X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=cb3870816a13d7b5eab42c3b3a5f57a65972d8c3;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=9be277572b72e3b32b5a6697b59325b3af4861a2;hpb=8c0737632c158907098990b81ac702710721e9f2;p=jalview.git
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index 9be2775..cb38708 100755
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@@ -1,81 +1,104 @@
-
-Alignment Window Menus
-
-
-Alignment Window View Menu
-
-
-
- - Font
- Change the font of the display from the "Choose Font"
- dialog box, which is shown when this item is selected. Select a "Monospaced"
- font for fast rendering of your alignment. The checkbox labelled "Monospaced"
- indicates whether the chosen font uses characters all of the same width.
-
- - Smooth Fonts
- If selected, the alignment will be drawn with anti-aliasing on which looks
- better, but performace is reduced.
-
- - Wrap
- When ticked, the alignment display is "wrapped"
- to the width of the alignment window. This is useful if your alignment has
- only a few sequences to view its full width at once.
- Options are available to show the residue numbering at the start and/or
- end of an alignment as well as showing the alignment position above each
- sequence row.
- NOTE: When in wrapped alignment view, the alignment cannot
- be edited or have regions selected on it.
-
- - Show Full Sequence ID
- If this box is selected the sequence name will have the start
- and end position of the sequence appended to the name, in the format NAME/START-END
-
- - Boxes
- If this is selected the background of a residue will be coloured using the
- selected background colour. Useful if used in conjunction with "Colour
- Text."
-
- - Text
- If this is selected the residues will be displayed using the
- standard 1 character amino acid alphabet.
-
- - Colour Text
- If this is selected the residues will be coloured according
- to the background colour associated with that residue. The colour is slightly
- darker than background so the amino acid symbol remains visible.
-
- - Show Gaps
- When this is selected, gap characters will be displayed as
- "." or "-". If unselected, then gap characters will
- appear as blank spaces.
- You may set the default gap character in preferences.
-
- - 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.
-
- - Sequence Features
- If the sequence names are Swissprot entries Jalview will use
- the names to retrieve sequence features
- from the EBI. Features which are 1 residue in length are coloured red, sequences
- longer than 1 residue are coloured blue. Move the mouse over a coloured
- feature to display the details of the feature.
- Note: The retrieved information will update the sequence start and end labels
- if they are incorrect.
-
- - Seqence Settings
- If features have been added to the alignment then the priority of rendering
- the features can be altered so that overlapping features can be displayed
- or hidden. See Sequence Features.
-
- - 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 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.
+ - Show All Annotations
+ Show all available annotations on the alignment. You can selectively hide these from the Popup
+ or Annotation menus. (Since Jalview 2.8.2)
+ - Hide All Annotations
+ Hide all annotations on the alignment. (Since Jalview 2.8.2)
+ - 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.
+ - Sequence 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.
+
+
+
+