Alignment Window View Menu
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-- Font
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- 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
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- If selected, the alignment will be drawn with anti-aliasing on which looks - better, but performace is reduced.
-- Wrap
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- 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
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- 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
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- 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
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- If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
-- Colour Text
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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.