3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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/>.
20 <title>Annotation Panel Menus</title>
23 <p><strong>Annotation Panel Menus</strong></p>
25 <li> <strong>Annotation Label Popup Menu</strong><br>
26 <em>This menu is opened by clicking anywhere on the annotation row labels
27 area (below the sequence ID area).</em>
29 <li><strong> Add New Row</strong><br>
30 <em>Adds a new, named annotation row (a dialog box will pop up for you
31 to enter the label for the new row). </em> </li>
32 <li><strong>Hide Row</strong><br>
33 <em>Hides the annotation row whose label was clicked in order to bring
34 up the menu.</em> </li>
35 <li><strong>Delete Row</strong><br>
36 <em>Deletes the annotation row whose label was clicked in order to bring
37 up the menu.</em> </li>
38 <li><strong>Show All Hidden Rows</strong><br>
39 <em>Shows all hidden annotation rows.</em> </li>
40 <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
41 <em>Annotations can be saved to file or output to a text window in either the
42 Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
43 <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
44 <em>Opens a text box with a list of comma-separated values corresponding
45 to the annotation (numerical or otherwise) at each position in the row.
46 This is useful to export alignment quality measurements for further analysis.</em>
49 <em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em>
51 <li><strong>Ignore Gaps in Consensus</strong><br>
52 If this checkbox is selected, all consensus calculations performed in
53 the current Alignment window will be done without counting gaps as a consensus
55 <li><strong>Show Consensus Histogram<br></strong>
56 Enable or disable the display of the histogram above the consensus sequence.
59 <strong>Show Consensus Logo<br></strong>
60 Enable or disable the display of the sequence logo above the consensus sequence.
62 <li><strong>Normalise Consensus Logo<br>
63 </strong><em>When enabled, scales all logo stacks to the same height,
64 making it easier to compare symbol diversity in highly variable
68 <li><strong>Copy Consensus Sequence</strong><br>
69 Copies the consensus sequence to the clipboard in Fasta format, to allow
70 the consensus sequence to be added to an alignment. Note the copied sequence
71 is not accessible to other programs if Jalview is running as an applet
75 <li><strong>Annotation Popup Menu<br>
76 </strong><em>This menu is opened when right-clicking on the selected positions
77 of an annotation.</em>
79 <li><strong>Helix</strong><br>
80 <em>Mark selected positions with a helix glyph (a red oval), and optional
81 text label (see below). Consecutive ovals will be rendered as an unbroken
83 <li><strong>Sheet</strong><br>
84 <em>Mark selected positions with a sheet glyph (a green arrow oriented
85 from left to right), and optional text label (see below). Consecutive
86 arrows will be joined together to form a single green arrow.</em> </li>
87 <li><strong>Label</strong><br>
88 <em>Sets the text label at the selected positions. If more that one consecutive
89 position is marked with the same label, only the first position's label
90 will be rendered.</em> </li>
91 <li><strong>Colour</strong><br>
92 <em>Changes the colour of the annotation text label.</em> </li>
93 <li><strong>Remove Annotation</strong><br>
94 <em>Blanks any annotation at the selected positions on the row. Note:
95 <strong>This cannot be undone</strong></em> </li>