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

jprocter [Sun, 26 Mar 2006 17:07:33 +0000 (17:07 +0000)]

latest version is Beta. but we might change this :)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@214 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Sun, 26 Mar 2006 17:06:51 +0000 (17:06 +0000)]

added new constructor and File object accessor to make VamsasFile usable with VamsasArchive.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@213 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 24 Mar 2006 19:16:26 +0000 (19:16 +0000)]

fixed (hopefully) locking/read problems in test.simpleclient.VamsasArchive/Watcher classes and commented out the RandomAccess based reading/writing for mo.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@212 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 24 Mar 2006 19:13:22 +0000 (19:13 +0000)]

fixed leaky lock (answers todo about verifying that channel.close() should be called before lock.release())

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@211 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 24 Mar 2006 19:04:20 +0000 (19:04 +0000)]

new target - jar, and added an 'exclude' for Pierre's java5 vamav code (for the moment)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@210 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 24 Mar 2006 19:03:00 +0000 (19:03 +0000)]

simple test of locked IO based on ArchiveWatcher. Extend this to quickly incorporate vamsas dataset updates into a program (? really)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@209 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 24 Mar 2006 19:01:45 +0000 (19:01 +0000)]

commented out stream constructor for vamsasArchive.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@208 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Fri, 24 Mar 2006 15:40:31 +0000 (15:40 +0000)]

vamsas api example classes - AstexViewer@MSD-EBI

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@207 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 24 Mar 2006 10:21:36 +0000 (10:21 +0000)]

developing streamReader tests.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@206 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 23 Mar 2006 19:27:57 +0000 (19:27 +0000)]

still dealing with JarInputStream issues.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@205 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 23 Mar 2006 14:13:46 +0000 (14:13 +0000)]

fixed exception when trying to cancel unwritten archives.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@204 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 23 Mar 2006 14:10:51 +0000 (14:10 +0000)]

debug output - just incase strange things are happening when trying to read jars

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@203 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Thu, 23 Mar 2006 13:48:35 +0000 (13:48 +0000)]

fix call of the argument parsing - '!' missing

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@202 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 23 Mar 2006 11:41:09 +0000 (11:41 +0000)]

locking for windows (XP) partly debugged. ClientsFileTest watchers do not behave perfectly yet.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@201 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Wed, 22 Mar 2006 17:29:00 +0000 (17:29 +0000)]

'!' missing for testing if the session directory is readeable.

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jprocter [Wed, 22 Mar 2006 17:04:50 +0000 (17:04 +0000)]

more fixes for clientdocument/simpleclient. Testign the vamsasArchive reader and sessionfile mechanism (windows patches)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@199 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 22 Mar 2006 14:12:54 +0000 (14:12 +0000)]

finished the Appdata/ClientDocument update mechanism. Untested!

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@198 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 22 Mar 2006 14:12:12 +0000 (14:12 +0000)]

added new method for writing an AppData jar entry directly from an InputStream.
Also reprioritised some TODOs and made comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@197 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 21 Mar 2006 17:18:41 +0000 (17:18 +0000)]

intermediate cjeckin - nfs woes!

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@196 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 21 Mar 2006 11:59:49 +0000 (11:59 +0000)]

rearranged some todos and preparing to implement SimpleClient and ClientDocument IO stuff.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@195 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 21 Mar 2006 11:58:54 +0000 (11:58 +0000)]

refactored generally useful higher level document IO methods to base class.

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jprocter [Mon, 20 Mar 2006 22:57:05 +0000 (22:57 +0000)]

SimpleClientAppdata implemented but untested.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@193 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 20 Mar 2006 17:11:43 +0000 (17:11 +0000)]

half implemented the SimpleClientAppdata interface.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@192 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 20 Mar 2006 15:58:47 +0000 (15:58 +0000)]

added for completeness, but may not be necessary.

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pmarguerite [Mon, 20 Mar 2006 13:51:27 +0000 (13:51 +0000)]

Add object casting for instrospection methods

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@190 be28352e-c001-0410-b1a7-c7978e42abec

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pmarguerite [Mon, 20 Mar 2006 13:43:07 +0000 (13:43 +0000)]

Remove local file Jim local file path for the current working directory.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@189 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 20 Mar 2006 13:03:34 +0000 (13:03 +0000)]

debugging the org.vamsas.client.SessionUrn selection mechanism (also partial bits for simpleclientDocument stuff)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@188 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Sun, 19 Mar 2006 18:01:33 +0000 (18:01 +0000)]

removed todo

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jprocter [Fri, 17 Mar 2006 09:27:31 +0000 (09:27 +0000)]

renamed base class for all vamsas document objects (now org.vamsas.client.Vobject)
there may be some incorrectly modified javadocs in unrelated files.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@186 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 16 Mar 2006 18:02:21 +0000 (18:02 +0000)]

changed semaphore implementation and session modified flag.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@185 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 16 Mar 2006 18:00:51 +0000 (18:00 +0000)]

simplification of some events and clarification.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@184 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 16 Mar 2006 12:16:43 +0000 (12:16 +0000)]

