* 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/>.
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-<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>
+-->
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