Hierarchy For All Packages

Package Hierarchies:

• org.forester.analysis,
• org.forester.application,
• org.forester.applications,
• org.forester.archaeopteryx,
• org.forester.archaeopteryx.phylogeny.data,
• org.forester.archaeopteryx.tools,
• org.forester.archaeopteryx.webservices,
• org.forester.datastructures,
• org.forester.development,
• org.forester.evoinference,
• org.forester.evoinference.distance,
• org.forester.evoinference.matrix.character,
• org.forester.evoinference.matrix.distance,
• org.forester.evoinference.parsimony,
• org.forester.evoinference.tools,
• org.forester.go,
• org.forester.go.etc,
• org.forester.io.parsers,
• org.forester.io.parsers.nexus,
• org.forester.io.parsers.nhx,
• org.forester.io.parsers.phyloxml,
• org.forester.io.parsers.phyloxml.data,
• org.forester.io.parsers.tol,
• org.forester.io.parsers.util,
• org.forester.io.writers,
• org.forester.msa,
• org.forester.msa_compactor,
• org.forester.pccx,
• org.forester.phylogeny,
• org.forester.phylogeny.data,
• org.forester.phylogeny.factories,
• org.forester.phylogeny.iterators,
• org.forester.protein,
• org.forester.rio,
• org.forester.sdi,
• org.forester.sequence,
• org.forester.species,
• org.forester.surfacing,
• org.forester.test,
• org.forester.test.examples,
• org.forester.tools,
• org.forester.util,
• org.forester.ws.hmmer,
• org.forester.ws.seqdb,
• org.forester.ws.wabi

Class Hierarchy

• java.lang.Object
  • org.forester.applications.aa
  • org.forester.applications.aaa
  • org.forester.phylogeny.data.Accession (implements java.lang.Comparable<T>, org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.AccessionParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.analysis.AncestralTaxonomyInference
  • org.forester.phylogeny.data.Annotation (implements java.lang.Comparable<T>, org.forester.phylogeny.data.MultipleUris, org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.AnnotationParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.application.annotator
  • org.forester.archaeopteryx.AptxUtil
  • org.forester.archaeopteryx.Archaeopteryx
  • org.forester.util.AsciiHistogram
  • org.forester.surfacing.BasicBinaryDomainCombination (implements org.forester.protein.BinaryDomainCombination)
    • org.forester.surfacing.AdjactantDirectedBinaryDomainCombination
    • org.forester.surfacing.DirectedBinaryDomainCombination
  • org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<S> (implements org.forester.evoinference.matrix.character.CharacterStateMatrix<S>)
  • org.forester.surfacing.BasicCombinableDomains (implements org.forester.surfacing.CombinableDomains)
    • org.forester.surfacing.AdjactantDirectedCombinableDomains
    • org.forester.surfacing.DirectedCombinableDomains
  • org.forester.util.BasicDescriptiveStatistics (implements org.forester.util.DescriptiveStatistics)
  • org.forester.protein.BasicDomain (implements org.forester.protein.Domain)
  • org.forester.surfacing.BasicDomainSimilarityCalculator (implements org.forester.surfacing.DomainSimilarityCalculator)
  • org.forester.pccx.BasicExternalNodeBasedCoverageExtender (implements org.forester.pccx.CoverageExtender)
  • org.forester.surfacing.BasicGenomeWideCombinableDomains (implements org.forester.surfacing.GenomeWideCombinableDomains)
  • org.forester.go.BasicGoRelationship (implements org.forester.go.GoRelationship)
  • org.forester.go.BasicGoSubset (implements org.forester.go.GoSubset)
  • org.forester.go.BasicGoTerm (implements org.forester.go.GoTerm)
  • org.forester.go.BasicGoXRef (implements org.forester.go.GoXRef)
  • org.forester.msa.BasicMsa (implements org.forester.msa.Msa)
    • org.forester.msa.DeleteableMsa
    • org.forester.msa.ResampleableMsa
  • org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient (implements org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient)
  • org.forester.protein.BasicProtein (implements org.forester.protein.Protein)
  • org.forester.sequence.BasicSequence (implements org.forester.sequence.MolecularSequence)
  • org.forester.species.BasicSpecies (implements org.forester.species.Species)
  • org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix (implements org.forester.evoinference.matrix.distance.DistanceMatrix)
  • org.forester.util.BasicTable<E>
  • org.forester.util.BasicTableParser
  • org.forester.phylogeny.data.BinaryCharacters (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.BinaryCharactersParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.archaeopteryx.tools.Blast
  • org.forester.evoinference.tools.BootstrapResampler
  • org.forester.phylogeny.data.BranchColor (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.pccx.BranchCountingBasedScoringMethod (implements org.forester.pccx.ScoringMethodForExternalNode)
    • org.forester.pccx.BranchLengthBasedScoringMethod
    • org.forester.pccx.LogBranchLengthBasedScoringMethod
  • org.forester.phylogeny.data.BranchData (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.phylogeny.data.BranchWidth (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.BranchWidthParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.application.check_fasta
  • org.forester.io.parsers.phyloxml.data.ColorParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity (implements org.forester.surfacing.PairwiseDomainSimilarity)
  • org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
  • org.forester.util.CommandLineArguments
  • org.forester.util.CommandProcessBuilder
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • org.forester.development.AbstractRenderer
          • org.forester.development.ResidueRenderer
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.forester.archaeopteryx.MainPanel (implements java.awt.event.ComponentListener)
          • org.forester.archaeopteryx.TreePanel (implements java.awt.event.ActionListener, java.awt.event.MouseWheelListener, java.awt.print.Printable)
        • org.forester.development.MsaRenderer
      • java.awt.Panel (implements javax.accessibility.Accessible)
        • java.applet.Applet
          • javax.swing.JApplet (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer)
            • org.forester.archaeopteryx.ArchaeopteryxA
            • org.forester.archaeopteryx.ArchaeopteryxE (implements java.awt.event.ActionListener)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.forester.msa_compactor.Chart (implements java.awt.event.ActionListener)
            • org.forester.archaeopteryx.FontChooser (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
            • org.forester.archaeopteryx.tools.PhyloInferenceDialog (implements java.awt.event.ActionListener)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.forester.archaeopteryx.MainFrame (implements java.awt.event.ActionListener)
              • org.forester.archaeopteryx.MainFrameApplet
              • org.forester.archaeopteryx.MainFrameApplication
  • org.forester.application.confadd
  • org.forester.phylogeny.data.Confidence (implements java.lang.Comparable<T>, org.forester.phylogeny.data.PhylogenyData)
  • org.forester.tools.ConfidenceAssessor
  • org.forester.io.parsers.phyloxml.data.ConfidenceParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.archaeopteryx.Configuration
  • org.forester.archaeopteryx.Constants
  • org.forester.applications.core_chars
  • org.forester.application.count_support
  • org.forester.surfacing.CountsBasedPairwiseDomainSimilarity (implements org.forester.surfacing.PairwiseDomainSimilarity)
  • org.forester.pccx.CoverageCalculator
  • org.forester.phylogeny.data.Date (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.DateParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.application.decorator
  • org.forester.application.decoratorX
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.forester.io.parsers.phyloxml.PhyloXmlHandler
    • org.forester.io.parsers.tol.TolXmlHandler
  • org.forester.development.DevelopmentTools
  • org.forester.phylogeny.data.Distribution (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.DistributionParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.evoinference.parsimony.DolloParsimony
  • org.forester.application.dom_dup
  • org.forester.phylogeny.data.DomainArchitecture (implements org.forester.phylogeny.data.PhylogenyData)
    • org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture (implements org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData)
  • org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
  • org.forester.io.parsers.phyloxml.data.DomainArchitectureParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
  • org.forester.surfacing.DomainCountsDifferenceUtil
  • org.forester.surfacing.DomainLengths
  • org.forester.surfacing.DomainLengthsTable