added simple semaphore file mechanism for session directory.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@183 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 16 Mar 2006 11:18:02 +0000 (11:18 +0000)]

null sessionUrn parameter to create a new session

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jprocter [Wed, 15 Mar 2006 19:35:11 +0000 (19:35 +0000)]

adding various state flags for events

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@181 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 14 Mar 2006 19:24:40 +0000 (19:24 +0000)]

partly finished analysis of vamsas client session events.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@180 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 14 Mar 2006 19:24:39 +0000 (19:24 +0000)]

partly finished analysis of vamsas client session events.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@179 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 14 Mar 2006 18:47:43 +0000 (18:47 +0000)]

trivial typo

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jprocter [Tue, 14 Mar 2006 18:25:13 +0000 (18:25 +0000)]

extended clientfactory interface for session discovery and default session connection

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@177 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 14 Mar 2006 17:59:32 +0000 (17:59 +0000)]

reprioritising TODOs and LATERs and fixing documentation typos.

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jprocter [Tue, 24 Jan 2006 19:34:48 +0000 (19:34 +0000)]

removed unnecessary createdummyVamsasDocument private method.

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jprocter [Tue, 24 Jan 2006 19:31:49 +0000 (19:31 +0000)]

initial org.vamsas.client.IClientAppData implementation phase.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@174 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 24 Jan 2006 19:31:24 +0000 (19:31 +0000)]

fixed a slight bug in AppData entry searching, and introduced generic AppData entry searching methods.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@173 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 24 Jan 2006 19:23:12 +0000 (19:23 +0000)]

introduced org.vamsas.client.IClientAppData interface to get and set app-global and user-specific appdata chunks.

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jprocter [Tue, 24 Jan 2006 16:40:47 +0000 (16:40 +0000)]

fixed probable bug

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@171 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 24 Jan 2006 16:29:56 +0000 (16:29 +0000)]

updated example application to handle IClient.getDocument() exceptions and ensured IVorbaIdFactory actually has object reference for the object it is registering.

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jprocter [Tue, 24 Jan 2006 15:16:26 +0000 (15:16 +0000)]

parameterised the default empty document construction

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jprocter [Tue, 24 Jan 2006 14:56:22 +0000 (14:56 +0000)]

SimpleClient creates dummy documents.

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jprocter [Tue, 24 Jan 2006 14:49:18 +0000 (14:49 +0000)]

note about making default provenance entries at same time as ensuring all Vorba Ids are made.

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jprocter [Mon, 23 Jan 2006 19:10:43 +0000 (19:10 +0000)]

implementing minimal set : SimpleClientFactory createSession method -> SimpleClient -> SimpleDocument + events.

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jprocter [Mon, 23 Jan 2006 14:14:59 +0000 (14:14 +0000)]

beginning refactoring of locked IO for lists.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@165 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 23 Jan 2006 14:14:45 +0000 (14:14 +0000)]

beginning refactoring of locked IO for lists.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@164 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 23 Jan 2006 10:54:24 +0000 (10:54 +0000)]

clarified the getSessionUrn function and added new importDocument method

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jprocter [Mon, 23 Jan 2006 10:53:19 +0000 (10:53 +0000)]

added some more comments about event types/implementation

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jprocter [Mon, 23 Jan 2006 10:52:24 +0000 (10:52 +0000)]

added asFile method to get urn path as a file object.
Need to fix this to deal with local/non local urns.

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jprocter [Mon, 23 Jan 2006 10:34:06 +0000 (10:34 +0000)]

urn classes for different kinds of vamsas object.

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jprocter [Mon, 23 Jan 2006 10:13:23 +0000 (10:13 +0000)]

urn classes for different kinds of vamsas object.

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jprocter [Fri, 20 Jan 2006 18:03:29 +0000 (18:03 +0000)]

partially implemented simpleclient.EventGenerator

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jprocter [Fri, 20 Jan 2006 18:01:37 +0000 (18:01 +0000)]

added Appender for the VAMSAS session.

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jprocter [Fri, 20 Jan 2006 16:19:45 +0000 (16:19 +0000)]

comments and removed spurious todo:

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jprocter [Fri, 20 Jan 2006 15:22:15 +0000 (15:22 +0000)]

tidying IO.

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jprocter [Fri, 20 Jan 2006 12:00:23 +0000 (12:00 +0000)]

added overwrite flag to VamsasArchive writer class (avoids loss of locks on file deletion)

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jprocter [Fri, 20 Jan 2006 11:05:28 +0000 (11:05 +0000)]

VamsasArchive tested. Locked IO routines to be implemented in ArchiveFile

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jprocter [Fri, 20 Jan 2006 09:57:33 +0000 (09:57 +0000)]

removed after schema modification,

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jprocter [Fri, 20 Jan 2006 08:50:30 +0000 (08:50 +0000)]

more locked IO performance tests.

