jprocter [Mon, 8 Jun 2009 12:28:08 +0000 (12:28 +0000)]
displayed urn is either vamsasdocument reference or local simpleclient session reference
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@500
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 8 Jun 2009 12:27:23 +0000 (12:27 +0000)]
new URN hold external session URI and internal reference to physical session location
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@499
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 12 May 2009 13:55:58 +0000 (13:55 +0000)]
added GPLv3 as per LGPL requirements.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@498
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 7 May 2009 15:46:53 +0000 (15:46 +0000)]
updated eclipse resources (under ganymede) and tidied up license files.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@497
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 7 May 2009 15:36:04 +0000 (15:36 +0000)]
applied LGPLv3 and source code formatting.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@496
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 7 May 2009 15:32:01 +0000 (15:32 +0000)]
schema documentation autogenerated using Oxygen v10.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@495
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 12 Nov 2008 16:02:23 +0000 (16:02 +0000)]
added SelectionMessage, Properties.isValid methods, and bug-fixed exceptions generated with regard to unreferenced AppData jar entry IO
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@493
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 12 Nov 2008 15:58:18 +0000 (15:58 +0000)]
new Selection message. This still needs work!
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@492
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 12 Nov 2008 15:57:33 +0000 (15:57 +0000)]
added validation method to perform minimal check that message class implementation is consistent for receiving its own generated messages.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@491
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 12 Nov 2008 15:53:49 +0000 (15:53 +0000)]
fix minor exception when syncing document with appdata references when no appdata is written.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@490
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 12 Nov 2008 15:51:01 +0000 (15:51 +0000)]
added more types and type validation method
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@489
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 12 Nov 2008 15:49:22 +0000 (15:49 +0000)]
apache license for the commons-zip code used to read and write vamsas documents
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@488
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 5 Nov 2008 10:50:15 +0000 (10:50 +0000)]
Proper README and LICENCE inclusion in vamsas-client.jar and creation of new build objects : vamsas-client-docs.jar vamsas-client-src-doc.jar
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@487
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 5 Nov 2007 16:17:49 +0000 (16:17 +0000)]
try to set sessionmodified flag if the client document was actually modified.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@486
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 5 Nov 2007 16:17:14 +0000 (16:17 +0000)]
requesttoclose event is raised if session modified flag is set.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@485
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 19 Oct 2007 13:05:10 +0000 (13:05 +0000)]
made SimpleClientConfig externally configurable and added mechanism to prevent invalid documents being written to session.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@484
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 13:17:16 +0000 (13:17 +0000)]
apache zip has no FileName method.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@483
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 13:08:12 +0000 (13:08 +0000)]
legalass-coverage (for use of third party and modified apache zip classes)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@482
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 13:06:28 +0000 (13:06 +0000)]
hack to minimise IO interruption when SimpleClient.finalize() is called whilst document IO is being performed on the event generator thread (as currently observed in ExampleApplication)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@481
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 13:04:39 +0000 (13:04 +0000)]
ultraparanoid zip entry safename function
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@480
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 13:03:38 +0000 (13:03 +0000)]
Switched to using pure java Apache Zip implementation
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@479
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 13:02:31 +0000 (13:02 +0000)]
imported from ant 1.7 source distribution
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@478
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 12:58:36 +0000 (12:58 +0000)]
made finalize check before zeroing self-references in SimpleClient (this is only necessary if finalize is called explicitly). Also fixed typo in warning message
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@477
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 27 Sep 2007 12:55:18 +0000 (12:55 +0000)]
Added test to ensure all bytes are transferred during backupSessionFile
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@476
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 24 Sep 2007 16:14:18 +0000 (16:14 +0000)]
test for property type and property type constants
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@475
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 18 Sep 2007 10:26:12 +0000 (10:26 +0000)]
fixed pathological vamsas archive issue related to periods in appDataRef entries derived from AppUrns.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@474
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 18 Sep 2007 10:24:42 +0000 (10:24 +0000)]
really simple test for accessibility of a zip file (used to check for pathological vamsas archives that are created but cannot then be re-opened leading to all session data being lost after an update).
