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-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:
-
-
- - 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
- Vamsas→"Session Update" menu entry
- to try to propagate the data to the other application.
-
-
- | Data Sharing Capability |
- Jalview 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 selections |
- 2.5 |
-
-
-
-
- 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.
-
-
-