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

jprocter [Fri, 19 Feb 2010 10:35:24 +0000 (10:35 +0000)]

java 1.5 build of vamsas client v0.2

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@518 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 19 Feb 2010 09:34:29 +0000 (09:34 +0000)]

verson 0.2 LGPL licensed jar for java 1.4

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@517 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 19 Feb 2010 09:24:11 +0000 (09:24 +0000)]

formatting

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@516 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 19 Feb 2010 09:22:11 +0000 (09:22 +0000)]

bugfix and new containment test method from jalview.utils.MapList in jalview 2.4 branch

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@515 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 15:37:57 +0000 (15:37 +0000)]

verson 0.2 LGPL licensed source and jars

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@514 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 15:35:30 +0000 (15:35 +0000)]

line rather than class output for info messages

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@513 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 13:46:17 +0000 (13:46 +0000)]

SAXTreeViewer requires java 1.5 or later.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@512 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 12:08:50 +0000 (12:08 +0000)]

vamsas API version 0.2 - allow new sessions or imported sessions to be created with a given session name

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@511 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 12:06:23 +0000 (12:06 +0000)]

flag for suppressing unresolved xmlId warnings

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@510 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 12:05:58 +0000 (12:05 +0000)]

suppress unresolved xmlId warnings for initial unmarshalling of vamsas document

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@509 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 12:03:20 +0000 (12:03 +0000)]

removed Appdata test TODO

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@508 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 12:00:27 +0000 (12:00 +0000)]

supress occasional null pointer exceptions (unverified fix)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@507 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 11:58:16 +0000 (11:58 +0000)]

efficiency

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@506 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 18 Feb 2010 11:53:36 +0000 (11:53 +0000)]

empty selection message not terminated with '\n'

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@505 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 8 Jun 2009 12:30:46 +0000 (12:30 +0000)]

use simpleclientsession handle rather than bare sessionhandle

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@504 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 8 Jun 2009 12:30:03 +0000 (12:30 +0000)]

locate first session or sessions for a given URN

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@503 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 8 Jun 2009 12:29:19 +0000 (12:29 +0000)]

locate simpleclientsession handle for any session URN

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@502 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 8 Jun 2009 12:28:41 +0000 (12:28 +0000)]

store simpleclientsession handle rather than bare sessionhandle

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@501 be28352e-c001-0410-b1a7-c7978e42abec

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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jprocter [Fri, 17 Aug 2007 14:45:35 +0000 (14:45 +0000)]

formatting changes

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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

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jprocter [Fri, 17 Aug 2007 14:38:52 +0000 (14:38 +0000)]

TODO comments

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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