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@473
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 18 Sep 2007 10:20:25 +0000 (10:20 +0000)]
Java ZipFile code does not cope with entries with lots of consecutive '.' - causes 'Exception when opening ZipFile' within native code.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@472
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 18 Sep 2007 10:19:22 +0000 (10:19 +0000)]
added retry mechanism for opening of vamsas archives before it's assumed that the archive contains no data.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@471
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 18 Sep 2007 10:17:53 +0000 (10:17 +0000)]
note on occasional null pointer exceptions raised on JVM shutdown
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@470
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 18 Sep 2007 10:01:18 +0000 (10:01 +0000)]
added two tests to ensure a vamsasArchive is readable and accessible as a Jar File.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@469
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:51:16 +0000 (13:51 +0000)]
added openSession from Stored Document ClientFactory methods.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@468
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:49:19 +0000 (13:49 +0000)]
tidied command line interface (a bit) and implement test for session document import into a new session.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@467
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:48:50 +0000 (13:48 +0000)]
implement low level functions for initialising a new vamsas session with a copy of an existing session document.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@466
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:48:09 +0000 (13:48 +0000)]
moved methods for opening a stored session document in a new vamsas session into the VamsasSession.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@465
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:47:14 +0000 (13:47 +0000)]
implement new client factory methods to open a stored session document in a new vamsas session.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@464
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:46:19 +0000 (13:46 +0000)]
todo on importDocument (whether to exclude from interface for initial api release)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@463
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:45:34 +0000 (13:45 +0000)]
added new client factory methods to open a stored session document in a new session.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@462
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 14 Sep 2007 13:40:24 +0000 (13:40 +0000)]
set printRootInfo so root labels are not lost.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@461
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 11 Sep 2007 20:47:56 +0000 (20:47 +0000)]
un-necessary spaces for bootstrap separator in root node.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@460
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 11 Sep 2007 20:44:48 +0000 (20:44 +0000)]
bootstrap value parsing/recovery only for nodes with unquoted non-negative integer in node name or after a space separated node name field (bugfix for regexes when moved from Jalview to j1.4+ pattern matching)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@459
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 11 Sep 2007 16:55:03 +0000 (16:55 +0000)]
refactored initialisation of new session with existing document code.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@458
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 11 Sep 2007 15:10:02 +0000 (15:10 +0000)]
todo for importing stored session as a new session
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@457
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 11 Sep 2007 09:14:29 +0000 (09:14 +0000)]
ensure that document updates only occur if the vamsas objects have been changed or an appdata has been written.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@456
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 4 Sep 2007 14:39:59 +0000 (14:39 +0000)]
made serializable
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@455
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 31 Aug 2007 16:12:25 +0000 (16:12 +0000)]
formatting
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@454
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 31 Aug 2007 16:11:15 +0000 (16:11 +0000)]
refactoring to enable initialisation of session from an existing vamsas archive and bug fix to store session document in an external file.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@453
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 31 Aug 2007 13:10:09 +0000 (13:10 +0000)]
bugfix for new appdata writes not overwriting existing appdata if the client has not checked for their existence or accessed them.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@452
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 31 Aug 2007 09:58:09 +0000 (09:58 +0000)]
vamsas client build with new ClientFactory methods and moderately debugged appdata IO.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@451
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 31 Aug 2007 09:57:17 +0000 (09:57 +0000)]
flags for reading/writing client or user appdata only.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@450
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 31 Aug 2007 09:55:48 +0000 (09:55 +0000)]
added newSession methods to create a new vamsas session and connect to it.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@449
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 28 Aug 2007 15:16:09 +0000 (15:16 +0000)]
last core object source generation on...