  • org.forester.applications.domainloss_replacement
  • org.forester.surfacing.DomainParsimonyCalculator
  • org.forester.surfacing.DomainSimilarity (implements java.lang.Comparable<T>)
  • org.forester.ws.seqdb.EbiDbEntry (implements org.forester.ws.seqdb.SequenceDatabaseEntry)
  • org.forester.phylogeny.data.Event (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.EventParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.test.examples.Example1
  • org.forester.test.examples.Example2
  • org.forester.test.examples.Example3
  • org.forester.test.examples.Example4
  • org.forester.test.examples.Example5
  • org.forester.phylogeny.iterators.ExternalForwardIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
  • org.forester.pccx.ExternalNodeBasedCoverage (implements org.forester.pccx.Coverage)
  • org.forester.pccx.ExternalNodeBasedCoverageMethod (implements org.forester.pccx.CoverageCalculationMethod)
  • org.forester.pccx.ExternalNodeBasedCoverageMethodOptions (implements org.forester.pccx.CoverageCalculationOptions)
  • org.forester.util.ExternalProgram
  • org.forester.application.fasta_split
  • org.forester.io.parsers.FastaParser
  • org.forester.evoinference.parsimony.FitchParsimony<STATE_TYPE>
  • org.forester.util.ForesterConstants
  • org.forester.util.ForesterUtil
  • org.forester.msa_compactor.GapContribution (implements java.lang.Comparable<T>)
  • org.forester.application.gene_tree_preprocess
  • org.forester.io.parsers.GeneralMsaParser
  • org.forester.util.GeneralTable<IDENTIFIER_TYPE,VALUE_TYPE>
  • org.forester.applications.genome_counts_for_once_appearing_dcs
  • org.forester.applications.get_distances
  • org.forester.applications.get_genome_counts_per_char
  • org.forester.applications.get_loss_nodes
  • org.forester.applications.get_shared_chars
  • org.forester.applications.get_subtree_specific_chars
  • org.forester.application.goac
  • org.forester.go.GoId (implements java.lang.Comparable<T>)
  • org.forester.go.GoNameSpace
  • org.forester.go.GoUtils
  • org.forester.application.gsdi
  • org.forester.sdi.GSDI (implements org.forester.sdi.GSDII)
  • org.forester.sdi.GSDIR (implements org.forester.sdi.GSDII)
  • org.forester.development.Hello3d
  • org.forester.development.HmmerRest
  • org.forester.io.parsers.HmmPfamOutputParser
  • org.forester.io.parsers.HmmscanPerDomainTableParser
  • org.forester.phylogeny.data.Identifier (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.IdentifierParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.archaeopteryx.tools.ImageLoader (implements java.lang.Runnable)
  • org.forester.archaeopteryx.tools.InferenceManager
  • org.forester.datastructures.IntMatrix
  • org.forester.applications.inverted_dcs
  • org.forester.phylogeny.iterators.LevelOrderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
  • org.forester.applications.map_lengths
  • org.forester.surfacing.MappingResults
  • org.forester.application.mcc
  • org.forester.application.meta_ontologizer
  • org.forester.go.etc.MetaOntologizer
  • org.forester.pccx.ModelingUtils
  • org.forester.application.msa_compactor
  • org.forester.msa_compactor.MsaCompactor
  • org.forester.msa.MsaInferrer
    • org.forester.msa.ClustalOmega
    • org.forester.msa.Mafft
  • org.forester.msa.MsaMethods
  • org.forester.msa_compactor.MsaProperties
  • org.forester.evoinference.distance.NeighborJoining
  • org.forester.evoinference.distance.NeighborJoiningF
  • org.forester.evoinference.distance.NeighborJoiningR
  • org.forester.development.neTest
  • org.forester.development.neTest.DoublePointer
  • org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
  • org.forester.io.parsers.nexus.NexusCharactersParser
  • org.forester.io.parsers.nexus.NexusConstants
  • org.forester.io.parsers.nexus.NexusPhylogeniesParser (implements org.forester.io.parsers.IteratingPhylogenyParser, org.forester.io.parsers.PhylogenyParser)
  • org.forester.io.parsers.nhx.NHXParser (implements org.forester.io.parsers.IteratingPhylogenyParser, org.forester.io.parsers.PhylogenyParser)
  • org.forester.io.parsers.nhx.NHXtags
  • org.forester.application.nj
  • org.forester.phylogeny.data.NodeData (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.phylogeny.data.NodeVisualData (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.application.obo_tool
  • org.forester.go.OBOparser
