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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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7 # Jalview is free software: you can redistribute it and/or
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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
36 <head><title>Alignment Annotation</title></head>
38 <p><strong>Alignment Annotation</strong></p>
40 <p>In addition to the definition of groups and sequence features,
41 Jalview can display symbols and graphs under the columns of an
42 alignment, and allow you to mark particular columns of an alignment and add symbols and text
43 in the annotation area shown below the alignment (which may be hidden if <strong>View→Show
44 Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up
45 menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
46 position with the left mouse button.</p>
47 <p>Web services can also add annotation to an alignment (see the
48 <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
49 annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
50 File</a> dragged into the alignment window or loaded from the
51 alignment's file menu.</p>
52 <p><strong>Interactive Alignment Annotation</strong></p>
54 Annotation rows are added using the <strong>Annotation Label</strong>
55 menu, which is obtained by clicking anywhere on the annotation row labels
56 area (below the sequence ID area).
60 <em>Adds a new, named annotation row (a dialog box will pop up for you to
61 enter the label for the new row). </em> </li>
63 <em>Hides the annotation row whose label was clicked in order to bring up
66 <em>Deletes the annotation row whose label was clicked in order to bring up
68 <li>Show All Hidden Rows<br>
69 <em>Shows all hidden annotation rows.</em> </li>
70 <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
71 <em>Annotations can be saved to file or output to a text window in either the
72 Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
73 <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
74 <em>Opens a text box with a list of comma-separated values corresponding
75 to the annotation (numerical or otherwise) at each position in the row.
76 This is useful to export alignment quality measurements for further analysis.</em>
78 <li><strong>Scale Label To Column</strong><em>(introduced in 2.5)</em><br>
79 <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>
82 <strong>Editing Label and secondary structure Annotation</strong></p>
84 Use the <strong>left mouse button</strong> to select a position along the row that are to
85 be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
86 with the left-click will select more than one position, or a range of
87 positions on the alignment.
89 <p>Once the desired position has been selected, use the <strong>right mouse
90 button</strong> to open the <strong>annotation menu</strong>:</p>
92 <li>Helix<br><em>Mark selected positions with a helix glyph (a red
93 oval), and optional text label (see below). A
94 dialog box will open for you to enter the text. Consecutive ovals
95 will be rendered as an unbroken red line.</em>
97 <li>Sheet<br><em>Mark selected positions with a sheet glyph (a green
98 arrow oriented from left to right), and optional text label (see
99 below). A dialog box will open for you to enter the text. Consecutive
100 arrows will be joined together to form a single green arrow.</em>
102 <li>Label<br><em>Set the text label at the selected positions. A
103 dialog box will open for you to enter the text. If
104 more that one consecutive position is marked with the same label, only
105 the first position's label will be rendered.</em>
107 <li>Colour<br><em>Changes the colour of the annotation text label.</em>
109 <li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
110 the row. Note: <strong>This cannot be undone</strong></em>
114 User defined annotation is stored and retrieved using <a
115 href="../features/jalarchive.html">Jalview Archives</a>.
117 <p><em>Current Limitations</em></p>
118 <p>As of version 2.5, the Jalview user interface does not support the
119 creation and editing quantitative annotation (histograms and line graphs), or
120 to create annotation associated with a specific sequence. It is also incapable of
121 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
122 <a href="annotationsFormat.html">Annotation file</a>.<br>