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

git://source.jalview.org / vamsas.git / commit

author	jprocter <jprocter@compbio.dundee.ac.uk>
	Thu, 7 May 2009 15:36:04 +0000 (15:36 +0000)
committer	jprocter <jprocter@compbio.dundee.ac.uk>
	Thu, 7 May 2009 15:36:04 +0000 (15:36 +0000)
commit	844ccad5a3fcbedec17b2af66d460f31abc7cff1
tree	18ca5d04105719488d9fd154c4bcc90fd51d7c04	tree \| snapshot
parent	6f33f705957d674dc2ab6c994a6ea87f7a91f40f	commit \| diff

applied LGPLv3 and source code formatting.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@496 be28352e-c001-0410-b1a7-c7978e42abec

221 files changed:

CONTRIB		diff \| blob \| history
COPYING.lesser	[new file with mode: 0644]	blob
README	[new file with mode: 0644]	blob
build.xml		diff \| blob \| history
packages/vamsas-client.jar		diff \| blob \| history
packages/vamsas-schema-and-doc.jar	[new file with mode: 0644]	blob
resources/README	[deleted file]	blob \| history
schemas/vamsas.xsd		diff \| blob \| history
schemas/vamsasDocument.xsd		diff \| blob \| history
src/org/apache/tools/zip/AsiExtraField.java		diff \| blob \| history
src/org/apache/tools/zip/ExtraFieldUtils.java		diff \| blob \| history
src/org/apache/tools/zip/JarMarker.java		diff \| blob \| history
src/org/apache/tools/zip/UnixStat.java		diff \| blob \| history
src/org/apache/tools/zip/UnrecognizedExtraField.java		diff \| blob \| history
src/org/apache/tools/zip/ZipEntry.java		diff \| blob \| history
src/org/apache/tools/zip/ZipExtraField.java		diff \| blob \| history
src/org/apache/tools/zip/ZipFile.java		diff \| blob \| history
src/org/apache/tools/zip/ZipLong.java		diff \| blob \| history
src/org/apache/tools/zip/ZipOutputStream.java		diff \| blob \| history
src/org/apache/tools/zip/ZipShort.java		diff \| blob \| history
src/uk/ac/vamsas/client/AppDataInputStream.java		diff \| blob \| history
src/uk/ac/vamsas/client/AppDataOutputStream.java		diff \| blob \| history
src/uk/ac/vamsas/client/ClientDocument.java		diff \| blob \| history
src/uk/ac/vamsas/client/ClientHandle.java		diff \| blob \| history
src/uk/ac/vamsas/client/Events.java		diff \| blob \| history
src/uk/ac/vamsas/client/IClient.java		diff \| blob \| history
src/uk/ac/vamsas/client/IClientAppdata.java		diff \| blob \| history
src/uk/ac/vamsas/client/IClientDocument.java		diff \| blob \| history
src/uk/ac/vamsas/client/IClientFactory.java		diff \| blob \| history
src/uk/ac/vamsas/client/IObjectUpdate.java		diff \| blob \| history
src/uk/ac/vamsas/client/IVorbaIdFactory.java		diff \| blob \| history
src/uk/ac/vamsas/client/Iapp.java		diff \| blob \| history
src/uk/ac/vamsas/client/InvalidSessionDocumentException.java		diff \| blob \| history
src/uk/ac/vamsas/client/InvalidSessionUrnException.java		diff \| blob \| history
src/uk/ac/vamsas/client/NoDefaultSessionException.java		diff \| blob \| history
src/uk/ac/vamsas/client/SessionHandle.java		diff \| blob \| history
src/uk/ac/vamsas/client/SessionUrn.java		diff \| blob \| history
src/uk/ac/vamsas/client/UserHandle.java		diff \| blob \| history
src/uk/ac/vamsas/client/Vobject.java		diff \| blob \| history
src/uk/ac/vamsas/client/Vobjhash.java		diff \| blob \| history
src/uk/ac/vamsas/client/VorbaId.java		diff \| blob \| history
src/uk/ac/vamsas/client/VorbaIdFactory.java		diff \| blob \| history
src/uk/ac/vamsas/client/VorbaXmlBinder.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/CustomMessage.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/IMessageHandler.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/IPickManager.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/Message.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/MouseOverMessage.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/PickEndPoint.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/PickServer.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/SelectionMessage.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/SocketManager.java		diff \| blob \| history
src/uk/ac/vamsas/client/picking/TestApp.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/ArchiveUrn.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/ClientDocument.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/ClientSessionFileWatcherElement.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/ClientsFile.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/EventGeneratorThread.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/FileLock.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/FileWatcher.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/IdFactory.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/ListFile.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/Lock.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/LockFactory.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/LockTimeoutException.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/LockedFileOutputStream.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/NativeLock.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SessionFile.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SessionFileWatcherElement.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SessionFlagFile.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SessionFlagWatcherElement.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SessionUrn.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SessionsFile.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleClient.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleClientConfig.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleClientFactory.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleDocument.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimplePickManager.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/SimpleSessionManager.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/VamsasArchiveReader.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/VamsasFile.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/VamsasFileWatcherElement.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/VamsasFileWatcherThread.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/VamsasSession.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/WatcherCallBack.java		diff \| blob \| history
src/uk/ac/vamsas/client/simpleclient/WatcherElement.java		diff \| blob \| history
src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java		diff \| blob \| history
src/uk/ac/vamsas/objects/EmptyDocumentUpdater.java		diff \| blob \| history
src/uk/ac/vamsas/objects/IDocumentUpdater.java		diff \| blob \| history
