X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fvamsas%2Findex.html;h=ef234899331cef61e0d8cb4a00385c0aa861b30b;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index e18e273..ef23489 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -1,7 +1,7 @@ + +VAMSAS Interoperation + + +

VAMSAS Interoperation

+

Jalview can interact with other applications using "the VAMSAS +Interoperation framework" which is an experimental model for +interoperation between bioinformatics applications (Visualization +and Analysis of Molecular Sequences, +Alignements and Structures). +Currently, the only other VAMSAS enabled application is TOPALi - a user friendly program for +phylogenetics and evolutionary analysis. +

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 Jalview Project Archive.

+
+Connecting to a VAMSAS session
+The VAMSAS functionality in Jalview is accessed through the Desktop's Vamsas +menu. The options available in this menu depend on whether the +application is currently interacting with a VAMSAS dataset in a VAMSAS +session. When the application is not connected to a session is active, +the menu options are as follows:
+ +
+VAMSAS and Firewalls: 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.
+
+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 Vamsas→"Session +Update" 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.
+Saving the current session
+You can save the current session as a VAMSAS Session archive using the Vamsas→"Session +Update". The file contains a snapshot of the current VAMSAS +session, including data from any other applications connected to the +session. Leaving a VAMSAS session
+A session can be disconnected from at any time using the Vamsas→"Stop +Session" 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.
+VAMSAS Session Persistence
+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 Vamsas→"Existing +session" sub menu.

+A quick Demo +
+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 +Vamsas→"Session Update" +menu entry to try to propagate the data to the other application. +
+ + + + + + + + + + + + + + + + + + + + + +
Data Sharing CapabilityJalview Version
Alignments, sequences and annotation, trees, database + references, cDNA/protein mappings.2.4
Mouseover location across linked DNA, protein and structure + positions.2.4
Jalview project settings (Multiple views, groups, tree + partitions, colouring, window positions)2.5
Sequence region and column selections2.5
+
+

Version 0.2 of the VAMSAS client library is used in Jalview +2.5. For further details about the VAMSAS framework, please check the +VAMSAS website. 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.  

+ +