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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+
+ 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.
+
+
+
+