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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
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+ * This file is part of Jalview.
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+ * Jalview is free software: you can redistribute it and/or
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+ * of the License, or (at your option) any later version.
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+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<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
+ <li><strong>Font...</strong><br>
+ <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></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:</em>
+ <ul>
+ <li><strong>Scale Left</strong><br>
+ <em>Show the sequence position for the first aligned residue in each row
+ in the left column of the alignment.</em></li>
+ <li><strong>Scale Right</strong><br>
+ <em>Show the sequence position for the last aligned residue in each row
+ in the right-most column of the alignment.</em></li>
+ <li><strong>Scale Above</strong><br>
+ <em>Show the alignment column position scale.</em></li>
+ </ul>
+ <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.</em></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.</em></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>
+ <li><strong>Centre Column Labels<br>
+ </strong><em>When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
+ </em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
+ </em></li>
+
</ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff