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[Treebase-guts] SF.net SVN: treebase:[246] trunk/treebase-core/src/main/java/org/cipres/ treebase
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From: <rv...@us...> - 2009-11-04 16:51:01
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Revision: 246
http://treebase.svn.sourceforge.net/treebase/?rev=246&view=rev
Author: rvos
Date: 2009-11-04 16:50:37 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Removed outdated CIPRES/SDSC disclaimers
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java
trunk/treebase-core/src/main/java/org/cipres/treebase/ContextManager.java
trunk/treebase-core/src/main/java/org/cipres/treebase/RangeExpression.java
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/treebase-core/src/main/java/org/cipres/treebase/Version.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Action.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ActionParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AddMetaDataAction.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AlternationParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AnalysisSectionParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentSequenceParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuthorParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxData.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxiliaryDataParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CheckMatrixNChars.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CommitStudy.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ConcatenationParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Filter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/FilterParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/FilterTrivial.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Generator.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/GenericAction.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/GenericAuxDataAction.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/HeadlineParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/HistoryParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/IOParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/InputMatrixParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/LazyList.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/MatrixParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/MultipleMatchError.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/OptionalParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/OutputTreeParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/RDParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/RDParserArgumentFailureException.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/RDParserFailure.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/RDParserResult.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/RepeatedParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/SideCondition.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/SimpleSectionParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/SingleTokenParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/SpecificHeadlineParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/StudyItemParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/StudyParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Token.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/TokenReader.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/TokenSequenceParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/TreeStudyMapping.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/TreebaseStreamTokenizer.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Value.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueAnalysisSection.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueAssignment.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueAssignmentMap.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueHeadline.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueNone.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueSection.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueSequence.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueStudy.java
trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ValueToken.java
trunk/treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/AbstractDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/admin/HelpDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/admin/PersonDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/admin/UserDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/CompoundElementJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ItemDefinitionJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixColumnJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixRowJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/NexusDataSetJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/PhyloTreeJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/CharacterDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/ItemDefinitionDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixColumnDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDataTypeDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixElementDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixRowDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/RowSegmentDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/AlgorithmDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/AnalysisDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/AnalysisStepDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/AnalyzedDataDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/CitationDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/CitationStatusDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyStatusDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/SubmissionDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractQueryCriteria.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/DomainHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TBPersistable.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/EmailAddress.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/EmailAddressPropertyEditor.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/Help.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/HelpHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/HelpService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/Person.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/PersonHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/PersonService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/RemotePersonServiceImp.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/User.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/UserHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/UserRole.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/UserService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/AncStateSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/AncestralState.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CSTree.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CSTreeNode.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharGroup.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharPartition.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharWeight.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharWeightSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CodonPositionSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ColumnRange.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CompoundMatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousAncState.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousChar.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ContinuousMatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteAncState.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteChar.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteCharState.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DiscreteMatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ExcludedCharSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/GapMode.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/GeneticCode.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/GeneticCodeRecord.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/GeneticCodeSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/IntegerCharWeight.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ItemDefinition.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ItemDefinitionHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/ItemValue.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumnHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumnService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixDataType.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixDataTypeHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElementHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElementService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixKind.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRowHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRowService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/PhyloChar.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/PolyTCount.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/PredefinedCharSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/PredefinedCharType.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RealCharWeight.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegmentHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegmentService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/SequenceMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StandardMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StateChangeSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StateFormat.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StateModifier.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StateSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StepMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/StepMatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/TypeSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserType.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserTypeRecord.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/AbstractNexusConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusDataSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusParserConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusParserFinder.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/ColumnRangeConvertHelper.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteContinuousMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteDistanceMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteStandardMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/ncl/NCLContinuousMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/ncl/NCLDistanceMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/ncl/NCLMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/ncl/NCLNexusConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/ncl/NCLStandardMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/MatrixSearchResults.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchResultsFrozen.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchResultsType.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/StudySearchResults.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TaxonSearchResults.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TreeSearchResults.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/UnknownSearchResultsTypeError.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Algorithm.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AlgorithmHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Analysis.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStep.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStepHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStepService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedData.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedDataHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedDataService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedMatrixHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedTree.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedTreeHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/ArticleCitation.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/BookCitation.