X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fvamsas%2Findex.html;h=8341ed9fadb2c982b89a7a3568cc81641e0de4b9;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=ab31958cb7dc6733246b35236a78f4afc3a36f60;hpb=1d5612858f8384e57ff461990d8bafb149898073;p=jalview.git diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index ab31958..8341ed9 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -1,119 +1,158 @@ - - -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 -2.4.1. 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: +
+ +
+ 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.   +

+ +