X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fvamsas%2Findex.html;h=ef234899331cef61e0d8cb4a00385c0aa861b30b;hb=7daa9e81a5e0c71271c1b135ff47cfa7bd367635;hp=ab31958cb7dc6733246b35236a78f4afc3a36f60;hpb=1d5612858f8384e57ff461990d8bafb149898073;p=jalview.git
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index ab31958..ef23489 100644
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+++ b/help/html/vamsas/index.html
@@ -1,119 +1,136 @@
-
-
-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 2.5Sessions 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
-2.4.1. 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 will be released under the
-LGPL license.
-
-
+
+
+
+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.
+
+