Download treemachine Free Java Code

.gitignore//from  www . j  a va  2s  .  co  m
README.md
build_and_test.sh
doc/Queries-Synthesis-API.txt
example.nexson
example/README.txt
example/grehan_schwartz_2009.tre
example/ncbi_primates.txt
example/sarich_wilson_1967.tre
mvn_cmdline.sh
mvn_serverplugins.sh
pom.serverplugins.xml
pom.xml
run_example.sh
run_import_tests.sh
run_longbitarray_tests.sh
scripts/compare_normalized_original_names_in_taxonomy.py
scripts/process_names_from_nexson.py
scripts/subset_taxonomy.py
src/main/java/jade/JSONMessageLogger.java
src/main/java/jade/MessageLogger.java
src/main/java/jade/tree/JadeNode.java
src/main/java/jade/tree/JadeTree.java
src/main/java/jade/tree/NexsonReader.java
src/main/java/jade/tree/NodeObject.java
src/main/java/jade/tree/TreeFileReader.java
src/main/java/jade/tree/TreeReader.java
src/main/java/jade/tree/TreeSimulator.java
src/main/java/jade/tree/TreeUtils.java
src/main/java/opentree/AncestorUtil.java
src/main/java/opentree/ChildNumberEvaluator.java
src/main/java/opentree/FilterByPropertyRelIterator.java
src/main/java/opentree/GeneralUtils.java
src/main/java/opentree/GraphBase.java
src/main/java/opentree/GraphDatabaseAgent.java
src/main/java/opentree/GraphExplorer.java
src/main/java/opentree/GraphExporter.java
src/main/java/opentree/GraphImporter.java
src/main/java/opentree/GraphInitializer.java
src/main/java/opentree/GraphJanitor.java
src/main/java/opentree/JSONExporter.java
src/main/java/opentree/LicaBipartEvaluator.java
src/main/java/opentree/LicaBipartEvaluatorBS.java
src/main/java/opentree/LicaContainsAllEvaluator.java
src/main/java/opentree/LicaContainsAllEvaluatorBS.java
src/main/java/opentree/LicaEvaluator.java
src/main/java/opentree/LicaEvaluatorBS.java
src/main/java/opentree/LicaUtil.java
src/main/java/opentree/LongArrayPropertyContainsAllEvaluator.java
src/main/java/opentree/MainRunner.java
src/main/java/opentree/PhylografterConnector.java
src/main/java/opentree/SpeciesEvaluator.java
src/main/java/opentree/TLongBitArray.java
src/main/java/opentree/TaxaListEvaluator.java
src/main/java/opentree/constants/GeneralConstants.java
src/main/java/opentree/constants/GraphProperty.java
src/main/java/opentree/constants/NodeProperty.java
src/main/java/opentree/constants/RelProperty.java
src/main/java/opentree/constants/RelType.java
src/main/java/opentree/constants/SourceProperty.java
src/main/java/opentree/exceptions/AmbiguousTaxonException.java
src/main/java/opentree/exceptions/DataFormatException.java
src/main/java/opentree/exceptions/MultipleHitsException.java
src/main/java/opentree/exceptions/NullComparisonException.java
src/main/java/opentree/exceptions/OttIdNotFoundException.java
src/main/java/opentree/exceptions/StoredEntityNotFoundException.java
src/main/java/opentree/exceptions/TaxonNotFoundException.java
src/main/java/opentree/exceptions/TreeIngestException.java
src/main/java/opentree/exceptions/TreeNotFoundException.java
src/main/java/opentree/plugins/GetJsons.java
src/main/java/opentree/plugins/GetSASJsons.java
src/main/java/opentree/plugins/GoLS.java
src/main/java/opentree/plugins/PhylografterUpdater.java
src/main/java/opentree/synthesis/DraftTreePathExpander.java
src/main/java/opentree/synthesis/SourcePropertyValue.java
src/main/java/opentree/synthesis/SynthesisExpander.java
src/main/java/opentree/synthesis/SynthesisUtils.java
src/main/java/opentree/synthesis/conflictresolution/RankResolutionMethod.java
src/main/java/opentree/synthesis/conflictresolution/RankResolutionMethodInferredPath.java
src/main/java/opentree/synthesis/conflictresolution/RelationshipConflictResolver.java
src/main/java/opentree/synthesis/conflictresolution/ResolutionMethod.java
src/main/java/opentree/synthesis/conflictresolution/TreeMakingBandB.java
src/main/java/opentree/synthesis/conflictresolution/TreeMakingExhaustivePairs.java
src/main/java/opentree/synthesis/filtering/Directive.java
src/main/java/opentree/synthesis/filtering/FilterCriterion.java
src/main/java/opentree/synthesis/filtering/FilterCriterionOLD.java
src/main/java/opentree/synthesis/filtering/RelationshipFilter.java
src/main/java/opentree/synthesis/filtering/SetComparison.java
src/main/java/opentree/synthesis/filtering/SingleValueComparison.java
src/main/java/opentree/synthesis/filtering/SourcePropertySetTest.java
src/main/java/opentree/synthesis/filtering/SourcePropertySingleValueTest.java
src/main/java/opentree/synthesis/filtering/Test.java
src/main/java/opentree/synthesis/filtering/TestValue.java
src/main/java/opentree/synthesis/filtering/TestValueSet.java
src/main/java/opentree/synthesis/ranking/RankingCriterion.java
src/main/java/opentree/synthesis/ranking/RankingOrder.java
src/main/java/opentree/synthesis/ranking/RelationshipRanker.java
src/main/java/opentree/synthesis/ranking/SourcePropertyPrioritizedRankingCriterion.java
src/main/java/opentree/synthesis/ranking/SourcePropertyRankingCriterion.java
src/main/java/opentree/testing/TreeUtils.java
src/main/java/org/neo4j/server/rest/repr/ArgusonRepresentationConverter.java
src/main/java/org/neo4j/server/rest/repr/GeneralizedMappingRepresentation.java
src/main/java/org/neo4j/server/rest/repr/OpenTreeMachineRepresentationConverter.java
src/main/resources/archive-files/services/org.neo4j.server.plugins.ServerPlugin
src/main/resources/log4j.properties
src/main/resources/tracelog4j.properties
src/test/java/opentree/AncestorUtilTest.java