-<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 "the <strong>VAMSAS\r
-Interoperation framework</strong>" which is an experimental model for\r
-interoperation between bioinformatics applications (<strong>V</strong>isualization\r
-and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,\r
-<strong>Alignements</strong> and <strong>S</strong>tructures).\r
-Currently, the only other VAMSAS enabled application is <a\r
- href="http://www.topali.org">TOPALi</a> - a user friendly program for\r
-phylogenetics and evolutionary analysis.\r
-<p>VAMSAS enabled applications access a shared bioinformatics\r
-dataset containing sequences, alignments, annotation and trees, which\r
-can be represented by an XML document analogous to a <a\r
- href="../features/jalarchive.html">Jalview Project Archive</a>.</p>\r
-<br>\r
-<strong>Connecting to a VAMSAS session</strong><br>\r
-The VAMSAS functionality in Jalview is accessed through the Desktop's <strong>Vamsas</strong>\r
-menu. The options available in this menu depend on whether the\r
-application is currently interacting with a VAMSAS dataset in a <strong>VAMSAS\r
-session</strong>. When the application is not connected to a session is active,\r
-the menu options are as follows:<br>\r
-<ul>\r
- <li><em>Connect to an existing session</em><br>\r
- If visible, this submenu contains a list of existing sessions that the\r
- VAMSAS framework has discovered on your computer. <br>\r
- 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\r
- VAMSAS session archive from which a new session will be created.<br />\r
- <em>New in 2.5</em>Sessions created from an imported document inherit\r
- the file or URL for the document.</li>\r
-\r
-</ul>\r
-<br>\r
-<strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to\r
-communicate between different programs. This means that after starting a\r
-session, your firewall software may ask you whether to allow the java\r
-executable access to the internet (port 53782). If you do not allow\r
-this, messages will not be exchanged with other VAMSAS applications.</br>\r
-<br>\r
-Once you have successfully connected to a VAMSAS session, any data made\r
-available by other VAMSAS applications will be automatically imported\r
-into Jalview. However, in order to share the data in Jalview with other\r
-VAMSAS applications, you must manually select the <strong>Vamsas→"Session\r
-Update"</strong> entry that is visible when a session is active. Selecting\r
-this option will update the VAMSAS session document, with the data\r
-loaded into Jalview. Any new alignments, trees and annotation will be\r
-written to the session, in addition to any edits you have made to data\r
-originally stored in the document. <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\r
-Update"</strong>. The file contains a snapshot of the current VAMSAS\r
-session, including data from any other applications connected to the\r
-session. <strong>Leaving a VAMSAS session</strong><br>\r
-A session can be disconnected from at any time using the <strong>Vamsas→"Stop\r
-Session"</strong> option. Selecting this option will only disconnect Jalview\r
-from the session - any other applications will remain connected to the\r
-session. If Jalview is the only application connected to the session and\r
-you have not yet saved the VAMSAS session then you will be prompted with\r
-an optional 'Save VAMSAS session...' dialog box, allowing the session to\r
-be saved and returned to at a later date. <br>\r
-<strong>VAMSAS Session Persistence</strong><br>\r
-VAMSAS sessions are persistent - this means that they exist\r
-independently of any VAMSAS applications that are connected to them.\r
-This means that if something goes wrong with a VAMSAS application and it\r
-crashes or otherwise fails, the VAMSAS session it is connected to will\r
-(hopefully) be unaffected. For instance, if Jalview is killed or crashes\r
-whilst it is still connected to a session, that session can be recovered\r
-in a new Jalview instance using the <strong>Vamsas→"Existing\r
-session"</strong> sub menu.</p>\r
-<strong>A quick Demo</strong>\r
-<br>\r
-Jalview can talk to itself through VAMSAS. Simply start two copies of\r
-the application, create a new vamsas session in one, and connect to the\r
-new session in the other. Then load your data into one of the\r
-applications, and use the\r
-<strong>Vamsas→"Session Update"</strong>\r
-menu entry to try to propagate the data to the other application.\r
-<br>\r
-<table>\r
- <tr>\r
- <td>Data Sharing Capability</td>\r
- <td>Jalview Version</td>\r
- </tr>\r
- <tr>\r
- <td>Alignments, sequences and annotation, trees, database\r
- references, cDNA/protein mappings.</td>\r
- <td>2.4</td>\r
- </tr>\r
- <tr>\r
- <td>Mouseover location across linked DNA, protein and structure\r
- positions.</td>\r
- <td>2.4</td>\r
- </tr>\r
- <tr>\r
- <td>Jalview project settings (Multiple views, groups, tree\r
- partitions, colouring, window positions)</td>\r
- <td>2.5</td>\r
- </tr>\r
- <tr>\r
- <td>Sequence region and column selections</td>\r
- <td>2.5</td>\r
- </tr>\r
-</table>\r
-<br />\r
-<p>Version 0.2 of the VAMSAS client library is used in <em>Jalview\r
-2.4.1</em>. For further details about the VAMSAS framework, please check the\r
-<a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS\r
-framework is implemented as a Java 1.4 Library and depends on a number\r
-of other open source projects. Its source is will be released under the\r
-LGPL license. </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<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