Alignment Window View Menu

• View

• 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.
  
• 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.