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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.<br />If the <strong>Per-sequence
- only</strong> tick box is not greyed out, then ticking it will limit the
- available annotation rows to just those that are sequence associated
- (e.g. T-COFFEE scores and <a
- href="../webServices/proteinDisorder.html">protein disorder
- predictions</a>), which will colour each sequence according to its own
- per-residue scores.<br />
- <em>Per-sequence associated annotation colouring was introduced
- in Jalview 2.8</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>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>
+ <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>
+ <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>
git://source.jalview.org / jalview.git / blobdiff