X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwformat.html;h=ab5fd7417843eb677ae7163f9d45cdb6bd7482c2;hb=cb03edaa1450e5716bd37ca5cc430a46c245e9db;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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+
+Alignment Window Format Menu
+
+ - Font...
+ Opens the "Choose Font" dialog box, in order to change the font
+ of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster
+ alignment rendering.
+ - 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.
+ Additional options for display of sequence numbering and scales are also visible
+ in wrapped layout mode:
+
+ - Scale Left
+ Show the sequence position for the first aligned residue in each row
+ in the left column of the alignment.
+ - Scale Right
+ Show the sequence position for the last aligned residue in each row
+ in the right-most column of the alignment.
+ - Scale Above
+ Show the alignment column position scale.
+
+ - Show Sequence Limits
+ 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
+ - Right Align Sequence ID
+ If this box is selected then the sequence names displayed in
+ the sequence label area will be aligned against the left-hand edge of the
+ alignment display, rather than the left-hand edge of the alignment window.
+ - Show Hidden Markers
+ When this box is selected, positions in the alignment where rows
+ and columns are hidden will be marked by blue arrows.
+ - 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.
+ - Centre Column Labels
+ When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
+
+ - Show Unconserved
+ When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
+
+
+
+
+