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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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+<head>
+<title>VAMSAS Interoperation</title>
+</head>
+<body>
+<p><strong>VAMSAS Interoperation</strong></p>
+<p>Jalview can interact with other applications using "the <strong>VAMSAS
+Interoperation framework</strong>" which is an experimental model for
+interoperation between bioinformatics applications (<strong>V</strong>isualization
+and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
+<strong>Alignements</strong> and <strong>S</strong>tructures).
+Currently, the only other VAMSAS enabled application is <a
+ href="http://www.topali.org">TOPALi</a> - a user friendly program for
+phylogenetics and evolutionary analysis.
+<p>VAMSAS enabled applications access a shared bioinformatics
+dataset containing sequences, alignments, annotation and trees, which
+can be represented by an XML document analogous to a <a
+ href="../features/jalarchive.html">Jalview Project Archive</a>.</p>
+<br>
+<strong>Connecting to a VAMSAS session</strong><br>
+The VAMSAS functionality in Jalview is accessed through the Desktop's <strong>Vamsas</strong>
+menu. The options available in this menu depend on whether the
+application is currently interacting with a VAMSAS dataset in a <strong>VAMSAS
+session</strong>. When the application is not connected to a session is active,
+the menu options are as follows:<br>
+<ul>
+ <li><em>Connect to an existing session</em><br>
+ If visible, this submenu contains a list of existing sessions that the
+ VAMSAS framework has discovered on your computer. <br>
+ Choose one to connect to it.</li>
+ <li><em>New VAMSAS Session</em><br>
+ This option will create a new session on your computer.</li>
+ <li><em>Load VAMSAS Session...</em><br>
+ This option will open a file browser window allowing you to select a
+ VAMSAS session archive from which a new session will be created.<br/>
+ <em>New in 2.5:</em>Sessions created from an imported document inherit
+ the file or URL for the document.</li>
+
+</ul>
+<br>
+<strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to
+communicate between different programs. This means that after starting a
+session, your firewall software may ask you whether to allow the java
+executable access to the internet (port 53782). If you do not allow
+this, messages will not be exchanged with other VAMSAS applications.</br>
+<br>
+Once you have successfully connected to a VAMSAS session, any data made
+available by other VAMSAS applications will be automatically imported
+into Jalview. However, in order to share the data in Jalview with other
+VAMSAS applications, you must manually select the <strong>Vamsas→"Session
+Update"</strong> entry that is visible when a session is active. Selecting
+this option will update the VAMSAS session document, with the data
+loaded into Jalview. Any new alignments, trees and annotation will be
+written to the session, in addition to any edits you have made to data
+originally stored in the document. <br>
+<strong>Saving the current session</strong><br>
+You can save the current session as a VAMSAS Session archive using the <strong>Vamsas→"Session
+Update"</strong>. The file contains a snapshot of the current VAMSAS
+session, including data from any other applications connected to the
+session. <strong>Leaving a VAMSAS session</strong><br>
+A session can be disconnected from at any time using the <strong>Vamsas→"Stop
+Session"</strong> option. Selecting this option will only disconnect Jalview
+from the session - any other applications will remain connected to the
+session. If Jalview is the only application connected to the session and
+you have not yet saved the VAMSAS session then you will be prompted with
+an optional 'Save VAMSAS session...' dialog box, allowing the session to
+be saved and returned to at a later date. <br>
+<strong>VAMSAS Session Persistence</strong><br>
+VAMSAS sessions are persistent - this means that they exist
+independently of any VAMSAS applications that are connected to them.
+This means that if something goes wrong with a VAMSAS application and it
+crashes or otherwise fails, the VAMSAS session it is connected to will
+(hopefully) be unaffected. For instance, if Jalview is killed or crashes
+whilst it is still connected to a session, that session can be recovered
+in a new Jalview instance using the <strong>Vamsas→"Existing
+session"</strong> sub menu.</p>
+<strong>A quick Demo</strong>
+<br>
+Jalview can talk to itself through VAMSAS. Simply start two copies of
+the application, create a new vamsas session in one, and connect to the
+new session in the other. Then load your data into one of the
+applications, and use the
+<strong>Vamsas→"Session Update"</strong>
+menu entry to try to propagate the data to the other application.
+<br>
+<table>
+ <tr>
+ <td>Data Sharing Capability</td>
+ <td>Jalview Version</td>
+ </tr>
+ <tr>
+ <td>Alignments, sequences and annotation, trees, database
+ references, cDNA/protein mappings.</td>
+ <td>2.4</td>
+ </tr>
+ <tr>
+ <td>Mouseover location across linked DNA, protein and structure
+ positions.</td>
+ <td>2.4</td>
+ </tr>
+ <tr>
+ <td>Jalview project settings (Multiple views, groups, tree
+ partitions, colouring, window positions)</td>
+ <td>2.5</td>
+ </tr>
+ <tr>
+ <td>Sequence region and column selections</td>
+ <td>2.5</td>
+ </tr>
+</table>
+<br />
+<p>Version 0.2 of the VAMSAS client library is used in <em>Jalview
+2.5</em>. For further details about the VAMSAS framework, please check the
+<a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS
+framework is implemented as a Java 1.4 Library and depends on a number
+of other open source projects. Its source is released under the
+LGPL license. </p>
+</body>
+</html>
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