X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2Falwview.html;h=cb3870816a13d7b5eab42c3b3a5f57a65972d8c3;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=b5334524441a7735843dc667057383ad98a5cfb4;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index b533452..cb38708 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.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.
+ -->
Alignment Window Menus
@@ -39,6 +42,11 @@
If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the conservation
calculation, quality calculation and consensus values as bar charts.
+ Show All Annotations
+ Show all available annotations on the alignment. You can selectively hide these from the Popup
+ or Annotation menus. (Since Jalview 2.8.2)
+ Hide All Annotations
+ Hide all annotations on the alignment. (Since Jalview 2.8.2)
Autocalculated Annotation
Settings for the display of autocalculated annotation.
-
Apply to all groups
@@ -49,10 +57,15 @@
Enable or disable the display of the histogram above the consensus sequence.
-
- Show Consensus Profile
+ 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.
+
+ -
Group Conservation
When ticked, display a conservation row for all groups (only available for protein alignments).
@@ -69,7 +82,7 @@
Show Sequence Features
Show or hide sequence features on this alignment.
- Seqence Feature Settings...
+ Sequence Feature Settings...
Opens the Sequence Feature Settings dialog box to control the colour and display
of sequence features on the alignment, and configure and retrieve features
from DAS annotation servers.