-<html>\r
-<head><title>Desktop Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Desktop Menus</strong></p>\r
-<ul>\r
- <li><strong>File</strong><em> </em> \r
- <ul>\r
- <li><strong>Input Alignment from</strong><em> (See more on <a href="../io/index.html">file \r
- formats</a>) </em> \r
- <ul>\r
- <li><strong>File</strong><br>\r
- <em>open file(s) on your local file system</em></li>\r
- <li><strong>URL</strong><br>\r
- <em>open a file from a website. The URL MUST start with http://</em></li>\r
- <li><strong>Textbox</strong><br>\r
- <em>copy and paste an alignment into a text window</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Fetch Sequence<br>\r
- </strong><em>Shows a dialog window in which you can select known ids from \r
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by \r
- the European Bioinformatics Institute.</em></li>\r
- <li><strong>Save Project</strong><br>\r
- <em>Saves all currently open alignment windows with their current view \r
- settings and any associated trees, as a <a href="../features/jalarchive.html">Jalview \r
- Archive</a> (which has a .jar extension).</em></li>\r
- <li><strong>Load Project</strong><br>\r
- <em>Loads Jalview archives <strong>only</strong>.</em></li>\r
- <li><strong>Quit</strong><br>\r
- <em>Close Jalview. Warning - any annotations you have made on alignments \r
- will be lost unless you Save your work before quitting.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Tools </strong> \r
- <ul>\r
- <li><strong><a href="../features/preferences.html">Preferences<br>\r
- </a></strong><em>Change the default visual settings for opening new alignment \r
- windows.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Help </strong> \r
- <ul>\r
- <li><strong>About<br>\r
- </strong><em>Displays the version and creation date of the application, \r
- as well as acknowledgements and a citation reference. </em></li>\r
- <li><strong>Documentation<br>\r
- </strong><em>Displays help files as a browseable, searchable set of pages \r
- with a table of contents. </em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Window<br>\r
- </strong><em>Each time a new window is added to the Jalview Desktop a new \r
- menu item will be added to the "Window" menu. If you are working \r
- with several alignments, trees or other types of windows use the "Window" \r
- menu to bring your window of choice to the top of the pile if it has been \r
- hidden by other windows. </em></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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>Desktop Menus</title>
+</head>
+
+<body>
+ <p>
+ <strong>Desktop Menus</strong>
+ </p>
+ <ul>
+ <li><em> <strong>File</strong></em>
+ <ul>
+ <li><strong>Input Alignment from</strong><em> (See
+ more on <a href="../io/index.html">file formats</a>)
+ </em>
+ <ul>
+ <li><strong>File (Control O)</strong><br> <em>open
+ file(s) on your local file system</em></li>
+ <li><strong>URL</strong><br> <em>open a file
+ from a website. The URL MUST start with http://</em></li>
+ <li><strong>Textbox</strong><br> <em>copy and
+ paste an alignment into a text window</em></li>
+ </ul></li>
+ <li><strong>Fetch Sequence<br>
+ </strong><em>Shows a dialog window in which you can select known ids
+ from Uniprot, EMBL, EMBLCDS or PDB database using Web
+ Services provided by the European Bioinformatics Institute.</em></li>
+ <li><strong>Save Project</strong><br> <em>Saves
+ all currently open alignment windows with their current view
+ settings and any associated trees, as a <a
+ href="../features/jalarchive.html"
+ >Jalview Archive</a> (which has a .jar extension).
+ </em></li>
+ <li><strong>Load Project</strong><br> <em>Loads
+ Jalview archives <strong>only</strong>.
+ </em></li>
+ <li><strong>Quit</strong><br> <em>Close Jalview.
+ <br> <strong>Note - any annotation you have
+ made on alignments will be lost unless you Save your work
+ before quitting.</strong>
+ </em><br></li>
+ </ul></li>
+ <li><strong>Tools</strong>
+ <ul>
+ <li><strong><a href="../features/preferences.html">Preferences<br>
+ </a></strong><em>Change the default visual settings for opening new
+ alignment windows.</em></li>
+ <li><strong>Show Memory Usage<br></strong> <em>When
+ ticked, the currently available memory will be displayed in
+ the bottom right of the desktop background area.<br>
+ See the <a href="../memory.html">help on Jalview memory
+ settings</a> for more information.
+ </em></li>
+ <li><strong>Collect Garbage<br></strong> <em>Selecting
+ this will initiate the Java Virtual Machine garbage
+ collector, which might help free up some memory... perhaps.
+ </em></li>
+ <li><strong>Java Console<br /></strong> <em>Toggles
+ the display of a the Jalview Java Console window. This
+ setting will be remembered in your user preferences.</em></li>
+ <li><strong>Jalview News<br /></strong> <em>Opens the
+ <a href="../webServices/newsreader.html">Jalview News</a>
+ dialog box.
+ </em></li>
+ <li><strong>Groovy Console...<em> (only
+ available if groovy is on the classpath)</em><br></strong> <em>Open's
+ the <a href="../groovy.html">Groovy Console</a> for
+ interactive scripting.
+ </em><strong><br></strong></li>
+
+ </ul></li>
+ <li><strong>Vamsas</strong> <em>For more details, read the
+ <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br />
+ When no session is active, the menu provides options for
+ initiating a new VAMSAS session:
+ </em>
+ <ul>
+ <li><strong>Connect to<br /></strong> <em>Connect to
+ one of the existing sessions available.</em></li>
+ <li><strong>New VAMSAS session<br /></strong> <em>Initiates
+ a new local VAMSAS session.</em></li>
+ <li><strong>Load VAMSAS session...<br /></strong> <em>Opens
+ a file browser allowing you to choose a VAMSAS document to
+ import into a new local session.</em></li>
+ </ul> <em>When Jalview is joined to a VAMSAS session, the menu
+ contains the following:</em>
+ <ul>
+ <li><strong>Session Update<br /></strong> <em>Sends
+ alignment data in the Jalview desktop to the VAMSAS session.</em></li>
+ <li><strong>Save VAMSAS Session...<br /></strong> <em>Saves
+ the current session to a VAMSAS document archive.</em></li>
+ <li><strong>Stop VAMSAS Session<br /></strong> <em>Disconnects
+ from the current session. You may be asked if you want to
+ save the current session's data if no other VAMSAS clients
+ are connected.</em></li>
+ </ul></li>
+ <li><strong>Help </strong>
+ <ul>
+ <li><strong>About<br>
+ </strong><em>Displays the version and creation date of the
+ application, as well as acknowledgements and a citation
+ reference. </em></li>
+ <li><strong>Documentation<br>
+ </strong><em>Displays help files as a browseable, searchable set of
+ pages with a table of contents. </em><strong><br> </strong></li>
+ </ul></li>
+ <li><strong>Window</strong><br> <em>Each time a new
+ window is added to the Jalview Desktop a corresponding menu item
+ will be added to the "Window" menu that will bring the
+ window to the top of the pile when it is selected.
+ <ul>
+ <li><strong>Close All</strong><br> Close all
+ alignment and analysis windows.<br>
+ <strong>Note: This will erase all alignments from
+ memory, and cannot be undone!</strong></li>
+ <li><strong>Raise Associated Windows</strong><br>
+ Bring all windows associated with the current alignment to
+ the top of the pile.</li>
+ <li><strong>Minimise Associated Windows</strong><br>
+ Hide all windows related to the current alignment behind
+ icons on the Jalview Desktop.
+ </ul>
+ </em></li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff