X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=4b8904946ea4cf0ac07f41b3a13c71401f435172;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=b604c892b2a030a4002a06dd192cef1fd84fa89e;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index b604c89..4b89049 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Annotation Panel Menus
@@ -46,12 +49,26 @@
This is useful to export alignment quality measurements for further analysis.
- The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:
+ The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:
+
- Ignore Gaps in Consensus
If this checkbox is selected, all consensus calculations performed in
the current Alignment window will be done without counting gaps as a consensus
character.
+ - Show Consensus Histogram
+ Enable or disable the display of the histogram above the consensus sequence.
+
+ -
+ Show Consensus Logo
+ Enable or disable the display of the sequence logo above the consensus sequence.
+
+ - Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
+
+ -
- Copy Consensus Sequence
Copies the consensus sequence to the clipboard in Fasta format, to allow
the consensus sequence to be added to an alignment. Note the copied sequence