3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Alignment Annotation</title></head>
21 <p><strong>Alignment Annotation</strong></p>
23 <p>In addition to the definition of groups and sequence features,
24 Jalview can display symbols and graphs under the columns of an
25 alignment, and allow you to mark particular columns of an alignment and add symbols and text
26 in the annotation area shown below the alignment (which may be hidden if <strong>View→Show
27 Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up
28 menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
29 position with the left mouse button.</p>
30 <p>Web services can also add annotation to an alignment (see the
31 <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
32 annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
33 File</a> dragged into the alignment window or loaded from the
34 alignment's file menu.</p>
35 <p><strong>Interactive Alignment Annotation</strong></p>
37 Annotation rows are added using the <strong>Annotation Label</strong>
38 menu, which is obtained by clicking anywhere on the annotation row labels
39 area (below the sequence ID area).
43 <em>Adds a new, named annotation row (a dialog box will pop up for you to
44 enter the label for the new row). </em> </li>
46 <em>Hides the annotation row whose label was clicked in order to bring up
49 <em>Deletes the annotation row whose label was clicked in order to bring up
51 <li>Show All Hidden Rows<br>
52 <em>Shows all hidden annotation rows.</em> </li>
53 <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
54 <em>Annotations can be saved to file or output to a text window in either the
55 Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
56 <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
57 <em>Opens a text box with a list of comma-separated values corresponding
58 to the annotation (numerical or otherwise) at each position in the row.
59 This is useful to export alignment quality measurements for further analysis.</em>
61 <li><strong>Scale Label To Column</strong><em>(introduced in 2.5)</em><br>
62 <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>
65 <strong>Editing Label and secondary structure Annotation</strong></p>
67 Use the <strong>left mouse button</strong> to select a position along the row that are to
68 be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
69 with the left-click will select more than one position, or a range of
70 positions on the alignment.
72 <p>Once the desired position has been selected, use the <strong>right mouse
73 button</strong> to open the <strong>annotation menu</strong>:</p>
75 <li>Helix<br><em>Mark selected positions with a helix glyph (a red
76 oval), and optional text label (see below). A
77 dialog box will open for you to enter the text. Consecutive ovals
78 will be rendered as an unbroken red line.</em>
80 <li>Sheet<br><em>Mark selected positions with a sheet glyph (a green
81 arrow oriented from left to right), and optional text label (see
82 below). A dialog box will open for you to enter the text. Consecutive
83 arrows will be joined together to form a single green arrow.</em>
85 <li>Label<br><em>Set the text label at the selected positions. A
86 dialog box will open for you to enter the text. If
87 more that one consecutive position is marked with the same label, only
88 the first position's label will be rendered.</em>
90 <li>Colour<br><em>Changes the colour of the annotation text label.</em>
92 <li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
93 the row. Note: <strong>This cannot be undone</strong></em>
97 User defined annotation is stored and retrieved using <a
98 href="../features/jalarchive.html">Jalview Archives</a>.
100 <p><em>Current Limitations</em></p>
101 <p>As of version 2.5, the Jalview user interface does not support the
102 creation and editing quantitative annotation (histograms and line graphs), or
103 to create annotation associated with a specific sequence. It is also incapable of
104 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
105 <a href="annotationsFormat.html">Annotation file</a>.<br>