3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Desktop Menus</title>
24 <p><strong>Desktop Menus</strong></p>
26 <li><em> <strong>File</strong></em>
28 <li><strong>Input Alignment from</strong><em> (See more on <a
29 href="../io/index.html">file formats</a>) </em>
31 <li><strong>File (Control O)</strong><br>
32 <em>open file(s) on your local file system</em></li>
33 <li><strong>URL</strong><br>
34 <em>open a file from a website. The URL MUST start with http://</em></li>
35 <li><strong>Textbox</strong><br>
36 <em>copy and paste an alignment into a text window</em></li>
39 <li><strong>Fetch Sequence<br>
40 </strong><em>Shows a dialog window in which you can select known ids from
41 Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
42 the European Bioinformatics Institute.</em></li>
43 <li><strong>Save Project</strong><br>
44 <em>Saves all currently open alignment windows with their current
45 view settings and any associated trees, as a <a
46 href="../features/jalarchive.html">Jalview Archive</a> (which has a
47 .jar extension).</em></li>
48 <li><strong>Load Project</strong><br>
49 <em>Loads Jalview archives <strong>only</strong>.</em></li>
50 <li><strong>Quit</strong><br>
51 <em>Close Jalview. <br>
52 <strong>Note - any annotation you have made on alignments will be lost
53 unless you Save your work before quitting.</strong></em><br>
57 <li><strong>Tools</strong>
59 <li><strong><a href="../features/preferences.html">Preferences<br>
60 </a></strong><em>Change the default visual settings for opening new alignment
62 <li><strong>Show Memory Usage<br></strong>
63 <em>When ticked, the currently available memory will be displayed in the
64 bottom right of the desktop background area.<br>
65 See the <a href="../memory.html">help on jalview memory settings</a> for more information.</em></li>
66 <li><strong>Collect Garbage<br></strong>
67 <em>Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
69 <li><strong>Java Console<br/></strong>
70 <em>Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.</em></li>
71 <li><strong>Jalview News<br/></strong>
72 <em>Opens the <a href="../webServices/newsreader.html">Jalview News</a> dialog box. </em></li>
73 <li><strong>Groovy Console...<em> (only available if groovy is on the classpath)</em><br></strong>
74 <em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
78 <li><strong>Vamsas</strong>
79 <em>For more details, read the <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br/>
80 When no session is active, the menu provides options for initiating a new VAMSAS session:</em>
82 <li><strong>Connect to<br/></strong>
83 <em>Connect to one of the existing sessions available.</em></li>
84 <li><strong>New VAMSAS session<br/></strong>
85 <em>Initiates a new local VAMSAS session.</em></li>
86 <li><strong>Load VAMSAS session...<br/></strong>
87 <em>Opens a file browser allowing you to choose a VAMSAS document to import into a new local session.</em></li>
89 <em>When Jalview is joined to a VAMSAS session, the menu contains the following:</em>
91 <li><strong>Session Update<br/></strong>
92 <em>Sends alignment data in the Jalview desktop to the VAMSAS session.</em></li>
93 <li><strong>Save VAMSAS Session...<br/></strong>
94 <em>Saves the current session to a VAMSAS document archive.</em></li>
95 <li><strong>Stop VAMSAS Session<br/></strong>
96 <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>
99 <li><strong>Help </strong>
101 <li><strong>About<br>
102 </strong><em>Displays the version and creation date of the application, as
103 well as acknowledgements and a citation reference. </em></li>
104 <li><strong>Documentation<br>
105 </strong><em>Displays help files as a browseable, searchable set of pages
106 with a table of contents. </em><strong><br>
110 <li><strong>Window</strong><br>
111 <em>Each time a new window is added to the Jalview Desktop a
112 corresponding menu item will be added to the "Window" menu
113 that will bring the window to the top of the pile when it is selected.
115 <li><strong>Close All</strong><br>
116 Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>
117 <li><strong>Raise Associated Windows</strong><br>
118 Bring all windows associated with the current alignment to the top of the pile.
120 <li><strong>Minimise Associated Windows</strong><br>
121 Hide all windows related to the current alignment behind icons on the Jalview Desktop.