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

amwaterhouse [Thu, 3 Nov 2005 11:12:28 +0000 (11:12 +0000)]

Application data has choice of data or dataRef

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@86 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 2 Nov 2005 16:11:46 +0000 (16:11 +0000)]

refactored common locked IO methods from ClientsFile to SessionFile

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@85 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 2 Nov 2005 15:31:53 +0000 (15:31 +0000)]

doc comment about lock holding across session client processes.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@84 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 2 Nov 2005 15:21:39 +0000 (15:21 +0000)]

propagate changes from schema update.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@83 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 1 Nov 2005 17:42:25 +0000 (17:42 +0000)]

creates and holds all the watcher/io objects for a session.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@82 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 1 Nov 2005 17:41:36 +0000 (17:41 +0000)]

partially updated comments (and repurposing of class).

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@81 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 28 Oct 2005 16:03:13 +0000 (16:03 +0000)]

refactored documentHandler to VamsasFile to indicate similarity with ClientFile handler class.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@80 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Fri, 28 Oct 2005 12:50:10 +0000 (12:50 +0000)]

DatasetAnnotations begin and end set as integers

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@79 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 27 Oct 2005 17:03:51 +0000 (17:03 +0000)]

javadoc typo

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@78 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 25 Oct 2005 13:28:45 +0000 (13:28 +0000)]

added more extantLock methods and test for clientList monitoring (using FileWatcher.setState())

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@77 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 24 Oct 2005 16:01:07 +0000 (16:01 +0000)]

typo fix.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@76 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 24 Oct 2005 13:32:28 +0000 (13:32 +0000)]

new fileWatcher method passes lock for changed file back to the caller.
ClientsFile methods extended to take an existing lock as a parameter.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@75 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 24 Oct 2005 13:31:23 +0000 (13:31 +0000)]

added automatic channel closure for failed locks. (suggest this class becomes a singleton?)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@74 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 24 Oct 2005 10:10:02 +0000 (10:10 +0000)]

forgot to release a trial lock that failed.
Should consider automatically closing/releasing if lock fails.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@73 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Sat, 22 Oct 2005 21:58:11 +0000 (21:58 +0000)]

debugged fileWatcher logic and Lock release function.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@72 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 20 Oct 2005 16:51:28 +0000 (16:51 +0000)]

better time delay in command execution.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@71 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 20 Oct 2005 10:16:16 +0000 (10:16 +0000)]

fixed change test.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@70 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 20 Oct 2005 10:06:36 +0000 (10:06 +0000)]

better builder

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@69 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 20 Oct 2005 10:00:35 +0000 (10:00 +0000)]

added better check for file change (length + last modified)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@68 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 20 Oct 2005 09:58:13 +0000 (09:58 +0000)]

slackened lock_release success requirement.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@67 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Fri, 14 Oct 2005 15:45:59 +0000 (15:45 +0000)]

Dataset should not contain gaps

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@66 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 12 Oct 2005 15:41:53 +0000 (15:41 +0000)]

franks data and topali analysis

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@65 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 12 Oct 2005 15:36:46 +0000 (15:36 +0000)]

updated core objects from latest schema (dbRef)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@64 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Wed, 12 Oct 2005 10:57:01 +0000 (10:57 +0000)]

Dbref attributes are of type string

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@63 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 12 Oct 2005 10:46:59 +0000 (10:46 +0000)]

modified FileWatcher to only register file change after a lock release (incurs a momentary file lock).
tested multi-process watching.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@62 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 11 Oct 2005 21:15:55 +0000 (21:15 +0000)]

ClientsFileTest debugged and verified.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@61 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 11 Oct 2005 17:35:29 +0000 (17:35 +0000)]

added test config for eclipse

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@60 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 11 Oct 2005 17:34:09 +0000 (17:34 +0000)]

test clientsFile handlers.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@59 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 11 Oct 2005 09:57:51 +0000 (09:57 +0000)]

quick update

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@58 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 11 Oct 2005 09:57:32 +0000 (09:57 +0000)]

quick update

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@57 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Sat, 8 Oct 2005 09:22:45 +0000 (09:22 +0000)]

accidental deletion of vamsas Client build config (now renamed)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@56 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 7 Oct 2005 15:14:53 +0000 (15:14 +0000)]

random bits and pieces whilst in hamburg - beginnings of file handliongimpmementation.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@55 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Thu, 6 Oct 2005 15:54:00 +0000 (15:54 +0000)]

Provenance must contain 1 entry, Alignment may have multiple AlignmentAnnotations

