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

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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@331 be28352e-c001-0410-b1a7-c7978e42abec

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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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@328 be28352e-c001-0410-b1a7-c7978e42abec

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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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@321 be28352e-c001-0410-b1a7-c7978e42abec

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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.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@315 be28352e-c001-0410-b1a7-c7978e42abec

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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.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@313 be28352e-c001-0410-b1a7-c7978e42abec

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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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@312 be28352e-c001-0410-b1a7-c7978e42abec

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

added usage notes about removing specific object bindings

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@311 be28352e-c001-0410-b1a7-c7978e42abec

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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.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@310 be28352e-c001-0410-b1a7-c7978e42abec

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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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@304 be28352e-c001-0410-b1a7-c7978e42abec

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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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@303 be28352e-c001-0410-b1a7-c7978e42abec

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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).

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@302 be28352e-c001-0410-b1a7-c7978e42abec

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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

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@301 be28352e-c001-0410-b1a7-c7978e42abec

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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

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

refactored org to uk

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

broken refactoring

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

backtrack

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

refactored from org.vamsas to uk.ac.vamsas

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

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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

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

quick commit before refactoring

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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

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

Updated docs and logging for the picking api.

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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

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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.

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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.

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

IObjectUpdate interface introduction.

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

Mapping element added

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jprocter [Tue, 12 Dec 2006 23:52:36 +0000 (23:52 +0000)]

first round of todos for codefest

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jprocter [Tue, 12 Dec 2006 23:49:50 +0000 (23:49 +0000)]

basic ideas for per-object update interface

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jprocter [Tue, 12 Dec 2006 23:43:21 +0000 (23:43 +0000)]

added todo for making library automatically construct the user handle

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jprocter [Tue, 12 Dec 2006 11:02:13 +0000 (11:02 +0000)]

new stuff for vamsas hack.

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jprocter [Sun, 17 Sep 2006 14:42:32 +0000 (14:42 +0000)]

show vamsasId for aligments.

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jprocter [Sun, 17 Sep 2006 14:42:13 +0000 (14:42 +0000)]

tidier file locks - lock file is removed on JVM exit.

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jprocter [Sun, 17 Sep 2006 14:41:31 +0000 (14:41 +0000)]

ensured that hash binding vorbaIds is passed to client document object for vorba object lookup methods.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@244 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 13 Sep 2006 14:25:32 +0000 (14:25 +0000)]

jalview'esque vamsas session example for org.vamsas.test.simpleclient.ArchiveClient test model.

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jprocter [Wed, 13 Sep 2006 14:24:57 +0000 (14:24 +0000)]

bug fix to ensure valid and vorbaIds are generated and stored in vamsas object model

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@242 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 12 Sep 2006 10:20:55 +0000 (10:20 +0000)]

objects regenerated with valid schema (without excess id field cancelled in previous commit)

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jprocter [Tue, 12 Sep 2006 10:19:48 +0000 (10:19 +0000)]

removed excess id field (cancels previous commit)

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jprocter [Tue, 12 Sep 2006 10:07:11 +0000 (10:07 +0000)]

bugfixed org.vamsas.test.simpleclient.ArchiveClient and made VorbaId mechanism more rigorous.

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jprocter [Tue, 12 Sep 2006 10:04:04 +0000 (10:04 +0000)]

added id for RangeAnnotation types.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@238 be28352e-c001-0410-b1a7-c7978e42abec