  • org.forester.go.etc.OntologizerResult (implements java.lang.Comparable<T>)
  • org.forester.archaeopteryx.Options
  • org.forester.evoinference.distance.PairwiseDistanceCalculator
  • org.forester.surfacing.PairwiseGenomeComparator
  • org.forester.phylogeny.factories.ParserBasedPhylogenyFactory (implements org.forester.phylogeny.factories.PhylogenyFactory)
  • org.forester.io.parsers.util.ParserUtils
  • org.forester.io.parsers.nexus.PaupLogParser
  • org.forester.application.pccx
  • org.forester.application.pfam_go
  • org.forester.application.pfam2go_extractor
  • org.forester.application.pfamacc2go
  • org.forester.application.pfamacc2pfamid
  • org.forester.go.PfamToGoMapping (implements org.forester.go.Mapping)
  • org.forester.go.PfamToGoParser
  • org.forester.applications.phylo2coloredgraphics
  • org.forester.applications.phylo2graphics
  • org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
  • org.forester.phylogeny.Phylogeny
  • org.forester.phylogeny.PhylogenyBranch
  • org.forester.phylogeny.data.PhylogenyDataUtil
  • org.forester.tools.PhylogenyDecorator
  • org.forester.phylogeny.PhylogenyMethods
  • org.forester.phylogeny.PhylogenyNode (implements java.lang.Comparable<T>)
  • org.forester.io.writers.PhylogenyWriter
  • org.forester.application.phylostrip
  • org.forester.application.phyloxml_converter
  • org.forester.io.parsers.phyloxml.PhyloXmlMapping
  • org.forester.io.writers.PhyloXmlNodeWriter
  • org.forester.io.parsers.phyloxml.PhyloXmlParser (implements org.forester.io.parsers.PhylogenyParser)
  • org.forester.io.parsers.phyloxml.PhyloXmlUtil
  • org.forester.phylogeny.data.Point (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.PointParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.phylogeny.data.Polygon (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.PolygonParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.phylogeny.iterators.PostOrderStackObject
  • org.forester.phylogeny.iterators.PostorderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
  • org.forester.phylogeny.iterators.PreorderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
  • org.forester.archaeopteryx.tools.ProcessPool
  • org.forester.archaeopteryx.tools.ProcessRunning
  • org.forester.phylogeny.data.PropertiesMap (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.phylogeny.data.Property (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.PropertyParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
  • org.forester.phylogeny.data.ProteinDomain (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.ProteinDomainParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.protein.ProteinId (implements java.lang.Comparable<T>)
  • org.forester.datastructures.Queue
  • org.forester.development.RandomThing
  • org.forester.phylogeny.data.Reference (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.ReferenceParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.applications.reinv_count
  • org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence (implements org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData)
  • org.forester.archaeopteryx.phylogeny.data.RenderableVector (implements org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData)
  • org.forester.ws.wabi.RestUtil
  • org.forester.application.rio
  • org.forester.rio.RIO
  • org.forester.archaeopteryx.tools.RunnableProcess (implements java.lang.Runnable)
    • org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer
    • org.forester.archaeopteryx.tools.PhylogeneticInferrer
    • org.forester.archaeopteryx.tools.SequenceDataRetriver
    • org.forester.analysis.TaxonomyDataManager
  • org.forester.evoinference.parsimony.SankoffParsimony<STATE_TYPE>
  • org.forester.evoinference.distance.Sarray
  • org.forester.sdi.SDI
  • org.forester.sdi.SDIR
  • org.forester.sdi.SDIutil
  • org.forester.phylogeny.data.Sequence (implements java.lang.Comparable<T>, org.forester.phylogeny.data.MultipleUris, org.forester.phylogeny.data.PhylogenyData)
  • org.forester.util.SequenceAccessionTools
  • org.forester.ws.seqdb.SequenceDbWsTools
  • org.forester.io.parsers.phyloxml.data.SequenceParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.phylogeny.data.SequenceRelation (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.SequenceRelationParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.io.writers.SequenceWriter
