-<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
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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/>.
+ * 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