* 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>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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