  • org.forester.applications.set_comparator
  • org.forester.applications.shared_chars_in_ext_nodes
  • org.forester.applications.simple_node_processor
  • org.forester.surfacing.SimpleDomain (implements org.forester.protein.Domain)
  • org.forester.evoinference.distance.Sset
  • org.forester.util.StringInt
  • org.forester.util.StringInt.DescendingIntComparator (implements java.util.Comparator<T>)
  • org.forester.applications.subtree_feature_count
  • org.forester.application.support_statistics
  • org.forester.application.support_transfer
  • org.forester.tools.SupportCount
  • org.forester.application.surfacing
  • org.forester.surfacing.SurfacingConstants
  • org.forester.surfacing.SurfacingUtil
  • org.forester.io.parsers.SymmetricalDistanceMatrixParser
  • org.forester.util.SystemCommandExecutor
  • org.forester.application.table2fasta
  • org.forester.applications.tax_code_cleaner
  • org.forester.phylogeny.data.Taxonomy (implements java.lang.Comparable<T>, org.forester.phylogeny.data.MultipleUris, org.forester.phylogeny.data.PhylogenyData)
  • org.forester.util.TaxonomyColors
  • org.forester.io.parsers.phyloxml.data.TaxonomyParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.util.TaxonomyUtil
  • org.forester.development.Test
  • org.forester.test.Test
  • org.forester.ws.hmmer.Test
  • org.forester.go.TestGo
  • org.forester.sdi.TestGSDI
  • org.forester.pccx.TestPccx
  • org.forester.evoinference.TestPhylogenyReconstruction
  • org.forester.rio.TestRIO
  • org.forester.surfacing.TestSurfacing
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.forester.analysis.AncestralTaxonomyInferenceException
      • java.io.IOException
        • org.forester.msa.MsaFormatException
        • org.forester.io.parsers.nexus.NexusFormatException
        • org.forester.io.parsers.nhx.NHXFormatException
        • org.forester.io.parsers.util.PhylogenyParserException
        • org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
      • org.forester.rio.RIOException
      • java.lang.RuntimeException
        • org.forester.util.FailedConditionCheckException
        • java.lang.IllegalArgumentException
          • org.forester.util.IllegalFormatUseException
        • org.forester.io.parsers.phyloxml.PhyloXmlException
      • org.forester.sdi.SDIException
  • org.forester.development.Time
  • org.forester.io.parsers.tol.TolParser (implements org.forester.io.parsers.PhylogenyParser)
  • org.forester.io.parsers.tol.TolXmlMapping
  • org.forester.archaeopteryx.TreeColorSet
  • org.forester.archaeopteryx.TreeFontSet
  • org.forester.archaeopteryx.TreePanelUtil
  • org.forester.tools.TreeSplitMatrix
  • org.forester.ws.wabi.TxSearch
  • org.forester.ws.seqdb.UniProtEntry (implements org.forester.ws.seqdb.SequenceDatabaseEntry)
  • org.forester.ws.seqdb.UniProtTaxonomy
  • org.forester.phylogeny.data.Uri (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.data.UriParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
  • org.forester.archaeopteryx.UrlTreeReader (implements java.lang.Runnable)
  • org.forester.ws.wabi.WabiTools
  • org.forester.archaeopteryx.webservices.WebservicesManager
  • org.forester.archaeopteryx.webservices.WebserviceUtil
  • org.forester.applications.wiki_examples
  • org.forester.util.WindowsUtils
  • java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
    • java.io.BufferedWriter
      • org.forester.util.EasyWriter
  • org.forester.io.parsers.phyloxml.XmlElement

Interface Hierarchy

• org.forester.evoinference.matrix.character.CharacterStateMatrix<S>
• org.forester.surfacing.CombinableDomains
• java.lang.Comparable<T>
  • org.forester.protein.BinaryDomainCombination
  • org.forester.protein.Domain
  • org.forester.go.GoRelationship
  • org.forester.go.GoSubset
  • org.forester.go.GoTerm (also extends org.forester.phylogeny.data.PhylogenyData)
  • org.forester.go.GoXRef
  • org.forester.go.Mapping
  • org.forester.species.Species
• org.forester.pccx.Coverage
• org.forester.pccx.CoverageCalculationMethod
• org.forester.pccx.CoverageCalculationOptions
• org.forester.pccx.CoverageExtender
• org.forester.util.DescriptiveStatistics
• org.forester.evoinference.matrix.distance.DistanceMatrix
• org.forester.surfacing.DomainSimilarityCalculator
• org.forester.surfacing.GenomeWideCombinableDomains
