--- /dev/null
+<html>
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
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+ * Jalview is distributed in the hope that it will be useful, but
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+ * You should have received a copy of the GNU General Public License
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+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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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