help/html/menus/desktopMenu.html

   1 <html>
   2 <head>
   3 <title>Desktop Menus</title>
   4 </head>
   5
   6 <body>
   7 <p><strong>Desktop Menus</strong></p>
   8 <ul>
   9         <li><em> <strong>File</strong></em>
  10         <ul>
  11                 <li><strong>Input Alignment from</strong><em> (See more on <a
  12                         href="../io/index.html">file formats</a>) </em>
  13                 <ul>
  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>
  20                 </ul>
  21                 </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>
  37       </li>
  38         </ul>
  39         </li>
  40         <li><strong>Tools </strong>
  41         <ul>
  42                 <li><strong><a href="../features/preferences.html">Preferences<br>
  43                 </a></strong><em>Change the default visual settings for opening new alignment
  44                 windows.</em></li>
  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.
  51                 </em></li>
  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>
  54
  55         </ul>
  56         </li>
  57         <li><strong>Help </strong>
  58         <ul>
  59                 <li><strong>About<br>
  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>
  65                 </strong></li>
  66         </ul>
  67         </li>
  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 &quot;Window&quot; menu
  71         that will bring the window to the top of the pile when it is selected.
  72         <ul>
  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.
  77                 </li>
  78                 <li><strong>Minimise Associated Windows</strong><br>
  79                 Hide all windows related to the current alignment behind icons on the Jalview Desktop.
  80                 </ul>
  81                 </em></li>
  82         </ul>
  83 </body>
  84 </html>