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:
- Connect to an existing session
If visible, this submenu contains a list of existing sessions that the
VAMSAS framework has discovered on your computer.
Choose one to connect to it.
- New VAMSAS Session
This option will create a new session on your computer.
- Load VAMSAS Session...
This option will open a file browser window allowing you to select a
VAMSAS session archive from which a new session will be created.
New in 2.5:Sessions created from an imported document inherit
the file or URL for the document.
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
menu entry to try to propagate the data to the other application.
|Data Sharing Capability
|Alignments, sequences and annotation, trees, database
references, cDNA/protein mappings.
|Mouseover location across linked DNA, protein and structure
|Jalview project settings (Multiple views, groups, tree
partitions, colouring, window positions)
|Sequence region and column selections
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