X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=3d2d3beeb3ab0666dbc18b98762025e00c0b4abe;hb=e5cbd35e13f46ae1d59a08b0af1086677418141d;hp=93ef54468115e492a5155cf87104e4cbc5cbe17f;hpb=10229aa22853c5d605a1924130704dc49b0a6e42;p=jalview.git
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+
Alignment Window Menus
@@ -14,20 +34,57 @@
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 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).
+
+ -
+ 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
+ pointer in a linked alignment or structure view.
+
Show Sequence Features
Show or hide sequence features on this alignment.
Seqence 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.
+ Sequence ID Tooltip (application only)
+
This submenu's options allow the inclusion or exclusion of
+ non-positional sequence features or database cross references
+ from the tooltip shown when the mouse hovers over the sequence ID panel.
Alignment Properties...
Displays some simple statistics computed for the
current alignment view and any named properties defined on the