X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwview.html;h=b5334524441a7735843dc667057383ad98a5cfb4;hb=1335a93a7eb656ab1bd08572d4be2b386a9043c9;hp=4cc5c1509f83ff4b3acb1f2f4920df468461cc2e;hpb=3e0eb5fe92f38828607594c7b70dfdf012e4d3dc;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
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@@ -1,4 +1,21 @@
+
Alignment Window Menus
@@ -14,14 +31,37 @@
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
calculation, quality calculation and consensus values as bar charts.
+ Autocalculated Annotation
Settings for the display of autocalculated annotation.
+ -
+ Apply to all groups
+ 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
+ Enable or disable the display of the sequence logo above the consensus sequence.
+
+ -
+ Group Conservation
+ When ticked, display a conservation row for all groups (only available for protein alignments).
+
+ -
+ Apply to all groups
+ When ticked, display a consensus row for all groups.
+
+
+
Automatic Scrolling
When selected, the view will automatically scroll to display the
highlighted sequence position corresponding to the position under the mouse