X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=e229214881e6157a2d00936c1500c88ce41c05c7;hb=3f2b8374416a4e6388984481ddcddd6e61c458f5;hp=197a1f3e4c7f2a2d0493fe0cb48d6ed4a0db90fe;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 197a1f3..e229214 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,7 +1,7 @@
+-->
Annotation Panel Menus
@@ -46,12 +46,26 @@
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