+++ /dev/null
-<html>
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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
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- * Jalview is free software: you can redistribute it and/or
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- * The Jalview Authors are detailed in the 'AUTHORS' file.
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-<head>
-<p>
- <strong>Alignment Window Format Menu</strong>
-</p>
-<ul>
- <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