+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * 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>
- <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 that 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>
git://source.jalview.org / jalview.git / blobdiff