3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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23 <title>Annotation Colouring</title>
28 <strong> Annotation Colouring </strong>
30 <p>Jalview allows the columns of an alignment to be coloured using
31 any numerical annotation rows added to that alignment.</p>
32 Select "Colour"
33 <strong>→</strong> "by Annotation..." to bring up the
34 Colour by Annotation settings window.
36 <br>You can also apply Colour by annotation for a particular annotation
37 (or per-sequence set) by right-clicking an annotation row's label and selecting "Colour by Annotation..." or "Colour by Annotation (per Sequence)..." from the
38 <strong>Annotation label popup menu</strong>. (<em>Since Jalview 2.11.3</em>)
41 <img src="../features/annotationsubmenucolbyannot.png" width="414" height="266">
43 <p><strong>The Colour by Annotation Settings Window</strong></p>
46 <img src="annotationColourSetting.gif" width="471" height="256">
49 <li>Select which annotation to base the colouring scheme on
50 using the top left selection box. Sequence associated alignment
51 annotation are shown with the seuqence's name appended.<br />If
52 the <strong>Per-sequence only</strong> tick box is not greyed out,
53 then ticking it will limit the list of available annotation rows
54 to just the labels for those that are sequence associated.
55 Annotation rows on each sequence with the same label (e.g.
56 T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
57 disorder predictions</a>) will then be used to colour its
58 corresponding positions in the alignment.<br /> <em>Per-sequence
59 associated annotation colouring is currently only available in
62 <li>If the "Use Original Colours" box is selected,
63 the colouring scheme will use the colouring scheme present on the
64 alignment before the Annotation Colour Settings window was
65 displayed. <br /> <em><strong>Please Note:</strong> If no
66 colour scheme was applied previously, then the colours for lines
67 and labels at each position in the annotation row will be used,
68 for secondary structure symbols and graphs, this may be black by
69 default, so your alignment will be coloured black.</em>
71 <li><em>Secondary structure annotation colouring</em><br />By
72 default, Jalview will employ the helix or sheet colours to shade
73 sequences and columns by available secondary structure annotation
74 tracks. In the case of RNA, each structure is processed to
75 identify distinct RNA helices and rendered in the same way as the
76 <a href="rnahelicesColouring.html">RNA Helices shading scheme</a>.
77 <em>Structure based sequence shading was added in Jalview
79 <li>The colour scheme can display a colour gradient from a
80 colour representing the minimum value in the selected annotation
81 to a colour representing the maximum value in the selected
82 annotation. Use the "Min Colour" and "Max
83 Colour" to set the colour gradient range.
85 <li>Press the "Defaults" button to reset the
86 minimum and maximum colours to their default settings (these
87 are configured in the applet's parameters or the <a
88 href="../features/preferences.html">application's
89 user preferences</a>.).<br /> <em>Default min and max
90 colours were introduced in Jalview 2.7</em>
94 <li>Select whether to colour the alignment above or below an
95 adjustable threshold with the selection box center left of the
97 <li>Change the threshold value with the slider, or enter the
98 exact value in the text box.</li>
99 <li>Select the "Threshold is Min/Max" checkbox to
100 assign colours using the thresholded range's minimum and maximum
101 values, otherwise the scale will be defined by the range of values
102 in the annotation row.</li>
105 <img src="annotationColours.gif" width="582" height="464">