<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 2.9)
+ * 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.
- *
+ * 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>
<title>Sequence feature colour schemes</title>
</head>
<body>
-<p><strong>Sequence feature colour schemes</strong></p>
-<p>Jalview can visualize annotation present on parts of a sequence by
-overlaying colours according to the annotation present at each position.
-It allows features to be colored either according to type, or for a
-particular type, according to an individual feature's associated label
-or score. The <a href="featuresettings.html">Feature Settings dialog
-box</a> controls the order and display of each sequence annotation type, and
-also allows the colour scheme used for the the feature to be changed <em>via</em>
-the 'Graduated Colour' option in the sequence feature pop-up menu
-(obtained by right-clicking on a sequence feature).</p>
+ <p>
+ <strong>Sequence feature colour schemes</strong>
+ </p>
+ <p>
+ Jalview can visualize annotation present on parts of a sequence by
+ overlaying colours according to the annotation present at each
+ position. It allows features to be colored either according to type,
+ or for a particular type, according to an individual feature's
+ associated label or score. The <a href="featuresettings.html">Feature
+ Settings dialog box</a> controls the order and display of each
+ sequence annotation type, and also allows the colour scheme used for
+ the the feature to be changed <em>via</em> the 'Graduated Colour'
+ option in the sequence feature pop-up menu (obtained by
+ right-clicking on a sequence feature).
+ </p>
-<center><img src="featurecoloursettings.gif"><br/>Graduated
-feature colour scheme settings dialog box</img></center>
-<p>The Graduated Feature Colour dialog box has the following
-controls:
-<ul>
- <li><em>Colour by Label</em> - when checked this derives a colour
- for each feature based on the label text.</li>
- <li><em>Min and Max Color boxes</em> - Click on these boxes to set
- the minimum and maximum colours used to shade features by their
- associated score.</li>
- <li><em>Threshold type combo box</em> - Allows features to be
- hidden features if their score is below or above a given threshold.<br />
- <em>Set the threshold using the slider or type it in to the text
- box. The threshold cannot be set outside the available range of feature
- scores.</em>
- </li>
- <li><em>Threshold is Min/Max</em> - When checked, the threshold
- will be used as the upper or lower limit when shading the features
- according to their score using the Min and Max colour.</li>
-</ul>
-</p>
-<p><strong>Icon styles for graduated feature styles</strong><br/>
-<p>When a graduated colourscheme is applied to a feature, it is indicated in the feature settings or amend feature dialog box by the following types of icon:<br/>
-<center><table width="50%" border="1">
-<tr><td><strong>Type of Colouring</strong></td><td><strong>Icon</strong></td></tr>
-<tr><td><em>Graduated colour by Feature Score</em></td><td><img src="fcsminmax.gif"/></td></tr>
-<tr><td><em>Graduated colour thresholded (less than) by feature Score</em></td><td><img src="fcsltthan.gif"/></td></tr>
-<tr><td><em>Graduated colour thresholded (greater than) by feature Score</em></td><td><img src="fcsgtthan.gif"/></td></tr>
-<tr><td><em>Colour by Feature Label (may also be thresholded)</em></td><td><img src="fcsntlabel.gif"/></td></tr>
-<tr>
- <td align="center" colspan="2">
- <em>
- <strong>The current threshold is given in the
- icon's tooltip.</strong>
- </em>
- </td></tr></table></center></p>
-<em>Graduated feature colours were introduced in Jalview 2.5</em>
+ <center>
+ <img src="featurecoloursettings.gif"><br />Graduated feature
+ colour scheme settings dialog box</img>
+ </center>
+ <p>The Graduated Feature Colour dialog box has the following
+ controls:
+ <ul>
+ <li><em>Colour by Label</em> - when checked this derives a
+ colour for each feature based on the label text.</li>
+ <li><em>Min and Max Color boxes</em> - Click on these boxes to
+ set the minimum and maximum colours used to shade features by
+ their associated score.</li>
+ <li><em>Threshold type combo box</em> - Allows features to be
+ hidden features if their score is below or above a given
+ threshold.<br /> <em>Set the threshold using the slider or
+ type it in to the text box. The threshold cannot be set outside
+ the available range of feature scores.</em></li>
+ <li><em>Threshold is Min/Max</em> - When checked, the threshold
+ will be used as the upper or lower limit when shading the features
+ according to their score using the Min and Max colour.</li>
+ </ul>
+ </p>
+ <p>
+ <strong>Icon styles for graduated feature styles</strong><br />
+ <p>
+ When a graduated colourscheme is applied to a feature, it is
+ indicated in the feature settings or amend feature dialog box by the
+ following types of icon:<br />
+ <center>
+ <table width="50%" border="1">
+ <tr>
+ <td><strong>Type of Colouring</strong></td>
+ <td><strong>Icon</strong></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour by Feature Score</em></td>
+ <td><img src="fcsminmax.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour thresholded (less than) by
+ feature Score</em></td>
+ <td><img src="fcsltthan.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour thresholded (greater than) by
+ feature Score</em></td>
+ <td><img src="fcsgtthan.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Colour by Feature Label (may also be
+ thresholded)</em></td>
+ <td><img src="fcsntlabel.gif" /></td>
+ </tr>
+ <tr>
+ <td align="center" colspan="2"><em> <strong>The
+ current threshold is given in the icon's tooltip.</strong>
+ </em></td>
+ </tr>
+ </table>
+ </center>
+ </p>
+ <em>Graduated feature colours were introduced in Jalview 2.5</em>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff