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phyloGeoRef-master
phyloGeoRef
src
au
com
bytecode
opencsv
CSVParser.java
CSVReader.java
CSVWriter.java
ResultSetHelper.java
ResultSetHelperService.java
bean
ColumnPositionMappingStrategy.java
CsvToBean.java
HeaderColumnNameMappingStrategy.java
HeaderColumnNameTranslateMappingStrategy.java
MappingStrategy.java
nescent
DemoMain.java
DemoMain2.java
DemoMain3.java
phylogeoref
Calc3DTree.java
Magic.java
Quad.java
Triple.java
geodata
ParseCoords.java
ParseMetadata.java
gui
PhyloGeoRefWidget.java
Phylogeoref.java
processor
PhylogenyProcessor.java
ProcessorFactory.java
UnweightedPhylogenyProcessor.java
WeightedPhylogenyProcessor.java
utility
ComputeUtility.java
reader
CSVMetadataReader.java
GrandUnifiedReader.java
MetadataReader.java
MultiFormatReader.java
NeXMLEngine.java
NeXMLReader.java
PhylogenyKitchen.java
PhylogenyMould.java
TextMetadataReader.java
TreeReader.java
UniversalMetadataReader.java
UniversalTreeReader.java
utility
PhyloUtility.java
PhylogenyFactory.java
validator
PhylogenyValidator.java
exception
InvalidChildrenException.java
InvalidEdgeLengthException.java
InvalidLatitudeException.java
InvalidLongitudeException.java
LocationNotFoundException.java
MissingEdgeLengthException.java
SingleChildException.java
ZeroChildException.java
writer
AdvancedKmlWriter.java
HierarchicalKmlPainter.java
KmlPainter.java
KmlWriter.java
LevelwiseKmlPainter.java
PaintStyle.java
SimpleKmlWriter.java
utility
AMath.java
HTMLParlour.java
KmlConstants.java
KmlToolkit.java
KmlUtility.java
testMain.java
org
forester
application
confadd.java
count_support.java
decorator.java
get_distances.java
goac.java
meta_ontologizer.java
nhx_too.java
nj.java
obo_tool.java
pccx.java
perfume.java
pfam2go_extractor.java
pfam_go.java
phyloxml_converter.java
printAllSpecies.java
printSameOrder.java
rio.java
sdi.java
sdi_r.java
shin.java
strip.java
support_statistics.java
support_transfer.java
surf_paup.java
surfacing.java
surfacing_old.java
ta.java
archaeopteryx
Archaeopteryx.java
ArchaeopteryxA.java
ArchaeopteryxE.java
Blast.java
ColorSchemeChooser.java
Configuration.java
Constants.java
ControlPanel.java
FontChooser.java
MainFrame.java
MainFrameApplet.java
MainFrameApplication.java
MainPanel.java
MainPanelApplets.java
MouseListener.java
NodeEditPanel.java
NodeFrame.java
NodePanel.java
Options.java
PdfExporter.java
PdfWriter.java
Printer.java
TextFrame.java
TreeColorSet.java
TreeFontSet.java
TreePanel.java
UrlTreeReader.java
Util.java
WebLink.java
phylogeny
data
RenderableDomainArchitecture.java
RenderablePhylogenyData.java
webservices
BasicPhylogeniesWebserviceClient.java
PhylogeniesWebserviceClient.java
WebserviceUtil.java
WebservicesManager.java
datastructures
Queue.java
development
AminoAcid.java
AminoAcidSequence.java
BasicMsa.java
DevelopmentTools.java
Factory.java
Msa.java
MsaFactory.java
Sequence.java
SimpleMutableMsa.java
StreamBasedMsaFactory.java
SupportCount.java
Test.java
go
BasicGoRelationship.java
BasicGoSubset.java
BasicGoTerm.java
BasicGoXRef.java
GoId.java
