X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fvamsas%2Findex.html;h=f2794b6a1a007a014e5d31179fec890a00c891ae;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d9b5cb80255a60fd16ba05aab4c55a269ae6d388;hpb=e641357d074cf8f3b9ee877f47879d6e22ac1ce1;p=jalview.git diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index d9b5cb8..f2794b6 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -1,119 +1,137 @@ - - -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.  

- - + + + +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.  

+ +