X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwview.html;h=33ec77f9fc29279cfad23d4734f1148a8aa2ae3a;hb=refs%2Fheads%2Fbug%2FJAL-3120restoreFeatureColour;hp=4248f9a36d6ac5ae1bd287209124338996e3b0dc;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;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 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
- 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.
-
-
+
+ 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.
+ - 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.
+ - Sequence
+ Feature Settings...
Opens the Sequence
+ Feature Settings dialog box to control the colour and display of
+ sequence features on the alignment.
+ - 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.
+
+