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.
- Smooth Fonts
If selected, the alignment will be drawn with anti-aliasing on which looks
better, but performace is reduced.
- Show (all Columns / Sequences)
All hidden Columns / Sequences will be revealed.
- Hide (all Columns / Sequences)
Hides the all the currently selected Columns / Sequences
- 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.
- Fetch 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.
- Show Sequence Features
Show or hide sequence features on this alignment.
- Seqence Feature Settings...
Control the colour and display of sequence features on the alignment.
See Sequence Feature Settings.
- 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.