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

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

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

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

debugging on the haltWatch method

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@413 be28352e-c001-0410-b1a7-c7978e42abec

use of config class

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@412 be28352e-c001-0410-b1a7-c7978e42abec

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

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

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

end position not correctly set.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@408 be28352e-c001-0410-b1a7-c7978e42abec

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

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

less verbose default logging

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@405 be28352e-c001-0410-b1a7-c7978e42abec

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

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

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

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

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

test cdoc object retrieve by VorbaId and add timeout for hanging around (needs to be a specific command)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@399 be28352e-c001-0410-b1a7-c7978e42abec

todo doc

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@398 be28352e-c001-0410-b1a7-c7978e42abec

fix non-retrieval of vobject by vorba id on clientdoc interface

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@397 be28352e-c001-0410-b1a7-c7978e42abec

VamsasSession: fixed incorrectly stopping the EventGeneratorThread

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@396 be28352e-c001-0410-b1a7-c7978e42abec

VamsasSession: insure the RemoveClientWatchCallBack  handleWatchEvent method. no needed to check if there is no client in the client list,if the list does not have been modified

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@395 be28352e-c001-0410-b1a7-c7978e42abec

Added support for crashed client.
Crashed client are removed correctly from the session client.
When a new client joins a session, it adds itself to the session client list and ensures that it is still in the list while it is active.
When a client wants to remove itself from the session, the client clears the session client list to check if it is the last client. (all actives clients should readd themself to the list during two watcher cycles, if the list is still empty. The client consideres itself as the last client of the session and closes properly the session)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@394 be28352e-c001-0410-b1a7-c7978e42abec

better command line processing options (load, save) and slower update poll check.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@393 be28352e-c001-0410-b1a7-c7978e42abec

javadoc todo

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@392 be28352e-c001-0410-b1a7-c7978e42abec

removed old Mapping object dependency

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@391 be28352e-c001-0410-b1a7-c7978e42abec

build.xml: modified javadoc ant task to add ref to the lib directory

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@390 be28352e-c001-0410-b1a7-c7978e42abec

sequenceMapping added

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@389 be28352e-c001-0410-b1a7-c7978e42abec

castor-1.1 source generation

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@388 be28352e-c001-0410-b1a7-c7978e42abec

Descriptors live in uk.ac.vamsas.objects.core.descriptors in castor-1.1 xml binding.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@387 be28352e-c001-0410-b1a7-c7978e42abec

relatively silent debug state (have to sort out of this log4j or the one in resources is being used)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@386 be28352e-c001-0410-b1a7-c7978e42abec

pick manager and simulation of alignment modification within existing document.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@385 be28352e-c001-0410-b1a7-c7978e42abec

part-implemented and *untested*

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@384 be28352e-c001-0410-b1a7-c7978e42abec

introduced hashCode based object change detection that works (see vamsas.test.exampleApplication)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@383 be28352e-c001-0410-b1a7-c7978e42abec

attempt to fix occasional backupSessionFile exception.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@382 be28352e-c001-0410-b1a7-c7978e42abec

ambiguous import of 'Lock' removed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@381 be28352e-c001-0410-b1a7-c7978e42abec

incorrect update approach (attempt prior to hashCode fix in castor-1.1(v))

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@380 be28352e-c001-0410-b1a7-c7978e42abec

int to long type change in castor-1.1(v) objects

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@379 be28352e-c001-0410-b1a7-c7978e42abec

rebult for castor-1.1(vamsas version)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@378 be28352e-c001-0410-b1a7-c7978e42abec

updated to castor-1.1 + Vamsas Specific hashCode modification

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@377 be28352e-c001-0410-b1a7-c7978e42abec

fixed session log configuration

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@376 be28352e-c001-0410-b1a7-c7978e42abec

updated to castor-1.1 + Vamsas Specific hashCode modification

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@375 be28352e-c001-0410-b1a7-c7978e42abec

