove p1 gaps at the cursor position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-</table>\r
+<tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts\r
+one (or optionally <strong><em>p</em></strong>) gaps at the current position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
+<tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes\r
+one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
+<tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes\r
+one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr></table>\r
 <p>&nbsp;</p>\r
 <p>&nbsp;</p>\r
 </body>\r