source.jalview.org Git - vamsas.git/log

imilne [Wed, 7 Mar 2007 11:09:07 +0000 (11:09 +0000)]

Added shutdown() methods for the socket-based PickManager code.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@350 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 6 Mar 2007 12:57:09 +0000 (12:57 +0000)]

stub for the dom tree update event generator.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@349 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 6 Mar 2007 12:56:31 +0000 (12:56 +0000)]

added PickManager test code. Current state of library means this example app fails to shutdown after three instances have been started.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@348 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 6 Mar 2007 12:55:46 +0000 (12:55 +0000)]

synchronized methods to ensure thread safety for underlying SimplePickManager code. (not successful yet!)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@347 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 27 Feb 2007 22:19:12 +0000 (22:19 +0000)]

ensured single instance of vamsasarchive io handler to prevent lock contention.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@346 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 12 Feb 2007 14:33:21 +0000 (14:33 +0000)]

non-1.4 factory construtors removed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@345 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 2 Feb 2007 17:45:52 +0000 (17:45 +0000)]

Added generateClientUrn method to generate a urn from client name and version. Ensures that the client urn is generated, when one of the attribute is modified. And, add support for null attribute in the equals method

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@344 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 2 Feb 2007 17:39:51 +0000 (17:39 +0000)]

Avoid creation of ClientHandle and UserHandle objects with null attributes. Otherwise, problem with null pointer exception.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@343 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:54:01 +0000 (15:54 +0000)]

log config (with SESSIONLOG config too).
Need to separate SESSIONLOG in future.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@342 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:51:15 +0000 (15:51 +0000)]

SimpleClient implementation testable against uk.ac.vamsas.test.ExampleApplication

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@341 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:47:39 +0000 (15:47 +0000)]

fixed bug leaving copies of archive backups (no testcase for this)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@340 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:46:10 +0000 (15:46 +0000)]

extended to test against SimpleClient implementation

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@339 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:42:39 +0000 (15:42 +0000)]

added TODO for testing getAppData method before migration to simpleClient.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@338 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:39:22 +0000 (15:39 +0000)]

untested watcherElement for spotting changes in SessionFlagFile presence/absence.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@337 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:38:15 +0000 (15:38 +0000)]

formal polling thread for particular FileWatcher types (VamsasFile or SessionFile style)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@336 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:35:44 +0000 (15:35 +0000)]

method to get File object being watched

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@335 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:34:27 +0000 (15:34 +0000)]

fixed subtle bug in closeChannel behaviour on lock release and debug logging.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@334 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:26:43 +0000 (15:26 +0000)]

wrapper for conditionally passing picks onto the client application

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@333 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 15:26:11 +0000 (15:26 +0000)]

added (broken) haltPickManager methods

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@332 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 12 Jan 2007 13:29:45 +0000 (13:29 +0000)]

refactoring org->uk.ac

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pmarguerite [Fri, 5 Jan 2007 19:01:15 +0000 (19:01 +0000)]

VamsasSession: Fixed VamsasSession init/construction if the session directory exists and do not contains session files.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@330 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Thu, 4 Jan 2007 15:45:53 +0000 (15:45 +0000)]

when closing session, closes each associated VAMAV clients

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@329 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 15 Dec 2006 17:32:41 +0000 (17:32 +0000)]

more refactoring fallout

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pmarguerite [Fri, 15 Dec 2006 16:13:25 +0000 (16:13 +0000)]

Updated simple client sessionURN to use URI instead of URL to generate SessionURN (URI) from the session directory path (file location or vamsas session).
Updated SimpleClient to match modified constructor (MalformedURL not throw anymore)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@327 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 15 Dec 2006 15:58:04 +0000 (15:58 +0000)]

SessionURN fix asFile method now create the File object from the URI

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@326 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 15 Dec 2006 15:47:37 +0000 (15:47 +0000)]

Added TestSessionURN: to test the creation of a sessionURN and to retrieve a correct file from it.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@325 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 15 Dec 2006 15:46:51 +0000 (15:46 +0000)]

SessionUrn: modified to scope with windows (space ... in file name. Use URI instead of URL

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@324 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Fri, 15 Dec 2006 15:09:28 +0000 (15:09 +0000)]

