+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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...<br></strong> <em>Opens
- the <a href="../features/groovy.html">Groovy Console</a> for
- interactive scripting.
- </em><strong><br></strong></li>
- <!-- <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em> -->
-
- </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