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/CitationHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/CitationService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/CitationStatus.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/CitationStatusHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/DistanceAlgorithm.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/InBookCitation.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/LikelihoodAlgorithm.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/OtherAlgorithm.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/ParsimonyAlgorithm.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Software.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyCriteria.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyStatus.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyStatusHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/SubmissionHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/SubmissionService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/UploadFileResult.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/LSIDTaxonLink.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/SpecimenLabel.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonAuthority.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelGroup.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelPartition.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLink.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonVariant.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TextTaxonLink.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/NodeAttribute.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeAttribute.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeGroup.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeKind.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeNode.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeNodeEdge.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreePartition.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeQuality.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeType.java
trunk/treebase-core/src/main/java/org/cipres/treebase/event/ProgressionListener.java
trunk/treebase-core/src/main/java/org/cipres/treebase/exception/UnimplementedMethodError.java
trunk/treebase-core/src/main/java/org/cipres/treebase/framework/ExecutionResult.java
trunk/treebase-core/src/main/java/org/cipres/treebase/framework/TSVFileParser.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/AbstractService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/AbstractServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/admin/HelpServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/admin/PersonServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/admin/UserServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/matrix/CharacterServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/matrix/MatrixColumnServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/matrix/MatrixElementServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/matrix/MatrixRowServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/matrix/MatrixServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/matrix/RowSegmentServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/search/SearchServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/AnalysisServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/AnalysisStepServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/AnalyzedDataServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/CitationServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/tree/PhyloTreeServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/AbstractStandalone.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/AnnotateTree.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/AuxiliaryDataImporter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/AuxiliaryDataImporterInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/BulkUpload.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CreateTaxon.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CreateTaxonVariant.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/DeleteObject.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/DeleteObjectInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/DeleteStudy.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/DestroySubmission.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/DidNexusFile.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/GetOpts.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/LoadTaxonData.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/MergeDuplicateTaxonLabels.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/MergeDuplicateTaxonLabelsInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/ObjectDeleter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/ObjectDeleterFactory.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/ObjectGroupMerger.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/OptionSettings.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/PseudoSubmission.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/PutbackReader.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RawNexusImporter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RawNexusImporterInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RegenerateTaxonLabelSetsInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RepatriateAuthors.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RepatriateData.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/Standalone.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/TaxonDeleter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/UnixOptions.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/WhatsMissing.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/WhatsMissingInterface.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/package.html
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,24 +1,3 @@
-/*
- * CIPRES Copyright (c) 2009, The Regents of the University of California All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification, are permitted
- * provided that the following conditions are met: * Redistributions of source code must retain the
- * above copyright notice, this list of conditions and the following disclaimer. * Redistributions
- * in binary form must reproduce the above copyright notice, this list of conditions and the
- * following disclaimer in the documentation and/or other materials provided with the distribution. *
- * Neither the name of the University of California or the San Diego Supercomputer Center nor the
- * names of its contributors may be used to endorse or promote products derived from this software
- * without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- * FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
- * WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
package org.cipres.treebase;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/ContextManager.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/ContextManager.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/ContextManager.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2005 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/RangeExpression.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/RangeExpression.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/RangeExpression.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2005 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/Version.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/Version.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/Version.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -39,6 +39,6 @@
*
*/
public class Version {
- public static final String VCSID = "##VCSID##";
- public static final String VCSDateString = "##VCSDATESTRING##";
+ public static final String VCSID = "245";
+ public static final String VCSDateString = "2009-11-04 15:03:06 +0000 (Wed, 04 Nov 2009)";
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Action.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Action.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Action.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2009 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase.auxdata;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ActionParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ActionParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ActionParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AddMetaDataAction.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AddMetaDataAction.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AddMetaDataAction.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2009 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase.auxdata;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AlternationParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AlternationParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AlternationParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AnalysisSectionParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AnalysisSectionParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AnalysisSectionParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentSequenceParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentSequenceParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AssignmentSequenceParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuthorParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuthorParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuthorParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxData.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxData.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxData.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxiliaryDataParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxiliaryDataParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/AuxiliaryDataParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase.auxdata;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CheckMatrixNChars.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CheckMatrixNChars.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CheckMatrixNChars.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2009 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase.auxdata;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CommitStudy.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CommitStudy.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/CommitStudy.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008, 2009 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
package org.cipres.treebase.auxdata;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ConcatenationParser.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ConcatenationParser.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/ConcatenationParser.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that the above copyright notice, this paragraph and the following two
- * paragraphs appear in all copies.
- *
- * Permission to incorporate this software into commercial products may be obtained by contacting
- * us: http://www.phylo.org/contactUs.html
- *
- * The software program and documentation are supplied "as is". In no event shall the CIPRES project
- * be liable to any party for direct, indirect, special, incidental, or consequential damages,
- * including lost profits, arising out of the use of this software and its documentation, even if
- * the CIPRES project has been advised of the possibility of such damage. The CIPRES project
- * specifically disclaims any warranties, including, but not limited to, the implied warranties of
- * merchantability and fitness for a particular purpose. The CIPRES project has no obligations to
- * provide maintenance, support, updates, enhancements, or modifications.
- */
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Filter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Filter.java 2009-11-04 15:03:06 UTC (rev 245)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/auxdata/Filter.java 2009-11-04 16:50:37 UTC (rev 246)
@@ -1,22 +1,3 @@
-/*
- * Copyright 2008 CIPRES project. http://www.phylo.org/ All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this software and its documentation for
- * educational, research and non-profit purposes, without fee, and without a written agreement is
- * hereby granted, provided that ...
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