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- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
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* WITHOUT ANY WARRANTY; without even the implied warranty
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+ * 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>
+
+ <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