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@54 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Sun, 25 Sep 2005 19:02:11 +0000 (19:02 +0000)]

implemented state flags and automatic call to VorbaIdFactory for unregistered (but registerable) vamsas objects.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@53 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 23 Sep 2005 17:43:17 +0000 (17:43 +0000)]

refactored schema (SequenceSet to DataSet and SequenceSetAnnotation to DataSetAnnotation).
More client implementation.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@52 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 23 Sep 2005 09:19:39 +0000 (09:19 +0000)]

added a pollUpdate method to kick the vamsas Document watcher thread when the application wants to be immediatly informed of a document update.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@51 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 22 Sep 2005 22:07:22 +0000 (22:07 +0000)]

event handler.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@50 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 22 Sep 2005 21:58:56 +0000 (21:58 +0000)]

refactored Client to simpleClient. Implemented many housekeeping functions.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@49 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 22 Sep 2005 16:17:33 +0000 (16:17 +0000)]

part implementation of simpleClient and refactoring of ClientDocument.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@48 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 22 Sep 2005 09:56:36 +0000 (09:56 +0000)]

added sourcegen entry for the vamsasDocument.xsd objects.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@47 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Thu, 22 Sep 2005 09:56:04 +0000 (09:56 +0000)]

created new schema to define the document XML file. Added two well formed schema examples.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@46 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 19:12:04 +0000 (19:12 +0000)]

made vamsas a proper root element in schema and added example document.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@45 be28352e-c001-0410-b1a7-c7978e42abec

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amwaterhouse [Tue, 20 Sep 2005 16:53:30 +0000 (16:53 +0000)]

Optional instead of min/max

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@44 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 16:41:10 +0000 (16:41 +0000)]

builder for eclipse

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@43 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 16:40:43 +0000 (16:40 +0000)]

changed vamsas.xsd filename.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@42 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 16:40:23 +0000 (16:40 +0000)]

transient file.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@41 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 16:38:27 +0000 (16:38 +0000)]

refactored to vamsas.xsd

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@40 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 16:37:09 +0000 (16:37 +0000)]

renamed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@39 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 16:33:50 +0000 (16:33 +0000)]

latest schema.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@38 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 10:13:56 +0000 (10:13 +0000)]

objects from refactored schema.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@37 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 10:00:58 +0000 (10:00 +0000)]

move to new eclipse version.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@36 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 09:49:07 +0000 (09:49 +0000)]

updated builders

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@35 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 09:48:35 +0000 (09:48 +0000)]

more comments.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@34 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 09:42:33 +0000 (09:42 +0000)]

refactored tree type to avoid conflicts.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@33 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Tue, 20 Sep 2005 09:42:13 +0000 (09:42 +0000)]

added source generator and builder

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@32 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 23:31:25 +0000 (23:31 +0000)]

updated to castor-0.9.9M2 and added some comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@31 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 23:26:31 +0000 (23:26 +0000)]

tried to resolve some namespace clashes and add xs:ID attributes where necessary.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@30 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 23:25:22 +0000 (23:25 +0000)]

updated to castor-0.9.9M2

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@29 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 18:16:16 +0000 (18:16 +0000)]

making more relocatable.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@28 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 18:13:52 +0000 (18:13 +0000)]

regenerate core objects

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@27 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 18:08:43 +0000 (18:08 +0000)]

renamed getId to avoid clashes.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@26 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 18:06:07 +0000 (18:06 +0000)]

changed sourcegenerator destination package

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@25 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 18:05:18 +0000 (18:05 +0000)]

refactored core objects and regenerated.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@24 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 16:19:59 +0000 (16:19 +0000)]

needed for castor sourcegenerator.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@23 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 16:19:41 +0000 (16:19 +0000)]

added castor sourcegenerator task.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@22 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 16:19:17 +0000 (16:19 +0000)]

default generation using sourcegen schema.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@21 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 14:19:27 +0000 (14:19 +0000)]

directory for runtime dependencies and non-java class data.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@20 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 14:15:55 +0000 (14:15 +0000)]

ant based sourcegen task

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@19 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 13:24:13 +0000 (13:24 +0000)]

log4j

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@18 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 13:20:36 +0000 (13:20 +0000)]

first attempt at object build.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@17 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 13:15:24 +0000 (13:15 +0000)]

latestish vamsas schema

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@16 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 13:14:58 +0000 (13:14 +0000)]

added a few more dependencies

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@15 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 13:13:07 +0000 (13:13 +0000)]

added comments concerning provenance

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@14 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 19 Sep 2005 13:12:29 +0000 (13:12 +0000)]

added for generation of vamsas classes

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@13 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 16 Sep 2005 15:26:43 +0000 (15:26 +0000)]

basic example application skeleton and SimpleClientFactory .

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@12 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Fri, 16 Sep 2005 13:38:28 +0000 (13:38 +0000)]

LGPL from FSF site.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@11 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 14 Sep 2005 16:24:26 +0000 (16:24 +0000)]

separate some interface methods into abstract classes to enforce access control

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@10 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 14 Sep 2005 15:25:38 +0000 (15:25 +0000)]

object registration functions return an Id for the object.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@9 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 14 Sep 2005 13:47:34 +0000 (13:47 +0000)]

renamed Iclient and others.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@8 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Wed, 14 Sep 2005 13:41:41 +0000 (13:41 +0000)]

first version sent out to Iain and Pierre

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@7 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 12 Sep 2005 09:36:10 +0000 (09:36 +0000)]

Initial revision

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@2 be28352e-c001-0410-b1a7-c7978e42abec

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jprocter [Mon, 12 Sep 2005 09:36:10 +0000 (09:36 +0000)]

New repository initialized by cvs2svn.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@1 be28352e-c001-0410-b1a7-c7978e42abec