-<html>\r
-<head>\r
-<title>Annotation Panel Menus</title>\r
-</head>\r
-<body>\r
-<p><strong>Annotation Panel Menus</strong></p>\r
-<ul>\r
- <li> <strong>Annotation Label Popup Menu</strong><br>\r
- <em>This menu is opened by clicking anywhere on the annotation row labels \r
- area (below the sequence ID area).</em> \r
- <ul>\r
- <li><strong> Add New Row</strong><br>\r
- <em>Adds a new, named annotation row (a dialog box will pop up for you \r
- to enter the label for the new row). </em> </li>\r
- <li><strong>Hide Row</strong><br>\r
- <em>Hides the annotation row whose label was clicked in order to bring \r
- up the menu.</em> </li>\r
- <li><strong>Delete Row</strong><br>\r
- <em>Deletes the annotation row whose label was clicked in order to bring \r
- up the menu.</em> </li>\r
- <li><strong>Show All Hidden Rows</strong><br>\r
- <em>Shows all hidden annotation rows.</em> </li>\r
- <li><strong>Export Annotation</strong><br>\r
- <em>Annotations can be saved to file or output to a text window in the \r
- Jalview annotations format. </em> </li>\r
- <li><strong>Ignore Gaps in Consensus</strong><br>\r
- If this checkbox is selected, all consensus calculations performed in \r
- the current Alignment window will be done without counting gaps as a consensus \r
- character.</li>\r
- <li><strong>Copy Consensus Sequence</strong><br>\r
- Copies the consensus sequence to the clipboard in Fasta format, to allow \r
- the consensus sequence to be added to an alignment. Note the copied sequence \r
- is not accessible to other programs if Jalview is running as an applet \r
- in a web page.</li>\r
- </ul>\r
- </li>\r
- <li><strong>Annotation Popup Menu<br>\r
- </strong><em>This menu is opened when right-clicking on the selected positions \r
- of an annotation.</em> \r
- <ul>\r
- <li><strong>Helix</strong><br>\r
- <em>Mark selected positions with a helix glyph (a red oval), and optional \r
- text label (see below). Consecutive ovals will be rendered as an unbroken \r
- red line.</em> </li>\r
- <li><strong>Sheet</strong><br>\r
- <em>Mark selected positions with a sheet glyph (a green arrow oriented \r
- from left to right), and optional text label (see below). Consecutive \r
- arrows will be joined together to form a single green arrow.</em> </li>\r
- <li><strong>Label</strong><br>\r
- <em>Sets the text label at the selected positions. If more that one consecutive \r
- position is marked with the same label, only the first position's label \r
- will be rendered.</em> </li>\r
- <li><strong>Colour</strong><br>\r
- <em>Changes the colour of the annotation text label.</em> </li>\r
- <li><strong>Remove Annotation</strong><br>\r
- <em>Blanks any annotation at the selected positions on the row. Note: \r
- <strong>This cannot be undone</strong></em> </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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>Hide Row</strong><br>
+ <em>Hides the annotation row whose label was clicked in order to bring
+ up the menu.</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 avalable 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>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