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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
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 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.
+
+
+ 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.
+