Modified CustomMessage.java so that tabs are used to separate message elements rather than underscores.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@323 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Fri, 15 Dec 2006 15:08:57 +0000 (15:08 +0000)]

Modified MouseOverMessage.java so that tabs are used to separate message elements rather than underscores.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@322 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 15 Dec 2006 15:07:30 +0000 (15:07 +0000)]

SessionHandle: added equals method to compare SessionHandles, based on the sessionUrn

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pmarguerite [Fri, 15 Dec 2006 15:06:25 +0000 (15:06 +0000)]

amsasSession: added addClient and removeClient to add and remove a client to/from the session client list.
Attached (as attribute) a SessionManager

Removes the currentSession of the active session list, if the client to removed is the last one of the list

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@320 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 15 Dec 2006 15:03:10 +0000 (15:03 +0000)]

Moves sessionFile management to SimpleSessionManager calling SessionsFile class (dealing directly with the file)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@319 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 15 Dec 2006 15:01:43 +0000 (15:01 +0000)]

SimpleClient: remove client of the session client list when closing/finalizing (finalizeClient method)
added get_session() to retrieve current vamsas session

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@318 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Fri, 15 Dec 2006 13:53:29 +0000 (13:53 +0000)]

Added comment about handling messages in the GUI event thread.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@317 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Fri, 15 Dec 2006 13:49:52 +0000 (13:49 +0000)]

Added getter methods to the MouseOverMessage class.
Added code to MouseOverMessage.java so it can reconstruct the message object from the raw data stream.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@316 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 15 Dec 2006 12:05:06 +0000 (12:05 +0000)]

internal flags for added and updated since last read for Vobjects tested with ArchiveClient code.

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imilne [Fri, 15 Dec 2006 11:52:41 +0000 (11:52 +0000)]

Checked in the document update handler interface and a concrete implementation of it (that contains empty methods).

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@314 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Fri, 15 Dec 2006 11:27:30 +0000 (11:27 +0000)]

Commented out all logging messages from the pick code to speed up message transfer.

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jprocter [Fri, 15 Dec 2006 11:12:32 +0000 (11:12 +0000)]

added a getter for the pickhandler interface in IClient

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jprocter [Fri, 15 Dec 2006 11:10:55 +0000 (11:10 +0000)]

added usage notes about removing specific object bindings

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jprocter [Fri, 15 Dec 2006 11:07:07 +0000 (11:07 +0000)]

extracted from the jalview.io.VamsasDatastore bindjv2obj and associated methods.

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pmarguerite [Fri, 15 Dec 2006 09:24:24 +0000 (09:24 +0000)]

SessionUrn: added a constructor to build a SessionURN from a String

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@309 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 15 Dec 2006 09:04:32 +0000 (09:04 +0000)]

javadoc not updated for refactored packages.

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pmarguerite [Thu, 14 Dec 2006 21:18:21 +0000 (21:18 +0000)]

created setURN to generated sessionUrn from a urn as String. Allow to be replaced by an inheriting class

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pmarguerite [Thu, 14 Dec 2006 21:15:09 +0000 (21:15 +0000)]

SessionHandle: made SessionHandle serializable to be able to store it into file

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pmarguerite [Thu, 14 Dec 2006 21:14:12 +0000 (21:14 +0000)]

SessionHandle: made SessionHandle serializable to be able to store it into file

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pmarguerite [Thu, 14 Dec 2006 21:13:31 +0000 (21:13 +0000)]

VamsasSession Fix session constructor/initialisation if the session directory already exists

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pmarguerite [Thu, 14 Dec 2006 21:13:03 +0000 (21:13 +0000)]

SimpleClientFactory Added support to create a IClient for a given Session to a given session URN

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imilne [Thu, 14 Dec 2006 19:29:20 +0000 (19:29 +0000)]

Picking API now has message classes and basic implementation of interfaces (for its own implementation and client-app message handling implementation).

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pmarguerite [Thu, 14 Dec 2006 19:21:21 +0000 (19:21 +0000)]

Fix session constructor/initialisation if the session directory already exists

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jprocter [Thu, 14 Dec 2006 19:07:00 +0000 (19:07 +0000)]

changed vamsasDocument and vamsas types namespaces.

