3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Annotation Panel Menus</title>
26 <p><strong>Annotation Panel Menus</strong></p>
28 <li> <strong>Annotation Label Popup Menu</strong><br>
29 <em>This menu is opened by clicking anywhere on the annotation row labels
30 area (below the sequence ID area).</em>
32 <li><strong> Add New Row</strong><br>
33 <em>Adds a new, named annotation row (a dialog box will pop up for you
34 to enter the label for the new row). </em> </li>
35 <li><strong>Edit Label/Description</strong><br>
36 <em>This opens a dialog where you can change the name (displayed label), or the description
37 (as shown on the label tooltip) of the clicked annotation. </em> </li>
38 <li><strong>Hide This Row</strong><br>
39 <em>Hides the annotation row whose label was clicked in order to bring up
41 <li><strong>Hide All <em><label></em></strong><br>
42 <em>Hides all annotation rows whose label matches the one clicked.
43 (This option is only shown for annotations that relate to individual sequences,
44 not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
45 <li><strong>Delete Row</strong><br>
46 <em>Deletes the annotation row whose label was clicked in order to bring
47 up the menu.</em> </li>
48 <li><strong>Show All Hidden Rows</strong><br>
49 <em>Shows all hidden annotation rows.</em> </li>
50 <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
51 <em>Annotations can be saved to file or output to a text window in either the
52 Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
53 <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
54 <em>Opens a text box with a list of comma-separated values corresponding
55 to the annotation (numerical or otherwise) at each position in the row.
56 This is useful to export alignment quality measurements for further analysis.</em>
59 <em>The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:</em>
62 <li><strong>Ignore Gaps in Consensus</strong><br>
63 If this checkbox is selected, all consensus calculations performed in
64 the current Alignment window will be done without counting gaps as a consensus
66 <li><strong>Show Consensus Histogram<br></strong>
67 Enable or disable the display of the histogram above the consensus sequence.
70 <strong>Show Consensus Logo<br></strong>
71 Enable or disable the display of the sequence logo above the consensus sequence.
73 <li><strong>Normalise Consensus Logo<br>
74 </strong><em>When enabled, scales all logo stacks to the same height,
75 making it easier to compare symbol diversity in highly variable
79 <li><strong>Copy Consensus Sequence</strong><br>
80 Copies the consensus sequence to the clipboard in Fasta format, to allow
81 the consensus sequence to be added to an alignment. Note the copied sequence
82 is not accessible to other programs if Jalview is running as an applet
86 <li><strong>Annotation Popup Menu<br>
87 </strong><em>This menu is opened when right-clicking on the selected positions
88 of an annotation.</em>
90 <li><strong>Helix</strong><br>
91 <em>Mark selected positions with a helix glyph (a red oval), and optional
92 text label (see below). Consecutive ovals will be rendered as an unbroken
94 <li><strong>Sheet</strong><br>
95 <em>Mark selected positions with a sheet glyph (a green arrow oriented
96 from left to right), and optional text label (see below). Consecutive
97 arrows will be joined together to form a single green arrow.</em> </li>
98 <li><strong>Label</strong><br>
99 <em>Sets the text label at the selected positions. If more that one consecutive
100 position is marked with the same label, only the first position's label
101 will be rendered.</em> </li>
102 <li><strong>Colour</strong><br>
103 <em>Changes the colour of the annotation text label.</em> </li>
104 <li><strong>Remove Annotation</strong><br>
105 <em>Blanks any annotation at the selected positions on the row. Note:
106 <strong>This cannot be undone</strong></em> </li>