From be80bb1a8c747f67cfbaa0d73ac4f31c7cd1b9b9 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 5 Aug 2008 16:52:03 +0000 Subject: [PATCH] vamsas documentation --- help/help.jhm | 1 + help/helpTOC.xml | 5 +++++ help/html/vamsas/index.html | 45 +++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 help/html/vamsas/index.html diff --git a/help/help.jhm b/help/help.jhm index ad04f64..2e7bec7 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -88,6 +88,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 1762e22..75eb7df 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -6,6 +6,7 @@ + @@ -71,6 +72,10 @@ + + + + diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html new file mode 100644 index 0000000..ce2dffc --- /dev/null +++ b/help/html/vamsas/index.html @@ -0,0 +1,45 @@ + + +VAMSAS Interoperation + + +

VAMSAS Interoperation

+

Jalview can interact with other applications using + "the VAMSAS Interoperaton 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.
    • +
+
+ 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.

+

+ For further details, please check the VAMSAS website. The VAMSAS framework is implemented as a Java 1.4 Library and its source is will be released under the LGPL license. +  

+ + -- 1.7.10.2