added annotationColouring to whats new and updated IO and cursorMode

[jalview.git] / help / html / io / index.html

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