<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).
+ <strong>Visualisation of Sequence Features</strong>
</p>
+ <p>Jalview can visualize sequence features - the positional
+ annotation present on parts of a sequence, as colours overlaid on
+ corresponding positions in the alignment. Features may be coloured
+ either according to their type, or for a particular type, according to
+ each feature's associated label, score, or other attributes.</p>
+ <p>
+ The <a href="featuresettings.html">Feature Settings dialog box</a>
+ controls the order and display of each feature type, and
+ also allows filters and colour schemes to be configured.
+ </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>
+
+ <div align="center">
+ <img src="featureDisplaySettings.png" /><br />
+ <em>Feature Display Settings dialog for 'sequence_variant'
+ features imported from VCF</em>
+ </div>
+ <p>The Feature Display Settings has the following controls:
+ <p><strong>Colour</strong></p>
+ <ul>
+ <li><em>Simple Colour</em> - select this to assign a given colour
+ to any features of this type. The assigned colour can be changed by
+ clicking on the colour box.</li>
+ <li><em>Colour by text</em> - this option derives a colour for
+ each feature based on its label, or any other attributes presented <em>via</em>
+ the drop-down menu.</li>
+ <li><em>Graduated Colour</em> - shade features according to
+ associated score, or other numeric attribute.
+ <ul>
+ <li><em>Min and Max Color boxes</em> - Click on these boxes to
+ set the minimum and maximum colours for the shading scheme.</li>
+ <li><em>Threshold type combo box</em> - Specify an exclusion
+ threshold.<br />Set the threshold using the slider or
+ type it in to the text box. The threshold cannot be set outside
+ the available range of values observed for the selected attribute.</li>
+ <li><em>Threshold is Min/Max</em> - When checked, the threshold
+ will be used as the upper or lower limit for shading using the Min
+ and Max colour.</li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong><em>Filters</em></strong><br /> Any number of filter
+ conditions may be specified to select features based on one or more
+ attributes. The <strong>join</strong> condition specifies whether all
+ filters must apply (<strong><em>And</em></strong>) or whether any one
+ filter must apply (<strong><em>Or</em></strong>) for a feature to be
+ selected.
+ </p>
+ <p>The filters available depend on the type of attribute:</p>
+ <ul>
+ <li><strong>Numeric</strong> - specify a threshold above, equal
+ to or below which a feature will be selected or ignored.</li>
+ <li><strong>String</strong> - select or ignore features based on
+ presence, absence, equivalence, or containment of a string (not case sensitive).</li>
+ </ul>
+ <p>
+ The filters and colour schemes active for a particular feature type
+ are shown in the <em>Colour</em> and <em>Configuration</em> columns in
+ the feature settings dialog. Styles and filters can be saved as a
+ Jalview Feature Colours file, and are also exported and imported via <a
+ href="featuresFormat.html">Jalview Feature files</a>.
+
+ <p>
+ <strong>Icon styles for feature rendering styles</strong><br />
+
+ <p>
+ When a graduated colour scheme is applied to a feature according to
+ the value of a particular attribute, it is indicated in the feature
+ settings or amend feature dialog box by the following types of icon:<br />
+
+ <div align="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 (or other attribute)</em></td>
+ <td><img src="fcsltthan.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour thresholded (greater than) by
+ feature Score (or other attribute)</em></td>
+ <td><img src="fcsgtthan.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Colour by Feature Label</em></td>
+ <td><img src="fcsntlabel.gif" /></td>
+ </tr>
+ <tr>
+ <td align="center" colspan="2"><em> <strong>The
+ current threshold and attribute is shown in the icon's tooltip.</strong>
+ </em></td>
+ </tr>
+ </table>
+ </div>
+ </p>
+ <em>Graduated feature colours were introduced in Jalview 2.5.
+ Attribute based colouring and filters were added in Jalview 2.11.</em>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff