<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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