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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
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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>
+ <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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