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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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