-<html>\r
-\r
-<head><title>Annotation Colouring</title></head>\r
-\r
-<body>\r
-<p><strong> Annotation Colouring </strong></p>\r
-<p>Jalview 2.08 allows an alignment to be coloured on a per-column basis based \r
- on any numerical annotation added to that alignment. </p>\r
-Select "Colour" <strong>→</strong> ".. \r
- by Annotation" to bring up the Colour by Annotation settings window. <br>\r
- <br><div align="center">\r
- <img src="annotationColourSetting.jpg" width="426" height="140"> </div>\r
-<ul>\r
- <li>Select which annotation to base the colouring scheme on using the top left \r
- selection box.</li>\r
- <li> If the "Use Original Colours" box is selected, the colouring \r
- scheme will use the colouring scheme present on the alignment before the Annotation \r
- Colour Settings window was displayed. </li>\r
- <li>The colour scheme can display a colour gradient from a colour representing \r
- the minimum value in the selected annotation to a colour representing the \r
- maximum value in the selected annotation. Use the "Min Colour" and \r
- "Max Colour" to set the colour gradient range.</li>\r
- <li>Select whether to colour the alignment above or below an adjustable threshold \r
- with the selection box center left of the window. </li>\r
- <li>Change the threshold value with the slider, or enter the exact value in \r
- the text box. </li>\r
-</ul>\r
-<p align="center"><img src="annotationColours.jpg" width="475" height="262"> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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>
+<title>Annotation Colouring</title>
+</head>
+
+<body>
+ <p>
+ <strong> Annotation Colouring </strong>
+ </p>
+ <p>Jalview allows the columns of an alignment to be coloured using
+ any numerical annotation rows added to that alignment.</p>
+ Select "Colour"
+ <strong>→</strong> ".. by Annotation" to bring up the
+ Colour by Annotation settings window.
+ <br>
+ <br>
+ <div align="center">
+ <img src="annotationColourSetting.gif" width="471" height="256">
+ </div>
+ <ul>
+ <li>Select which annotation to base the colouring scheme on
+ using the top left selection box.<br />If the <strong>Per-sequence
+ only</strong> tick box is not greyed out, then ticking it will limit the
+ available annotation rows to just those that are sequence
+ associated (e.g. T-COFFEE scores and <a
+ href="../webServices/proteinDisorder.html"
+ >protein disorder predictions</a>), which will colour each sequence
+ according to its own per-residue scores.<br /> <em>Per-sequence
+ associated annotation colouring was introduced in Jalview 2.8</em>
+ </li>
+ <li>If the "Use Original Colours" box is selected,
+ the colouring scheme will use the colouring scheme present on the
+ alignment before the Annotation Colour Settings window was
+ displayed. <br /> <em><strong>Please Note:</strong> If no
+ colour scheme was applied previously, then the colours for lines
+ and labels at each position in the annotation row will be used,
+ for secondary structure symbols and graphs, this may be black by
+ default, so your alignment will be coloured black.</em>
+ </li>
+ <li><em>Secondary structure annotation colouring</em><br />By
+ default, Jalview will employ the helix or sheet colours to shade
+ sequences and columns by available secondary structure annotation
+ tracks. In the case of RNA, each structure is processed to
+ identify distinct RNA helices and rendered in the same way as the
+ <a href="rnahelicesColouring.html">RNA Helices shading scheme</a>.
+ <em>Structure based sequence shading was added in Jalview
+ 2.8.2</em></li>
+ <li>The colour scheme can display a colour gradient from a
+ colour representing the minimum value in the selected annotation
+ to a colour representing the maximum value in the selected
+ annotation. Use the "Min Colour" and "Max
+ Colour" to set the colour gradient range.
+ <ul>
+ <li>Press the "Defaults" button to reset the
+ minimum and maximum colours to their default settings (these
+ are configured in the applet's parameters or the <a
+ href="../features/preferences.html"
+ >application's user preferences</a>.).<br /> <em>Default min
+ and max colours were introduced in Jalview 2.7</em>
+ </ul>
+ </li>
+
+ <li>Select whether to colour the alignment above or below an
+ adjustable threshold with the selection box center left of the
+ window.</li>
+ <li>Change the threshold value with the slider, or enter the
+ exact value in the text box.</li>
+ <li>Select the "Threshold is Min/Max" checkbox to
+ assign colours using the thresholded range's minimum and maximum
+ values, otherwise the scale will be defined by the range of values
+ in the annotation row.</li>
+ </ul>
+ <p align="center">
+ <img src="annotationColours.gif" width="582" height="464">
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff