3 <title>Annotation Panel Menus</title>
6 <p><strong>Annotation Panel Menus</strong></p>
8 <li> <strong>Annotation Label Popup Menu</strong><br>
9 <em>This menu is opened by clicking anywhere on the annotation row labels
10 area (below the sequence ID area).</em>
12 <li><strong> Add New Row</strong><br>
13 <em>Adds a new, named annotation row (a dialog box will pop up for you
14 to enter the label for the new row). </em> </li>
15 <li><strong>Hide Row</strong><br>
16 <em>Hides the annotation row whose label was clicked in order to bring
17 up the menu.</em> </li>
18 <li><strong>Delete Row</strong><br>
19 <em>Deletes the annotation row whose label was clicked in order to bring
20 up the menu.</em> </li>
21 <li><strong>Show All Hidden Rows</strong><br>
22 <em>Shows all hidden annotation rows.</em> </li>
23 <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
24 <em>Annotations can be saved to file or output to a text window in either the
25 Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
26 <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
27 <em>Opens a text box with a list of comma-separated values corresponding
28 to the annotation (numerical or otherwise) at each position in the row.
29 This is useful to export alignment quality measurements for further analysis.</em>
32 <em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em>
34 <li><strong>Ignore Gaps in Consensus</strong><br>
35 If this checkbox is selected, all consensus calculations performed in
36 the current Alignment window will be done without counting gaps as a consensus
38 <li><strong>Copy Consensus Sequence</strong><br>
39 Copies the consensus sequence to the clipboard in Fasta format, to allow
40 the consensus sequence to be added to an alignment. Note the copied sequence
41 is not accessible to other programs if Jalview is running as an applet
45 <li><strong>Annotation Popup Menu<br>
46 </strong><em>This menu is opened when right-clicking on the selected positions
47 of an annotation.</em>
49 <li><strong>Helix</strong><br>
50 <em>Mark selected positions with a helix glyph (a red oval), and optional
51 text label (see below). Consecutive ovals will be rendered as an unbroken
53 <li><strong>Sheet</strong><br>
54 <em>Mark selected positions with a sheet glyph (a green arrow oriented
55 from left to right), and optional text label (see below). Consecutive
56 arrows will be joined together to form a single green arrow.</em> </li>
57 <li><strong>Label</strong><br>
58 <em>Sets the text label at the selected positions. If more that one consecutive
59 position is marked with the same label, only the first position's label
60 will be rendered.</em> </li>
61 <li><strong>Colour</strong><br>
62 <em>Changes the colour of the annotation text label.</em> </li>
63 <li><strong>Remove Annotation</strong><br>
64 <em>Blanks any annotation at the selected positions on the row. Note:
65 <strong>This cannot be undone</strong></em> </li>