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