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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<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. Sequence associated alignment
- annotation are shown with the seuqence's name appended.<br />If
- the <strong>Per-sequence only</strong> tick box is not greyed out,
- then ticking it will limit the list of available annotation rows
- to just the labels for those that are sequence associated.
- Annotation rows on each sequence with the same label (e.g.
- T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
- disorder predictions</a>) will then be used to colour its
- corresponding positions in the alignment.<br /> <em>Per-sequence
- associated annotation colouring is currently only available in
- the Desktop.</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>
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