X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwview.html;h=75e3904384f58009f56d4103e4943f61a97c3159;hb=cb4b4b590add93fb0fb5c5ecd1d0532f1456ecc2;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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+
+Alignment Window Menus
+
+
+
+Alignment Window View Menu
+
+ - New View (Control T)
+ Creates a new view from the current alignment view.
+ - Expand Views (X)
+ Display each view associated with the alignment in its own alignment window,
+ allowing several views to be displayed simultaneously.
+ - 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 / 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
+ 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
+ whole alignment.
+ - Overview Window
+ A scaled version of the alignment will be displayed in a small
+ window. A red box will indicate the currently visible area of the alignment.
+ Move the visible region using the mouse.
+
+
+
+