src/uk/ac/vamsas/objects/IVorbaBinding.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Alignment.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/AlignmentSequence.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/AnnotationElement.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/AppData.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/ApplicationData.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Attachment.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Common.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/DataSet.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/DataSetAnnotations.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/DbRef.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Entry.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Glyph.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Input.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Instance.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Link.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Local.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/LockFile.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Map.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/MapList.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/MapRangeType.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/MapType.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Mapped.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Mapping.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Newick.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/NodeType.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Param.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Pos.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Property.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Provenance.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Range.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/RangeAnnotation.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/RangeType.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/ReferenceType.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Score.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Seg.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Sequence.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/SequenceMapping.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/SequenceType.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Tree.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Treenode.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/User.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/VAMSAS.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/VamsasDocument.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Vref.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/Vxref.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AlignmentAnnotationDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AlignmentDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AlignmentSequenceAnnotationDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AlignmentSequenceDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AnnotationElementDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AppDataDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/ApplicationDataDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/AttachmentDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/CommonDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/DataSetAnnotationsDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/DataSetDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/DbRefDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/EntryDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/GlyphDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/InputDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/InstanceDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/LinkDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/LocalDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/LockFileDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/MapDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/MapListDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/MapRangeTypeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/MapTypeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/MappedDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/MappingDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/NewickDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/NodeTypeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/ParamDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/PosDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/PropertyDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/ProvenanceDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/RangeAnnotationDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/RangeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/RangeTypeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/ReferenceTypeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/ScoreDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/SegDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/SequenceDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/SequenceMappingDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/SequenceTypeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/TreeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/TreenodeDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/UserDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/VAMSASDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/VamsasDocumentDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/VrefDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/core/descriptors/VxrefDescriptor.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/AppDataReference.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/DocumentStuff.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/Format.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/GlyphDictionary.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/MapList.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/Mapping.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/Properties.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/ProvenanceStuff.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/Range.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/Seq.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/SeqAln.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/SeqSet.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/SymbolDictionary.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/Trees.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/document/VersionEntries.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/trees/NewickFile.java		diff \| blob \| history
src/uk/ac/vamsas/objects/utils/trees/SequenceNode.java		diff \| blob \| history
src/uk/ac/vamsas/test/ExampleApplication.java		diff \| blob \| history
src/uk/ac/vamsas/test/objects/Core.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ArchiveClient.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ArchiveReader.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ArchiveReports.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ArchiveStreamReader.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ArchiveWatcher.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ArchiveWriter.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ClientDoc.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ClientsFileTest.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/CommandProcessor.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/TestSessionURN.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/VamsasArchive.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/ZipTest.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasClient.java		diff \| blob \| history
src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java		diff \| blob \| history

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