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@448
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 28 Aug 2007 15:15:34 +0000 (15:15 +0000)]
notional testing of client and user app data read and writing
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@447
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 28 Aug 2007 15:14:31 +0000 (15:14 +0000)]
more rar friendly appdata reference name and uniqueness check,
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@446
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 22 Aug 2007 16:34:22 +0000 (16:34 +0000)]
hacked castor to be a bit faster (IdentitySet and log message concatenation fix)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@445
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 22 Aug 2007 16:15:06 +0000 (16:15 +0000)]
Removed clientfile watcher elements in attempt to remove any locks after client is finalized (and formatting).
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@444
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 22 Aug 2007 16:14:29 +0000 (16:14 +0000)]
attempts to remove any locks after client is finalized
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@443
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 22 Aug 2007 12:50:47 +0000 (12:50 +0000)]
fixed regex and made 'improper' support for parsing NHX style trees TODO: FIX THIS
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@442
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Wed, 22 Aug 2007 09:30:19 +0000 (09:30 +0000)]
better 'main' test and support creation of treenodes for all or just 'associated' binarynodes.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@441
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 21 Aug 2007 16:03:27 +0000 (16:03 +0000)]
beginning of 'simple' interface for newick string based tree representation
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@440
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 21 Aug 2007 16:02:54 +0000 (16:02 +0000)]
refactored and new methods for making and processing treenode vector for parsed newick string
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@439
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 21 Aug 2007 16:01:45 +0000 (16:01 +0000)]
refactored from newickfile
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@438
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 21 Aug 2007 12:43:54 +0000 (12:43 +0000)]
newickfile class moved into its own package ready for refactoring public methods into Trees class.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@437
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 21 Aug 2007 12:42:22 +0000 (12:42 +0000)]
new marshaller instance ensures we use marshalling properties and correct validation methods.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@436
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 17 Aug 2007 14:45:35 +0000 (14:45 +0000)]
formatting changes
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@435
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 17 Aug 2007 14:41:01 +0000 (14:41 +0000)]
safety checks and informational Errors generated when IClientDocument is not stored at end of handling an update. Attempts to properly close all session file handles on finalization (Clients.obj.lck still locked and VamDoc.jar still locked after finalize though).
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@434
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 17 Aug 2007 14:38:52 +0000 (14:38 +0000)]
TODO comments
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@433
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 17 Aug 2007 13:52:40 +0000 (13:52 +0000)]
new method to test if a particular file is or is related to the target of a lock
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@432
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 17 Aug 2007 13:22:08 +0000 (13:22 +0000)]
portability issue error messages
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@431
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 17 Aug 2007 09:48:43 +0000 (09:48 +0000)]
fixed update of existing appdata jar entry bug (raised a Duplicate zipEnty exception)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@430
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 16 Aug 2007 17:21:32 +0000 (17:21 +0000)]
refactored IClientAppdata and implementation has been minimally tested and bugfixed - still outstanding issues are when an app updates an Appdata already written to session (throws a DuplicateZipEntryException).