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jprocter [Thu, 14 Dec 2006 18:58:50 +0000 (18:58 +0000)]

refactored org to uk

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jprocter [Thu, 14 Dec 2006 18:58:27 +0000 (18:58 +0000)]

refactored org to uk

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jprocter [Thu, 14 Dec 2006 18:57:20 +0000 (18:57 +0000)]

refactored org to uk

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jprocter [Thu, 14 Dec 2006 18:52:17 +0000 (18:52 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:51:35 +0000 (18:51 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:50:31 +0000 (18:50 +0000)]

refactoring org to uk - never use f**ng eclipse

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jprocter [Thu, 14 Dec 2006 18:49:23 +0000 (18:49 +0000)]

refactoring org to uk - never use f**ng eclipse

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jprocter [Thu, 14 Dec 2006 18:49:07 +0000 (18:49 +0000)]

refactoring org to uk - never use f**ng eclipse

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jprocter [Thu, 14 Dec 2006 18:48:08 +0000 (18:48 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:47:51 +0000 (18:47 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:47:18 +0000 (18:47 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:43:00 +0000 (18:43 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:42:43 +0000 (18:42 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:41:20 +0000 (18:41 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:40:16 +0000 (18:40 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:39:48 +0000 (18:39 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:27:53 +0000 (18:27 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:27:16 +0000 (18:27 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:26:15 +0000 (18:26 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:20:51 +0000 (18:20 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:18:43 +0000 (18:18 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:18:26 +0000 (18:18 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:17:24 +0000 (18:17 +0000)]

refactoring org to uk

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jprocter [Thu, 14 Dec 2006 18:16:54 +0000 (18:16 +0000)]

refactored org to uk

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jprocter [Thu, 14 Dec 2006 18:16:15 +0000 (18:16 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@275 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 18:16:14 +0000 (18:16 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@274 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 18:08:11 +0000 (18:08 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@273 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 18:05:40 +0000 (18:05 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@272 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:54:15 +0000 (17:54 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@271 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:52:40 +0000 (17:52 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@270 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:52:15 +0000 (17:52 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@269 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:51:17 +0000 (17:51 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@268 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:50:39 +0000 (17:50 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@267 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:50:38 +0000 (17:50 +0000)]

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@266 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:44:21 +0000 (17:44 +0000)]

broken refactoring

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@265 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:42:54 +0000 (17:42 +0000)]

backtrack

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@264 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:15:29 +0000 (17:15 +0000)]

refactored from org.vamsas to uk.ac.vamsas

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@263 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:11:07 +0000 (17:11 +0000)]

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@262 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 17:08:32 +0000 (17:08 +0000)]

refactored from org.vamsas to uk.ac.vamsas

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@261 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 16:40:55 +0000 (16:40 +0000)]

remove old ebi packages

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@260 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 16:21:49 +0000 (16:21 +0000)]

quick commit before refactoring

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@259 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Thu, 14 Dec 2006 16:19:27 +0000 (16:19 +0000)]

added SimpleClientFactory implementation and new class SessionsFile to deal with the list of active sessions

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@258 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Thu, 14 Dec 2006 16:15:36 +0000 (16:15 +0000)]

Updated docs and logging for the picking api.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@257 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 12:26:59 +0000 (12:26 +0000)]

modifiable attribute is now a string rather than a boolean. See 'locks' type documentation in vamsas.xsd

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@256 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Thu, 14 Dec 2006 11:56:17 +0000 (11:56 +0000)]

Picking code updated with full basic implementation of message sending and server restart code.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@255 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 14 Dec 2006 10:25:25 +0000 (10:25 +0000)]

refactored mapping to mapList type in both DbRef and SeqType object.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@254 be28352e-c001-0410-b1a7-c7978e42abec

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imilne [Wed, 13 Dec 2006 17:03:37 +0000 (17:03 +0000)]

First check-in of the picking api.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@253 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 13 Dec 2006 16:45:02 +0000 (16:45 +0000)]

IObjectUpdate interface introduction.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@252 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Wed, 13 Dec 2006 16:32:21 +0000 (16:32 +0000)]

Mapping element added

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@251 be28352e-c001-0410-b1a7-c7978e42abec