3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>Desktop Menus</title>
25 <p><strong>Desktop Menus</strong></p>
27 <li><em> <strong>File</strong></em>
29 <li><strong>Input Alignment from</strong><em> (See more on <a
30 href="../io/index.html">file formats</a>) </em>
32 <li><strong>File (Control O)</strong><br>
33 <em>open file(s) on your local file system</em></li>
34 <li><strong>URL</strong><br>
35 <em>open a file from a website. The URL MUST start with http://</em></li>
36 <li><strong>Textbox</strong><br>
37 <em>copy and paste an alignment into a text window</em></li>
40 <li><strong>Fetch Sequence<br>
41 </strong><em>Shows a dialog window in which you can select known ids from
42 Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
43 the European Bioinformatics Institute.</em></li>
44 <li><strong>Save Project</strong><br>
45 <em>Saves all currently open alignment windows with their current
46 view settings and any associated trees, as a <a
47 href="../features/jalarchive.html">Jalview Archive</a> (which has a
48 .jar extension).</em></li>
49 <li><strong>Load Project</strong><br>
50 <em>Loads Jalview archives <strong>only</strong>.</em></li>
51 <li><strong>Quit</strong><br>
52 <em>Close Jalview. <br>
53 <strong>Note - any annotation you have made on alignments will be lost
54 unless you Save your work before quitting.</strong></em><br>
58 <li><strong>Tools</strong>
60 <li><strong><a href="../features/preferences.html">Preferences<br>
61 </a></strong><em>Change the default visual settings for opening new alignment
63 <li><strong>Show Memory Usage<br></strong>
64 <em>When ticked, the currently available memory will be displayed in the
65 bottom right of the desktop background area.<br>
66 See the <a href="../memory.html">help on jalview memory settings</a> for more information.</em></li>
67 <li><strong>Collect Garbage<br></strong>
68 <em>Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
70 <li><strong>Java Console<br/></strong>
71 <em>Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.</em></li>
72 <li><strong>Jalview News<br/></strong>
73 <em>Opens the <a href="../webServices/newsreader.html">Jalview News</a> dialog box. </em></li>
74 <li><strong>Groovy Console...<em> (only available if groovy is on the classpath)</em><br></strong>
75 <em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
79 <li><strong>Vamsas</strong>
80 <em>For more details, read the <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br/>
81 When no session is active, the menu provides options for initiating a new VAMSAS session:</em>
83 <li><strong>Connect to<br/></strong>
84 <em>Connect to one of the existing sessions available.</em></li>
85 <li><strong>New VAMSAS session<br/></strong>
86 <em>Initiates a new local VAMSAS session.</em></li>
87 <li><strong>Load VAMSAS session...<br/></strong>
88 <em>Opens a file browser allowing you to choose a VAMSAS document to import into a new local session.</em></li>
90 <em>When Jalview is joined to a VAMSAS session, the menu contains the following:</em>
92 <li><strong>Session Update<br/></strong>
93 <em>Sends alignment data in the Jalview desktop to the VAMSAS session.</em></li>
94 <li><strong>Save VAMSAS Session...<br/></strong>
95 <em>Saves the current session to a VAMSAS document archive.</em></li>
96 <li><strong>Stop VAMSAS Session<br/></strong>
97 <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>
100 <li><strong>Help </strong>
102 <li><strong>About<br>
103 </strong><em>Displays the version and creation date of the application, as
104 well as acknowledgements and a citation reference. </em></li>
105 <li><strong>Documentation<br>
106 </strong><em>Displays help files as a browseable, searchable set of pages
107 with a table of contents. </em><strong><br>
111 <li><strong>Window</strong><br>
112 <em>Each time a new window is added to the Jalview Desktop a
113 corresponding menu item will be added to the "Window" menu
114 that will bring the window to the top of the pile when it is selected.
116 <li><strong>Close All</strong><br>
117 Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>
118 <li><strong>Raise Associated Windows</strong><br>
119 Bring all windows associated with the current alignment to the top of the pile.
121 <li><strong>Minimise Associated Windows</strong><br>
122 Hide all windows related to the current alignment behind icons on the Jalview Desktop.