GoNameSpace.java
GoRelationship.java
GoSubset.java
GoTerm.java
GoUtils.java
GoXRef.java
Mapping.java
OBOparser.java
PfamToGoMapping.java
PfamToGoParser.java
TestGo.java
etc
MetaOntologizer.java
OntologizerResult.java
io
parsers
HmmPfamOutputParser.java
HmmscanPerDomainTableParser.java
ParserUtils.java
PhylogenyParser.java
PhylogenyParserException.java
nexus
NexusBinaryStatesMatrixParser.java
NexusCharactersParser.java
NexusConstants.java
NexusFormatException.java
NexusPhylogeniesParser.java
PaupLogParser.java
nhx
NHXFormatException.java
NHXParser.java
NHXtags.java
phyloxml
PhyloXmlDataFormatException.java
PhyloXmlException.java
PhyloXmlHandler.java
PhyloXmlMapping.java
PhyloXmlParser.java
PhyloXmlUtil.java
XmlElement.java
phylogenydata
AccessionParser.java
AnnotationParser.java
BinaryCharactersParser.java
BranchWidthParser.java
ColorParser.java
ConfidenceParser.java
DateParser.java
DistributionParser.java
DomainArchitectureParser.java
EventParser.java
IdentifierParser.java
PhylogenyDataPhyloXmlParser.java
PointParser.java
PropertyParser.java
ProteinDomainParser.java
ReferenceParser.java
SequenceParser.java
SequenceRelationParser.java
TaxonomyParser.java
UriParser.java
tol
TolParser.java
TolXmlHandler.java
TolXmlMapping.java
writers
PhyloXmlNodeWriter.java
PhylogenyWriter.java
pccx
BasicExternalNodeBasedCoverageExtender.java
BranchCountingBasedScoringMethod.java
BranchLengthBasedScoringMethod.java
Coverage.java
CoverageCalculationMethod.java
CoverageCalculationOptions.java
CoverageCalculator.java
CoverageExtender.java
ExternalNodeBasedCoverage.java
ExternalNodeBasedCoverageMethod.java
ExternalNodeBasedCoverageMethodOptions.java
LogBranchLengthBasedScoringMethod.java
ModelingUtils.java
ScoringMethodForExternalNode.java
TestPccx.java
phylogeny
Edge.java
Phylogeny.java
PhylogenyBranch.java
PhylogenyMethods.java
PhylogenyNode.java
PhylogenyNodeI.java
data
Accession.java
Annotation.java
BinaryCharacters.java
BranchColor.java
BranchData.java
BranchWidth.java
Confidence.java
Date.java
Distribution.java
DomainArchitecture.java
Event.java
Identifier.java
NodeData.java
PhylogenyData.java
PhylogenyDataUtil.java
Point.java
PropertiesMap.java
Property.java
ProteinDomain.java
Reference.java
Sequence.java
SequenceRelation.java
Taxonomy.java
Uri.java
factories
BasicPhylogenyFactory.java
ParserBasedPhylogenyFactory.java
PhylogenyFactory.java
iterators
ChildNodeIteratorForward.java
ExternalForwardIterator.java
LevelOrderTreeIterator.java
PhylogenyNodeIterator.java
PostOrderStackObject.java
PostorderTreeIterator.java
PreorderTreeIterator.java
phylogenyinference
BasicCharacterStateMatrix.java
BasicSymmetricalDistanceMatrix.java
CharacterStateMatrix.java
DiscreteState.java
DistanceMatrix.java
DistanceMatrixParser.java
DistanceMethod.java
DolloParsimony.java
FitchParsimony.java
NeighborJoining.java
SankoffParsimony.java
SymmetricalDistanceMatrixParser.java
TestPhylogenyReconstruction.java
sdi
DistanceCalculator.java
GSDI.java
ORcount.java
RIO.java
RIOn.java
SDI.java
SDIR.java
SDIdirectory.java
SDIse.java
Shin.java