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jprocter [Thu, 19 Jan 2006 18:17:31 +0000 (18:17 +0000)]

introduced locked IO testing for Archive IO

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jprocter [Thu, 19 Jan 2006 18:17:04 +0000 (18:17 +0000)]

started on ClientDocument implementation and Locked IO tests for VamsasArchive

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jprocter [Thu, 19 Jan 2006 18:15:51 +0000 (18:15 +0000)]

added skeleton class for vorbaId methods and comments

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jprocter [Thu, 19 Jan 2006 13:32:33 +0000 (13:32 +0000)]

todo

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jprocter [Thu, 19 Jan 2006 12:12:42 +0000 (12:12 +0000)]

moved IClientDocument implementation into the simpleclient package.

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jprocter [Thu, 19 Jan 2006 12:12:04 +0000 (12:12 +0000)]

set correct get/Set VamsasRoots type, added addVamsasRoot, and some more TODOs

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jprocter [Thu, 19 Jan 2006 11:51:36 +0000 (11:51 +0000)]

generalised ArchiveReports functions to output on any stream.

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jprocter [Thu, 19 Jan 2006 11:31:56 +0000 (11:31 +0000)]

comments - explanation of bad heuristic that has to be fixed.

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jprocter [Tue, 17 Jan 2006 16:41:34 +0000 (16:41 +0000)]

added and tested simple document handling and update with test.ArchiveWriter.

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jprocter [Tue, 17 Jan 2006 12:17:30 +0000 (12:17 +0000)]

debugged VamsasArchive and rationalised debugging messages.

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jprocter [Tue, 17 Jan 2006 10:37:39 +0000 (10:37 +0000)]

fixed the User element and the form of the ApplicationData dataType.xsd definition.

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jprocter [Mon, 16 Jan 2006 20:25:49 +0000 (20:25 +0000)]

found cyclic dependency problems in schema and in VorbaId mechanism.

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jprocter [Mon, 16 Jan 2006 20:05:03 +0000 (20:05 +0000)]

minimally debugged idFactory and vorbaId mechanism. Inelegant!

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jprocter [Mon, 16 Jan 2006 11:19:16 +0000 (11:19 +0000)]

typo

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jprocter [Mon, 16 Jan 2006 10:25:52 +0000 (10:25 +0000)]

changed textual references for Class.class initializer for commons-logger

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jprocter [Mon, 16 Jan 2006 10:14:00 +0000 (10:14 +0000)]

refactored - Vorba object binding machinery and interfaces live in org.vamsas.client, specific clients now live in their own package.

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jprocter [Mon, 16 Jan 2006 09:37:30 +0000 (09:37 +0000)]

debug as far as test marshalling - a vorbaIdFactory is now required.

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jprocter [Sun, 15 Jan 2006 17:58:35 +0000 (17:58 +0000)]

debugging.

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jprocter [Sun, 15 Jan 2006 17:58:15 +0000 (17:58 +0000)]

debugging.

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jprocter [Sun, 15 Jan 2006 16:04:22 +0000 (16:04 +0000)]

minimal log.info output for commons-logging (commented out the specific org.vamsas logger so root logger takes precedence only)

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jprocter [Sun, 15 Jan 2006 13:18:21 +0000 (13:18 +0000)]

more verbose reports and demo VamsasDocument testing

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jprocter [Sun, 15 Jan 2006 13:17:45 +0000 (13:17 +0000)]

Controlled versionString vocabulary, newVamsasDocument construction methods and newAlignmentSequence methods

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jprocter [Fri, 13 Jan 2006 18:21:29 +0000 (18:21 +0000)]

save on nasty svn conflicts.

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jprocter [Fri, 13 Jan 2006 18:14:40 +0000 (18:14 +0000)]

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jprocter [Fri, 13 Jan 2006 18:14:04 +0000 (18:14 +0000)]

where packaged build will go

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jprocter [Fri, 13 Jan 2006 18:13:30 +0000 (18:13 +0000)]

eclipse builder

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jprocter [Fri, 13 Jan 2006 17:36:29 +0000 (17:36 +0000)]

refactored and incorporated basic io routines from vamsas web services stack.

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jprocter [Fri, 13 Jan 2006 16:35:54 +0000 (16:35 +0000)]

imported from the old vamsas webservices datatypes and adapted for new

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jprocter [Fri, 13 Jan 2006 16:35:09 +0000 (16:35 +0000)]

basic class defining symbol dictionaries

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jprocter [Fri, 13 Jan 2006 16:09:34 +0000 (16:09 +0000)]

more plus added VAMAS: tag for a policy decision

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jprocter [Fri, 13 Jan 2006 16:05:24 +0000 (16:05 +0000)]

added command line definition

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jprocter [Fri, 13 Jan 2006 15:52:34 +0000 (15:52 +0000)]

comments

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jprocter [Fri, 13 Jan 2006 15:50:56 +0000 (15:50 +0000)]

trivial

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jprocter [Fri, 13 Jan 2006 15:33:21 +0000 (15:33 +0000)]

trivial doc

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jprocter [Fri, 13 Jan 2006 15:26:52 +0000 (15:26 +0000)]

package for testing the core objects and their helper classes

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jprocter [Fri, 13 Jan 2006 15:24:25 +0000 (15:24 +0000)]

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@115 be28352e-c001-0410-b1a7-c7978e42abec