-<html>\r
-<head>\r
-<title>VAMSAS Interoperation</title>\r
-</head>\r
-<body>\r
-<p><strong>VAMSAS Interoperation</strong></p>\r
-<p>Jalview can interact with other applications using\r
- "the <strong>VAMSAS Interoperaton framework</strong>" \r
- which is an experimental model for interoperation between \r
- bioinformatics applications (<strong>V</strong>isualization \r
- and <strong>A</strong>nalysis of <strong>Molecular</strong> \r
- <strong>S</strong>equences, <strong>Alignements</strong> \r
- 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. \r
- <p>VAMSAS enabled applications access\r
- a shared bioinformatics dataset containing sequences, alignments,\r
- annotation and trees, which can be represented by an XML document \r
- analogous to a <a href="../features/jalarchive.html">Jalview \r
- Project Archive</a>.</p>\r
-<br><strong>Connecting to a VAMSAS session</strong><br>\r
-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>.\r
-When the application is not connected to a session is active, the menu options are as follows:<br>\r
-<ul><li><em>Connect to an existing session</em><br>\r
- 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>\r
-<li><em>New VAMSAS Session</em><br>\r
- This option will create a new session on your computer.</li>\r
-<li><em>Load VAMSAS Session...</em><br> \r
- This option will open a file browser window allowing you to select a VAMSAS session archive from which a new session will be created.</li>\r
- </ul>\r
- <br>\r
- 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, \r
- 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.\r
- <br>\r
- <strong>Saving the current session</strong><br>\r
- 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.\r
- <strong>Leaving a VAMSAS session</strong><br>\r
- 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.\r
- <br>\r
- <strong>VAMSAS Session Persistence</strong><br>\r
- VAMSAS sessions are persistent - this means that they exist independently of any VAMSAS applications that are connected to them.\r
- 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>\r
- <strong>A quick Demo</strong><br>\r
- 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.\r
- <br>\r
- <table>\r
- <tr><td>Data Sharing Capability</td><td>Jalview Version</td>\r
- </tr>\r
- <tr><td>Alignments, sequences and annotation, trees, database references, cDNA/protein mappings.</td><td>2.4</td></tr>\r
- <tr><td>Mouseover location across linked DNA, protein and structure positions.</td><td>2.4</td></tr>\r
- <tr><td>Jalview project settings (Multiple views, groups, tree partitions, colouring, window positions)</td><td>2.4.1</td></tr>\r
- <tr><td>Sequence region and column selections</td><td>2.4.1</td></tr>\r
- </table> \r
- \r
- <p>\r
- 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 will be released under the LGPL license. \r
- </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * 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.
+ *
+ * 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>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>
git://source.jalview.org / jalview.git / blobdiff