updated to castor-1.1 + Vamsas Specific hashCode modification

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@374 be28352e-c001-0410-b1a7-c7978e42abec

updated to castor-1.1 + Vamsas Specific hashCode modification

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@373 be28352e-c001-0410-b1a7-c7978e42abec

update detection mechanism based comparing the difference between the position of start and end tags of a Vobject between successive document unmarshallings.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@372 be28352e-c001-0410-b1a7-c7978e42abec

update detection mechanism based comparing the difference between the position of start and end tags of a Vobject between successive document unmarshallings.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@371 be28352e-c001-0410-b1a7-c7978e42abec

pass maintained hash of Vobject hash values to IdFactory so it can detect modified objects.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@370 be28352e-c001-0410-b1a7-c7978e42abec

commented out methods that might be used for accessing a list of updated objects stored in the vamsas session

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@369 be28352e-c001-0410-b1a7-c7978e42abec

javadoc

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@368 be28352e-c001-0410-b1a7-c7978e42abec

new constructor to pass hash of Vobject hash values to unmarshalling mechanism for comparison with document objects.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@367 be28352e-c001-0410-b1a7-c7978e42abec

trap exceptions during session events and ensure pick messages are blocked whilst document changed events occur

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@366 be28352e-c001-0410-b1a7-c7978e42abec

debug log output

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@365 be28352e-c001-0410-b1a7-c7978e42abec

switched picker shutdown to after finalize() call - simulating GUI shutdown after Vamsas session shutdown.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@364 be28352e-c001-0410-b1a7-c7978e42abec

WatcherElement reference should be nulled by caller of removeClient rather than within method.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@363 be28352e-c001-0410-b1a7-c7978e42abec

interrupt before wait sleep so haltWatchers is more likely to return after watchThread has stopped.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@362 be28352e-c001-0410-b1a7-c7978e42abec

Messages are thrown away when passThru is false (rather than receiver thread sleeping). Better shutdown behaviour (thread references are nulled)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@361 be28352e-c001-0410-b1a7-c7978e42abec

closing channel always releases lock (on windows anyhow)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@360 be28352e-c001-0410-b1a7-c7978e42abec

occasional null pointer exception

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@359 be28352e-c001-0410-b1a7-c7978e42abec

ensured backups are only made when backup==true

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@358 be28352e-c001-0410-b1a7-c7978e42abec

removed infinite loop on server shutdown

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@357 be28352e-c001-0410-b1a7-c7978e42abec

more debug messages.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@356 be28352e-c001-0410-b1a7-c7978e42abec

simplified and bugfixed occasional lock contention.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@355 be28352e-c001-0410-b1a7-c7978e42abec

bugfixes for shutdown and null message reception.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@354 be28352e-c001-0410-b1a7-c7978e42abec

utility functions for dealing with Range and Properties elements.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@353 be28352e-c001-0410-b1a7-c7978e42abec

remove unnecessary existence checks.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@352 be28352e-c001-0410-b1a7-c7978e42abec

remove unnecessary existence checks.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@351 be28352e-c001-0410-b1a7-c7978e42abec

Added shutdown() methods for the socket-based PickManager code.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@350 be28352e-c001-0410-b1a7-c7978e42abec

stub for the dom tree update event generator.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@349 be28352e-c001-0410-b1a7-c7978e42abec

added PickManager test code. Current state of library means this example app fails to shutdown after three instances have been started.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@348 be28352e-c001-0410-b1a7-c7978e42abec

synchronized methods to ensure thread safety for underlying SimplePickManager code. (not successful yet!)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@347 be28352e-c001-0410-b1a7-c7978e42abec

ensured single instance of vamsasarchive io handler to prevent lock contention.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@346 be28352e-c001-0410-b1a7-c7978e42abec

non-1.4 factory construtors removed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@345 be28352e-c001-0410-b1a7-c7978e42abec