TaxonomyAssigner.java
TestGSDI.java
Tuplet.java
surfacing
AdjactantDirectedBinaryDomainCombination.java
AdjactantDirectedCombinableDomains.java
BasicBinaryDomainCombination.java
BasicCombinableDomains.java
BasicDomain.java
BasicDomainSimilarityCalculator.java
BasicGenomeWideCombinableDomains.java
BasicProtein.java
BasicSpecies.java
BinaryDomainCombination.java
CombinableDomains.java
CombinationsBasedPairwiseDomainSimilarity.java
CombinationsBasedPairwiseDomainSimilarityCalculator.java
CountsBasedPairwiseDomainSimilarity.java
DirectedBinaryDomainCombination.java
DirectedCombinableDomains.java
Domain.java
DomainArchitectureBasedGenomeSimilarityCalculator.java
DomainCountsBasedPairwiseSimilarityCalculator.java
DomainCountsDifferenceUtil.java
DomainId.java
DomainLengths.java
DomainLengthsTable.java
DomainParsimonyCalculator.java
DomainSimilarity.java
DomainSimilarityCalculator.java
GenomeWideCombinableDomains.java
MappingResults.java
PairwiseDomainSimilarity.java
PairwiseDomainSimilarityCalculator.java
PairwiseGenomeComparator.java
PrintableDomainSimilarity.java
PrintableSpeciesSpecificDomainSimilariyData.java
Protein.java
ProteinCountsBasedPairwiseDomainSimilarityCalculator.java
ProteinId.java
SimpleDomain.java
Species.java
SpeciesSpecificDomainSimilariyData.java
SurfacingConstants.java
SurfacingUtil.java
TestSurfacing.java
test
Test.java
tools
ConfidenceAssessor.java
PhylogenyDecorator.java
TreeSplitMatrix.java
util
AsciiHistogram.java
BasicDescriptiveStatistics.java
BasicTable.java
BasicTableParser.java
CommandLineArguments.java
DescriptiveStatistics.java
ForesterConstants.java
ForesterUtil.java
GeneralTable.java
WindowsUtils.java
nexml
model
Annotatable.java
Annotation.java
CategoricalMatrix.java
Character.java
CharacterLinkable.java
CharacterState.java
CharacterStateSet.java
CompoundCharacterState.java
ContinuousMatrix.java
Document.java
DocumentFactory.java
Edge.java
FloatEdge.java
IntEdge.java
Matrix.java
MatrixCell.java
MolecularMatrix.java
Network.java
NetworkObject.java
NexmlWritable.java
Node.java
OTU.java
OTULinkable.java
OTUs.java
OTUsLinkable.java
PolymorphicCharacterState.java
Segmented.java
Tree.java
TreeBlock.java
UncertainCharacterState.java
impl
AnnotatableImpl.java
AnnotationImpl.java
CategoricalMatrixImpl.java
CharacterImpl.java
CharacterStateImpl.java
CharacterStateSetImpl.java
CompoundCharacterStateImpl.java
ContinuousMatrixImpl.java
DocumentImpl.java
EdgeImpl.java
FloatEdgeImpl.java
FloatNetworkImpl.java
FloatTreeImpl.java
IntEdgeImpl.java
IntNetworkImpl.java
IntTreeImpl.java
MatrixCellImpl.java
MatrixImpl.java
MolecularCharacterStateSetImpl.java
MolecularMatrixImpl.java
NetworkImpl.java
NexmlWritableImpl.java
NodeImpl.java
OTUImpl.java
OTULinkableImpl.java
OTUsImpl.java
OTUsLinkableImpl.java
PolymorphicCharacterStateImpl.java
SetManager.java
TreeBlockImpl.java
TreeImpl.java
UncertainCharacterStateImpl.java
test
nescent
phylogeoref
processor
utility
ComputeUtilityTest.java
package org.nexml.model; /** * Represents an OTU. */ public interface OTU extends Annotatable { }