X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwformat.html;h=62fdf9302ff8198c4b7b51bdc074f47ef5a7a8b3;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=0c45d465367de299a3f6e7ec259832a77a70a825;hpb=6aaed756a227469cc3f093e45c2bb38799450b60;p=jalview.git
diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html
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--- a/help/html/menus/alwformat.html
+++ b/help/html/menus/alwformat.html
@@ -1,56 +1,79 @@
+
-Alignment Window Menus
-
-
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 Above
Show the alignment column position scale.
- - 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.
-
- - 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 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.
+
+