2 <head><title>Alignment Annotation</title></head>
4 <p><strong>Alignment Annotation</strong></p>
6 <p>In addition to the definition of groups and sequence features,
7 Jalview can display symbols and graphs under the columns of an
8 alignment, and allow you to mark particular columns of an alignment and add symbols and text
9 in the annotation area shown below the alignment (which may be hidden if <strong>View→Show
10 Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up
11 menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
12 position with the left mouse button.</p>
13 <p>Web services can also add annotation to an alignment (see the
14 <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
15 annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
16 File</a> dragged into the alignment window or loaded from the
17 alignment's file menu.</p>
18 <p><strong>Interactive Alignment Annotation</strong></p>
20 Annotation rows are added using the <strong>Annotation Label</strong>
21 menu, which is obtained by clicking anywhere on the annotation row labels
22 area (below the sequence ID area).
26 <em>Adds a new, named annotation row (a dialog box will pop up for you to
27 enter the label for the new row). </em> </li>
29 <em>Hides the annotation row whose label was clicked in order to bring up
32 <em>Deletes the annotation row whose label was clicked in order to bring up
34 <li>Show All Hidden Rows<br>
35 <em>Shows all hidden annotation rows.</em> </li>
36 <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
37 <em>Annotations can be saved to file or output to a text window in either the
38 Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
39 <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
40 <em>Opens a text box with a list of comma-separated values corresponding
41 to the annotation (numerical or otherwise) at each position in the row.
42 This is useful to export alignment quality measurements for further analysis.</em>
44 <li><strong>Scale Label To Column</strong><em>(introduced in 2.4.1)</em><br>
45 <em>Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.</em></li>
48 <strong>Editing Label and secondary structure Annotation</strong></p>
50 Use the <strong>left mouse button</strong> to select a position along the row that are to
51 be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
52 with the left-click will select more than one position, or a range of
53 positions on the alignment.
55 <p>Once the desired position has been selected, use the <strong>right mouse
56 button</strong> to open the <strong>annotation menu</strong>:</p>
58 <li>Helix<br><em>Mark selected positions with a helix glyph (a red
59 oval), and optional text label (see below). A
60 dialog box will open for you to enter the text. Consecutive ovals
61 will be rendered as an unbroken red line.</em>
63 <li>Sheet<br><em>Mark selected positions with a sheet glyph (a green
64 arrow oriented from left to right), and optional text label (see
65 below). A dialog box will open for you to enter the text. Consecutive
66 arrows will be joined together to form a single green arrow.</em>
68 <li>Label<br><em>Set the text label at the selected positions. A
69 dialog box will open for you to enter the text. If
70 more that one consecutive position is marked with the same label, only
71 the first position's label will be rendered.</em>
73 <li>Colour<br><em>Changes the colour of the annotation text label.</em>
75 <li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
76 the row. Note: <strong>This cannot be undone</strong></em>
80 User defined annotation is stored and retrieved using <a
81 href="../features/jalarchive.html">Jalview Archives</a>.
83 <p><em>Current Limitations</em></p>
84 <p>As of version 2.4, the Jalview user interface does not support the
85 creation and editing quantitative annotation (histograms and line graphs), or
86 to create annotation associated with a specific sequence. It is also incapable of
87 annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an
88 <a href="annotationsFormat.html">Annotation file</a>.<br>