3 <title>Desktop Menus</title>
7 <p><strong>Desktop Menus</strong></p>
9 <li><em> <strong>File</strong></em>
11 <li><strong>Input Alignment from</strong><em> (See more on <a
12 href="../io/index.html">file formats</a>) </em>
14 <li><strong>File (Control O)</strong><br>
15 <em>open file(s) on your local file system</em></li>
16 <li><strong>URL</strong><br>
17 <em>open a file from a website. The URL MUST start with http://</em></li>
18 <li><strong>Textbox</strong><br>
19 <em>copy and paste an alignment into a text window</em></li>
22 <li><strong>Fetch Sequence<br>
23 </strong><em>Shows a dialog window in which you can select known ids from
24 Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
25 the European Bioinformatics Institute.</em></li>
26 <li><strong>Save Project</strong><br>
27 <em>Saves all currently open alignment windows with their current
28 view settings and any associated trees, as a <a
29 href="../features/jalarchive.html">Jalview Archive</a> (which has a
30 .jar extension).</em></li>
31 <li><strong>Load Project</strong><br>
32 <em>Loads Jalview archives <strong>only</strong>.</em></li>
33 <li><strong>Quit</strong><br>
34 <em>Close Jalview. <br>
35 <strong>Note - any annotation you have made on alignments will be lost
36 unless you Save your work before quitting.</strong></em><br>
40 <li><strong>Tools </strong>
42 <li><strong><a href="../features/preferences.html">Preferences<br>
43 </a></strong><em>Change the default visual settings for opening new alignment
45 <li><strong>Show Memory Usage<br></strong>
46 <em>When ticked, the currently available memory will be displayed in the
47 bottom right of the desktop background area.<br>
48 See the <a href="../memory.html">help on jalview memory settings</a> for more information.</em></li>
49 <li><strong>Collect Garbage<br></strong>
50 <em>Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
52 <li><strong>Groovy Console...<em> (only available if groovy is on the classpath)</em><br></strong>
53 <em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
57 <li><strong>Help </strong>
60 </strong><em>Displays the version and creation date of the application, as
61 well as acknowledgements and a citation reference. </em></li>
62 <li><strong>Documentation<br>
63 </strong><em>Displays help files as a browseable, searchable set of pages
64 with a table of contents. </em><strong><br>
68 <li><strong>Window</strong><br>
69 <em>Each time a new window is added to the Jalview Desktop a
70 corresponding menu item will be added to the "Window" menu
71 that will bring the window to the top of the pile when it is selected.
73 <li><strong>Close All</strong><br>
74 Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>
75 <li><strong>Raise Associated Windows</strong><br>
76 Bring all windows associated with the current alignment to the top of the pile.
78 <li><strong>Minimise Associated Windows</strong><br>
79 Hide all windows related to the current alignment behind icons on the Jalview Desktop.