X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwview.html;h=f59e0146b15420cccd3c1d5e6a00913c634a2d9a;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=10ab5112a0fc0d95dfeac4ee746c5620a59d4a4a;hpb=be5a6a44e9eb355110f3b414d6b0fd5419f5936c;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 10ab511..f59e014 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,4 +1,22 @@
+
Alignment Window Menus
@@ -14,10 +32,10 @@
Gather Views (G)
Each view associated with the alignment will be displayed within its own tab
on the current alignment window.
- Show→(all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
- Hide→(all Columns / Sequences)
- Hides the currently selected Columns / Sequences
+ Show→(all Columns / Sequences / Sequences and Columns )
+ All hidden Columns / Sequences / Sequences and Columns will be revealed.
+ Hide→(all Columns / Sequences / Selected Region / All but Selected Region)
+ Hides the currently selected Columns / Sequences / Region or everything but the selected Region.
Show Annotations
If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the conservation
@@ -25,17 +43,22 @@
Autocalculated Annotation
Settings for the display of autocalculated annotation.
-
Apply to all groups
- When ticked, any settings will be applied to all autocalculated annotation.
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
-
Show Consensus Histogram
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).