Added generateClientUrn method to generate a urn from client name and version. Ensures that the client urn is generated, when one of the attribute is modified. And, add support for null attribute in the equals method

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@344 be28352e-c001-0410-b1a7-c7978e42abec

Avoid creation of ClientHandle and UserHandle objects with null attributes. Otherwise, problem with null pointer exception.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@343 be28352e-c001-0410-b1a7-c7978e42abec

log config (with SESSIONLOG config too).
Need to separate SESSIONLOG in future.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@342 be28352e-c001-0410-b1a7-c7978e42abec

SimpleClient implementation testable against uk.ac.vamsas.test.ExampleApplication

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@341 be28352e-c001-0410-b1a7-c7978e42abec

fixed bug leaving copies of archive backups (no testcase for this)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@340 be28352e-c001-0410-b1a7-c7978e42abec

extended to test against SimpleClient implementation

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@339 be28352e-c001-0410-b1a7-c7978e42abec

added TODO for testing getAppData method before migration to simpleClient.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@338 be28352e-c001-0410-b1a7-c7978e42abec

untested watcherElement for spotting changes in SessionFlagFile presence/absence.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@337 be28352e-c001-0410-b1a7-c7978e42abec

formal polling thread for particular FileWatcher types (VamsasFile or SessionFile style)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@336 be28352e-c001-0410-b1a7-c7978e42abec

method to get File object being watched

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@335 be28352e-c001-0410-b1a7-c7978e42abec

fixed subtle bug in closeChannel behaviour on lock release and debug logging.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@334 be28352e-c001-0410-b1a7-c7978e42abec

wrapper for conditionally passing picks onto the client application

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@333 be28352e-c001-0410-b1a7-c7978e42abec

added (broken) haltPickManager methods

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@332 be28352e-c001-0410-b1a7-c7978e42abec

refactoring org->uk.ac

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

 VamsasSession: Fixed  VamsasSession init/construction if the session directory exists and do not contains session files.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@330 be28352e-c001-0410-b1a7-c7978e42abec

when closing session, closes each associated VAMAV clients

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@329 be28352e-c001-0410-b1a7-c7978e42abec

more refactoring fallout

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

Updated simple client sessionURN to use URI instead of URL to generate SessionURN (URI) from the session directory path (file location or vamsas session).
Updated SimpleClient to match modified constructor (MalformedURL not throw anymore)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@327 be28352e-c001-0410-b1a7-c7978e42abec

SessionURN fix asFile method now create the File object from the URI

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@326 be28352e-c001-0410-b1a7-c7978e42abec

Added TestSessionURN: to test the creation of a sessionURN and to retrieve a correct file from it.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@325 be28352e-c001-0410-b1a7-c7978e42abec

SessionUrn: modified to scope with windows  (space ... in file name. Use URI instead of URL

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@324 be28352e-c001-0410-b1a7-c7978e42abec

Modified CustomMessage.java so that tabs are used to separate message elements rather than underscores.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@323 be28352e-c001-0410-b1a7-c7978e42abec

Modified MouseOverMessage.java so that tabs are used to separate message elements rather than underscores.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@322 be28352e-c001-0410-b1a7-c7978e42abec

SessionHandle: added equals method to compare SessionHandles, based on the sessionUrn

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

amsasSession: added addClient and removeClient to add and remove a client to/from the session client list.
Attached (as attribute) a SessionManager

Removes  the currentSession of the active session list, if the client to removed is the last one of the list

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@320 be28352e-c001-0410-b1a7-c7978e42abec

Moves sessionFile management to SimpleSessionManager  calling SessionsFile class  (dealing directly with the file)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@319 be28352e-c001-0410-b1a7-c7978e42abec

SimpleClient: remove client of the session client list when closing/finalizing (finalizeClient method)
added get_session() to retrieve current vamsas session

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@318 be28352e-c001-0410-b1a7-c7978e42abec