+++ /dev/null
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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<head>
-<title>Annotation Panel Menus</title>
-</head>
-<body>
- <p>
- <strong>Annotation Panel Menus</strong>
- </p>
- <ul>
- <li><strong>Annotation Label Popup Menu</strong><br> <em>This
- menu is opened by clicking anywhere on the annotation row labels
- area (below the sequence ID area).</em> <br />
- <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
- the mouse/track pad is the same as a right-click. See your
- system's settings to configure your track-pad's corners to
- generate right-clicks.</em>
- <ul>
- <li><strong>Add New Row</strong><br> <em>Adds a
- new, named annotation row (a dialog box will pop up for you
- to enter the label for the new row). </em></li>
- <li><strong>Edit Label/Description</strong><br> <em>This
- opens a dialog where you can change the name (displayed
- label), or the description (as shown on the label tooltip)
- of the clicked annotation. </em></li>
- <li><strong>Hide This Row</strong><br> <em>Hides
- the annotation row whose label was clicked in order to bring
- up the menu.</em></li>
- <li><strong>Hide All <em><label></em></strong><br>
- <em>Hides all annotation rows whose label matches the one
- clicked. (This option is only shown for annotations that
- relate to individual sequences, not for whole alignment
- annotations. Since Jalview 2.8.2.)</em></li>
- <li><strong>Delete Row</strong><br> <em>Deletes
- the annotation row whose label was clicked in order to bring
- up the menu.</em></li>
- <li><strong>Show All Hidden Rows</strong><br> <em>Shows
- all hidden annotation rows.</em></li>
- <li><strong>Export Annotation</strong> <em>(Application
- only)</em><br> <em>Annotations can be saved to file or
- output to a text window in either the Jalview annotations
- format or as a spreadsheet style set of comma separated
- values (CSV). </em></li>
- <li><strong>Show Values in Text Box</strong> <em>(applet
- only)</em><br> <em>Opens a text box with a list of
- comma-separated values corresponding to the annotation
- (numerical or otherwise) at each position in the row. This
- is useful to export alignment quality measurements for
- further analysis.</em></li>
- </ul> <em>The following additional entries are available when the
- popup menu is opened on a consensus sequence annotation row:</em>
- <ul>
-
- <li><strong>Ignore Gaps in Consensus</strong><br> If
- this checkbox is selected, all consensus calculations
- performed in the current Alignment window will be done without
- counting gaps as a consensus character.</li>
- <li><strong>Show Consensus Histogram<br></strong>
- Enable or disable the display of the histogram above the
- consensus sequence.</li>
- <li><strong>Show Consensus Logo<br></strong> Enable or
- disable the display of the sequence logo above the consensus
- sequence.</li>
- <li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same
- height, making it easier to compare symbol diversity in
- highly variable regions.</em></li>
-
- <li>
- <li><strong>Copy Consensus Sequence</strong><br>
- Copies the consensus sequence to the clipboard in Fasta
- format, to allow the consensus sequence to be added to an
- alignment. Note the copied sequence is not accessible to other
- programs if Jalview is running as an applet in a web page.</li>
- </ul></li>
- <li><strong>Annotation Popup Menu<br>
- </strong><em>This menu is opened when right-clicking on the selected
- positions of an annotation.</em>
- <ul>
- <li><strong>Helix</strong><br> <em>Mark selected
- positions with a helix glyph (a red oval), and optional text
- label (see below). Consecutive ovals will be rendered as an
- unbroken red line.</em></li>
- <li><strong>Sheet</strong><br> <em>Mark selected
- positions with a sheet glyph (a green arrow oriented from
- left to right), and optional text label (see below).
- Consecutive arrows will be joined together to form a single
- green arrow.</em></li>
- <li><strong>Label</strong><br> <em>Sets the text
- label at the selected positions. If more than one
- consecutive position is marked with the same label, only the
- first position's label will be rendered.</em></li>
- <li><strong>Colour</strong><br> <em>Changes the
- colour of the annotation text label.</em></li>
- <li><strong>Remove Annotation</strong><br> <em>Blanks
- any annotation at the selected positions on the row. Note: <strong>This
- cannot be undone</strong>
- </em></li>
- </ul></li>
- </ul>
-</body>
-</html>
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