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

last core object source generation on...

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@448 be28352e-c001-0410-b1a7-c7978e42abec

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

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

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

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

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

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

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

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

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

refactored from  newickfile

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@438 be28352e-c001-0410-b1a7-c7978e42abec

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

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

formatting changes

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@435 be28352e-c001-0410-b1a7-c7978e42abec

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

TODO comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@433 be28352e-c001-0410-b1a7-c7978e42abec

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

portability issue error messages

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@431 be28352e-c001-0410-b1a7-c7978e42abec

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

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

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

updated classpath for eclipse project

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@427 be28352e-c001-0410-b1a7-c7978e42abec

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

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

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

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

debug message for default mapping

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@422 be28352e-c001-0410-b1a7-c7978e42abec

added mapType utilities.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@421 be28352e-c001-0410-b1a7-c7978e42abec

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

quieter logging

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@419 be28352e-c001-0410-b1a7-c7978e42abec

build on 28th June

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@418 be28352e-c001-0410-b1a7-c7978e42abec

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