• org.forester.sdi.GSDII
• org.forester.io.parsers.IteratingPhylogenyParser
• java.util.Iterator<E>
  • org.forester.phylogeny.iterators.PhylogenyNodeIterator
• org.forester.sequence.MolecularSequence
• org.forester.msa.Msa
• org.forester.phylogeny.data.MultipleUris
• org.forester.surfacing.PairwiseDomainSimilarity
• org.forester.surfacing.PairwiseDomainSimilarityCalculator
• org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
• org.forester.phylogeny.data.PhylogenyData
  • org.forester.go.GoTerm (also extends java.lang.Comparable<T>)
  • org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
• org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser
• org.forester.phylogeny.factories.PhylogenyFactory
• org.forester.io.parsers.PhylogenyParser
• org.forester.protein.Protein
• org.forester.pccx.ScoringMethodForExternalNode
• org.forester.ws.seqdb.SequenceDatabaseEntry

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.forester.phylogeny.data.Accession.Source
    • org.forester.archaeopteryx.AptxUtil.GraphicsExportType
    • org.forester.protein.BinaryDomainCombination.DomainCombinationType
    • org.forester.protein.BinaryDomainCombination.OutputFormat
    • org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates
    • org.forester.evoinference.matrix.character.CharacterStateMatrix.Format
    • org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates
    • org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates
    • org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON
    • org.forester.archaeopteryx.Configuration.UI
    • org.forester.evoinference.matrix.distance.DistanceMatrix.Format
    • org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
    • org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
    • org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
    • org.forester.surfacing.DomainSimilarity.PRINT_OPTION
    • org.forester.surfacing.DomainSimilarityCalculator.Detailedness
    • org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
    • org.forester.phylogeny.data.Event.EventType
    • org.forester.util.ForesterConstants.PhylogeneticTreeFormats
    • org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
    • org.forester.go.GoNameSpace.GoNamespaceType
    • org.forester.go.GoRelationship.Type
    • org.forester.go.GoSubset.Type
    • org.forester.go.GoXRef.Type
    • org.forester.io.parsers.HmmPfamOutputParser.FilterType
    • org.forester.io.parsers.HmmPfamOutputParser.ReturnType
    • org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
    • org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
    • org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
    • org.forester.sequence.MolecularSequence.TYPE
    • org.forester.msa.Msa.MSA_FORMAT
    • org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
    • org.forester.phylogeny.data.NodeDataField
    • org.forester.phylogeny.data.NodeVisualData.FontType
    • org.forester.phylogeny.data.NodeVisualData.NodeFill
    • org.forester.phylogeny.data.NodeVisualData.NodeShape
    • org.forester.go.OBOparser.ReturnType
    • org.forester.go.etc.OntologizerResult.TYPE
    • org.forester.archaeopteryx.Options.CLADOGRAM_TYPE
    • org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION
    • org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE
    • org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
    • org.forester.archaeopteryx.tools.PhylogeneticInferrer.MSA_PRG
    • org.forester.tools.PhylogenyDecorator.FIELD
    • org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY
    • org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField
    • org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE
    • org.forester.io.writers.PhylogenyWriter.FORMAT
    • org.forester.phylogeny.data.Property.AppliesTo
    • org.forester.rio.RIO.REROOTING
    • org.forester.sdi.SDIutil.ALGORITHM
    • org.forester.sdi.SDIutil.TaxonomyComparisonBase
    • org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
    • org.forester.io.writers.SequenceWriter.SEQ_FORMAT
    • org.forester.io.parsers.SymmetricalDistanceMatrixParser.InputMatrixType
    • org.forester.ws.wabi.TxSearch.RANKS
    • org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS
    • org.forester.ws.wabi.TxSearch.TAX_RANK
    • org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat