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[Treebase-guts] SF.net SVN: treebase:[216] trunk/oai-pmh_data_provider/data_provider_core
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From: <yo...@us...> - 2009-10-23 22:43:01
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Revision: 216
http://treebase.svn.sourceforge.net/treebase/?rev=216&view=rev
Author: youjun
Date: 2009-10-23 22:42:33 +0000 (Fri, 23 Oct 2009)
Log Message:
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Modified Paths:
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trunk/oai-pmh_data_provider/data_provider_core/.classpath
trunk/oai-pmh_data_provider/data_provider_core/.settings/org.eclipse.wst.common.component
Added Paths:
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trunk/oai-pmh_data_provider/data_provider_core/src/main/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/Constants.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/ContextManager.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/NamespacedGUID.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/PhyloWSPath.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/RangeExpression.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/TreebaseIDString.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/Version.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Action.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ActionParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AddMetaDataAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AlternationParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AnalysisSectionParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AssignmentParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AssignmentSequenceParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AuthorParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AuxData.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AuxiliaryDataParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/CheckMatrixNChars.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/CommitStudy.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/CompleteStudyAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ConcatenationParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Filter.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/FilterParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/FilterTrivial.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Generator.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/GenericAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/GenericAuxDataAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/HeadlineParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/HistoryParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/IOParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/InputMatrixParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/LazyList.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/MatrixParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/MultipleMatchError.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/OptionalParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/OutputTreeParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParserArgumentFailureException.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParserFailure.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParserResult.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RepeatedParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SideCondition.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SimpleSectionParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SingleTokenParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SpecificHeadlineParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/StudyItemParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/StudyParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Token.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TokenReader.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TokenSequenceParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TreeStudyMapping.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TreebaseStreamTokenizer.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Value.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueAnalysisSection.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueAssignment.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueAssignmentMap.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueHeadline.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueNone.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueSection.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueSequence.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueStudy.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ValueToken.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/core/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/AbstractDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/admin/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/admin/HelpDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/admin/PersonDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/admin/UserDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/CompoundElementJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/ItemDefinitionJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixColumnJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixRowJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/NexusDataSetJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/jdbc/PhyloTreeJDBC.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/CharacterDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/ItemDefinitionDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/MatrixColumnDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDataTypeDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/MatrixElementDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/MatrixRowDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/matrix/RowSegmentDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/AlgorithmDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/AnalysisDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/AnalysisStepDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/AnalyzedDataDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/CitationDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/CitationStatusDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/StudyStatusDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/study/SubmissionDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/taxon/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/taxon/TaxonDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/tree/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/AbstractQueryCriteria.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/DomainHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/TBPersistable.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/EmailAddress.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/EmailAddressPropertyEditor.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/Help.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/HelpHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/HelpService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/Person.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/PersonHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/PersonService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/RemotePersonServiceImp.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/User.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/UserHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/UserRole.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/admin/UserService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/AncStateSet.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/AncestralState.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CSTree.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CSTreeNode.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharGroup.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharPartition.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharSet.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharWeight.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharWeightSet.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharacterHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CharacterService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CodonPositionSet.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ColumnRange.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/CompoundMatrixElement.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousAncState.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousChar.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousMatrix.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousMatrixElement.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteAncState.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteChar.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteCharState.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteMatrix.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteMatrixElement.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrix.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrixElement.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ExcludedCharSet.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/GapMode.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/GeneticCode.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/GeneticCodeRecord.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/GeneticCodeSet.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/IntegerCharWeight.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ItemDefinition.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ItemDefinitionHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/ItemValue.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumnHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumnService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixDataType.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixDataTypeHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElementHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElementService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixKind.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRowHome.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRowService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/MatrixService.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/PhyloChar.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/domain/matrix/PolyTCount.java
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