-<html>
-<head>
-Alignment Window Menus
-</head>
-<body>
-<p><strong>Alignment Window Format Menu</strong></p>
-<ul>
- <li><strong>Font...<br>
- </strong><em>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. </em></li>
- <li><strong>Wrap<br>
- </strong><em>When ticked, the alignment display is "<a
- href="../features/wrap.html">wrapped</a>" 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.<br>
- Additional options for display of sequence numbering and scales are
- also visible in wrapped layout mode:<br>
- <ul>
- <li><strong>Scale Above</strong><br>Show the alignment column position scale.</li>
- <li><strong>Scale Left</strong><br>Show the sequence position for the first aligned residue in each row in the left column of the alignment.</li>
- <li><strong>Scale Right</strong><br>Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.</li>
- </em></li>
- <li><strong>Show Sequence Limits<br>
- </strong><em>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</em></li>
- <li><strong>Right Align Sequence ID<br>
- </strong><em>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.</li>
- <li><strong>Show Hidden Markers<br>
- </strong><em>When this box is selected, positions in the alignment where
- rows and columns are hidden will be marked by blue arrows.</li>
- <li><strong>Boxes</strong><em><br>
- 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." </em></li>
- <li><strong>Text<br>
- </strong><em>If this is selected the residues will be displayed using the
- standard 1 character amino acid alphabet.</em></li>
- <li><strong>Colour Text<br>
- </strong><em>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. </em></li>
- <li><strong>Show Gaps<br>
- </strong><em>When this is selected, gap characters will be displayed as
- "." or "-". If unselected, then gap characters will
- appear as blank spaces. <br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>.</em></li>
-</ul>
-</body>
-</html>
+<html>\r
+<head>\r
+<p><strong>Alignment Window Format Menu</strong></p>\r
+<ul>\r
+ <li><strong>Font...</strong><br>\r
+ <em>Opens the "Choose Font" dialog box, in order to change the font \r
+ of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster \r
+ alignment rendering. </em></em></li>\r
+ <li><strong>Wrap<br>\r
+ </strong><em>When ticked, the alignment display is "<a\r
+ href="../features/wrap.html">wrapped</a>" to the width of the alignment \r
+ window. This is useful if your alignment has only a few sequences to view \r
+ its full width at once.<br>\r
+ Additional options for display of sequence numbering and scales are also visible \r
+ in wrapped layout mode:</em>\r
+ <ul>\r
+ <li><strong>Scale Left</strong><br>\r
+ <em>Show the sequence position for the first aligned residue in each row \r
+ in the left column of the alignment.</em></li>\r
+ <li><strong>Scale Right</strong><br>\r
+ <em>Show the sequence position for the last aligned residue in each row \r
+ in the right-most column of the alignment.</em></li>\r
+ </ul>\r
+ \r
+ <li><strong>Scale Above</strong><br>\r
+ <em>Show the alignment column position scale.</em></li>\r
+ <li><strong>Show Sequence Limits<br>\r
+ </strong><em>If this box is selected the sequence name will have the start \r
+ and end position of the sequence appended to the name, in the format NAME/START-END</em></li>\r
+ <li><strong>Right Align Sequence ID<br>\r
+ </strong> <em>If this box is selected then the sequence names displayed in \r
+ the sequence label area will be aligned against the left-hand edge of the \r
+ alignment display, rather than the left-hand edge of the alignment window.</em></li>\r
+ <li><strong>Show Hidden Markers<br>\r
+ </strong><em>When this box is selected, positions in the alignment where rows \r
+ and columns are hidden will be marked by blue arrows.</em></li>\r
+ <li><strong>Boxes</strong><em><br>\r
+ If this is selected the background of a residue will be coloured using the \r
+ selected background colour. Useful if used in conjunction with "Colour \r
+ Text." </em></li>\r
+ <li><strong>Text<br>\r
+ </strong><em>If this is selected the residues will be displayed using the \r
+ standard 1 character amino acid alphabet.</em></li>\r
+ <li><strong>Colour Text<br>\r
+ </strong><em>If this is selected the residues will be coloured according to \r
+ the background colour associated with that residue. The colour is slightly \r
+ darker than background so the amino acid symbol remains visible. </em></li>\r
+ <li><strong>Show Gaps<br>\r
+ </strong><em>When this is selected, gap characters will be displayed as "." \r
+ or "-". If unselected, then gap characters will appear as blank \r
+ spaces. <br>\r
+ You may set the default gap character in <a\r
+ href="../features/preferences.html">preferences</a>.</em></li>\r
+</ul>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / blobdiff