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JAL-1701 first draft of help page for Split View (not linked in)
[jalview.git] / help / html / menus / alwcalculate.html
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 22387df..50bb37b 100755 (executable)
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -82,7 +82,15 @@
                                When selected, these numbers are parsed into sequence associated
                                annotation which can then be used to sort the alignment via the Sort
                                by&#8594;Score menu.</em> <br></li>
-
+               <li><strong>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments. 
+                       Selecting this option shows the DNA's calculated protein product in a new window. Note that the 
+                       translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
+                       standard <a href="../misc/geneticCode.html">genetic code</a> (any incomplete final codon is discarded). 
+                       You can perform this action on the whole alignment, 
+                       or selected rows, columns, or regions.</em> <br></li>
+               <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
+                       other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
+                       Select the database to view all cross-referenced sequences in a new window.</em> <br></li>
                <li><strong>Autocalculate Consensus</strong><br> <em>For
                                large alignments it can be useful to deselect &quot;Autocalculate
                                Consensus&quot; when editing. This prevents the sometimes lengthy