-<html>\r
-<head>\r
-<title>Desktop Menus</title>\r
-</head>\r
-\r
-<body>\r
-<p><strong>Desktop Menus</strong></p>\r
-<ul>\r
- <li><em> <strong>File</strong></em>\r
- <ul>\r
- <li><strong>Input Alignment from</strong><em> (See more on <a\r
- href="../io/index.html">file formats</a>) </em>\r
- <ul>\r
- <li><strong>File (Control O)</strong><br>\r
- <em>open file(s) on your local file system</em></li>\r
- <li><strong>URL</strong><br>\r
- <em>open a file from a website. The URL MUST start with http://</em></li>\r
- <li><strong>Textbox</strong><br>\r
- <em>copy and paste an alignment into a text window</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Fetch Sequence<br>\r
- </strong><em>Shows a dialog window in which you can select known ids from\r
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by\r
- the European Bioinformatics Institute.</em></li>\r
- <li><strong>Save Project</strong><br>\r
- <em>Saves all currently open alignment windows with their current\r
- view settings and any associated trees, as a <a\r
- href="../features/jalarchive.html">Jalview Archive</a> (which has a\r
- .jar extension).</em></li>\r
- <li><strong>Load Project</strong><br>\r
- <em>Loads Jalview archives <strong>only</strong>.</em></li>\r
- <li><strong>Quit</strong><br>\r
- <em>Close Jalview. <br>\r
- <strong>Note - any annotation you have made on alignments will be lost \r
- unless you Save your work before quitting.</strong></em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Tools </strong>\r
- <ul>\r
- <li><strong><a href="../features/preferences.html">Preferences<br>\r
- </a></strong><em>Change the default visual settings for opening new alignment\r
- windows.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Help </strong>\r
- <ul>\r
- <li><strong>About<br>\r
- </strong><em>Displays the version and creation date of the application, as\r
- well as acknowledgements and a citation reference. </em></li>\r
- <li><strong>Documentation<br>\r
- </strong><em>Displays help files as a browseable, searchable set of pages\r
- with a table of contents. </em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Window</strong><br>\r
- <em>Each time a new window is added to the Jalview Desktop a\r
- corresponding menu item will be added to the "Window" menu\r
- that will bring the window to the top of the pile when it is selected.\r
- <ul>\r
- <li><strong>Close All</strong><br>\r
- Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>\r
- <li><strong>Raise Associated Windows</strong><br>\r
- Bring all windows associated with the current alignment to the top of the pile. \r
- </li>\r
- <li><strong>Minimise Associated Windows</strong><br>\r
- Hide all windows related to the current alignment behind icons on the Jalview Desktop.\r
- </ul>\r
- </em></li>\r
- </ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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...<em> (only available if groovy is on the classpath)</em><br></strong>
+ <em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
+
+ </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