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@429
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 16 Aug 2007 17:20:15 +0000 (17:20 +0000)]
refactored AppData stream classes so they are returned from the IClientAppdata interface. This is not a great solution but at least makes the classes more usable for data IO.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@428
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 30 Jul 2007 14:19:50 +0000 (14:19 +0000)]
updated classpath for eclipse project
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@427
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 30 Jul 2007 14:17:24 +0000 (14:17 +0000)]
null pointer exception on attempt to release lock explicitly.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@426
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Sun, 15 Jul 2007 13:35:42 +0000 (13:35 +0000)]
vorbaId generator constructs valid ID strings (NCNames)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@425
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Fri, 29 Jun 2007 12:23:12 +0000 (12:23 +0000)]
0 to unbounded Dataset/Sequence/DbRef/Map elements. Allows alternate mappings between a sequence and its DbRef.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@424
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 20:17:38 +0000 (20:17 +0000)]
logic for debug message (if either or both mapped element has no defaults specified)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@423
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 20:16:43 +0000 (20:16 +0000)]
debug message for default mapping
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@422
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 20:12:32 +0000 (20:12 +0000)]
added mapType utilities.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@421
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 19:56:17 +0000 (19:56 +0000)]
imported utility classes for working with MapTypes from Jalview (v 2.3+ code)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@420
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:43:25 +0000 (14:43 +0000)]
quieter logging
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@419
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:42:33 +0000 (14:42 +0000)]
build on 28th June
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@418
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:41:19 +0000 (14:41 +0000)]
updated castor to castor-1.1-cycle
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@417
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:40:49 +0000 (14:40 +0000)]
prototype of Newick string parsing code and node binding utilities. Will be updated shortly with debugged routines from Jalview
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@416
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:38:55 +0000 (14:38 +0000)]
raise the DOCUMENT_REQUESTTOCLOSE event and debug output.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@415
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:38:02 +0000 (14:38 +0000)]
use the simpleClient's lockFactory for the client's lockfile to avoid platform dependent lock creation issues.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@414
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:37:02 +0000 (14:37 +0000)]
debugging on the haltWatch method
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@413
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:16:55 +0000 (14:16 +0000)]
use of config class
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@412
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:16:28 +0000 (14:16 +0000)]
beginnings of configuration settings class. Introduced to avoid validation overhead in castor-1.1-cycle-xml.jar
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@411
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:14:42 +0000 (14:14 +0000)]
modified warning for unresolved IDRef during castor un/marshalling. This message is unlikely to be observed if the cycle-patched castor is used
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@410
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:13:27 +0000 (14:13 +0000)]
added check for 'broken update' - where vamsas document file has been incorrectly written.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@409
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 14:12:30 +0000 (14:12 +0000)]
end position not correctly set.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@408
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 13:51:44 +0000 (13:51 +0000)]
sequence mappings and DbRef mapping objects unified and source binding for castor-1.1-cycle-xml.jar dependency
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@407
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 13:49:04 +0000 (13:49 +0000)]
cyclic IDREF patched castor-1.1.1 source
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@406
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Thu, 28 Jun 2007 13:11:26 +0000 (13:11 +0000)]
less verbose default logging
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@405
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 12 Jun 2007 14:42:02 +0000 (14:42 +0000)]
fixed regex to remove all kinds of file separators ('\' must be escaped correctly)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@404
be28352e-c001-0410-b1a7-
c7978e42abec
pmarguerite [Tue, 12 Jun 2007 10:40:53 +0000 (10:40 +0000)]
Added to mechanism to determine if a client closing is the last one of the session.
Each application creates a file with a lock on it in a subdirectory of the session.
When a client is closing, it checks if there is no other locked file.
If no file, it is the last one and closes the sessions.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@403
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Tue, 22 May 2007 15:16:26 +0000 (15:16 +0000)]
schema changes: provenance-entry-date is now an xmlSchema:dateTime bound directly to java.util.Date. Sequence and alignment sequence associated annotation takes an array of object references. Trees have a nodeMapping object to map between entities in the tree representation and objects in the document. Dataset sequences have Vxrefs which are named references to one or more other document objects.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@402
be28352e-c001-0410-b1a7-
c7978e42abec
jprocter [Mon, 21 May 2007 12:37:50 +0000 (12:37 +0000)]
log validation errors which cause the 'mergeRoots' call to fail.
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@401
be28352e-c001-0410-b1a7-
c7978e42abec
pmarguerite [Mon, 21 May 2007 09:56:26 +0000 (09:56 +0000)]
VamsasSession: increased time before considering the current client is the last one of the session (no modification on the client list).
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@400
be28352e-c001-0410-b1a7-
c7978e42abec
git://source.jalview.org / vamsas.git / log