Hierarchy For All Packages

Package Hierarchies:

phylonet, phylonet.algorithms.bipartitemaching, phylonet.algorithms.pairalignment, phylonet.algorithms.shortestpath, phylonet.app, phylonet.app.controller, phylonet.app.controller.datum, phylonet.app.model, phylonet.app.model.datum, phylonet.app.tool, phylonet.app.tool.charnet, phylonet.app.tool.cmpnets, phylonet.app.tool.component, phylonet.app.tool.countcoal, phylonet.app.tool.inferst, phylonet.app.tool.inferst.subpanel, phylonet.app.tool.lca, phylonet.app.tool.mast, phylonet.app.tool.netpars, phylonet.app.tool.recomp, phylonet.app.tool.rf, phylonet.app.tool.riatahgt, phylonet.app.util, phylonet.app.view, phylonet.app.view.datum, phylonet.bits, phylonet.cmdline, phylonet.cmdline.tool, phylonet.coalescent, phylonet.compatibility, phylonet.consensus, phylonet.fitchpars, phylonet.graph.io, phylonet.graph.model, phylonet.graph.model.sgi, phylonet.heaps, phylonet.ilp, phylonet.lca, phylonet.mast, phylonet.maxclique, phylonet.mct, phylonet.network.characterization, phylonet.network.gtdistribution, phylonet.network.io, phylonet.network.model, phylonet.network.model.bni, phylonet.network.util, phylonet.nj, phylonet.recomp, phylonet.recomp.comparator, phylonet.riatahgt, phylonet.riatahgt.viewer, phylonet.rpt, phylonet.rpt.io, phylonet.sequence.io, phylonet.sequence.model, phylonet.simulator, phylonet.symmdiff, phylonet.tree.io, phylonet.tree.model, phylonet.tree.model.sti, phylonet.tree.util, phylonet.tree.view.swing, phylonet.util

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • phylonet.app.tool.APhyloTool
      • phylonet.app.tool.charnet.CharnetTool
      • phylonet.app.tool.cmpnets.CmpnetsTool
      • phylonet.app.tool.countcoal.CountCoalTool
      • phylonet.app.tool.inferst.InferSTTool
      • phylonet.app.tool.lca.LCATool
      • phylonet.app.tool.mast.MastTool
      • phylonet.app.tool.netpars.NetparsTool
      • phylonet.app.tool.recomp.RecompTool
      • phylonet.app.tool.rf.RFTool
      • phylonet.app.tool.riatahgt.RIATAHGTTool
  • phylonet.app.model.datum.ADatum (implements java.lang.Comparable<T>, java.io.Serializable)
    • phylonet.app.model.datum.BatchDatum
    • phylonet.app.model.datum.HGTDatum
    • phylonet.app.model.datum.NetworkDatum
    • phylonet.app.model.datum.SequenceAlignmentDatum
    • phylonet.app.model.datum.TreeDatum
      • phylonet.app.model.datum.TreeWithBranchLengthsDatum
  • phylonet.app.controller.datum.ADatumController
    • phylonet.app.controller.datum.BatchDatumController
    • phylonet.app.controller.datum.HGTDatumController
    • phylonet.app.controller.datum.NetworkDatumController
    • phylonet.app.controller.datum.SequenceAlignmentDatumController
    • phylonet.app.controller.datum.TreeDatumController
  • phylonet.network.model.bni.BfsSearch<T> (implements java.lang.Iterable<T>)
  • phylonet.tree.util.Bipartitions
  • phylonet.bits.BitVector (implements java.lang.Iterable<T>, phylonet.rpt.Printable)
  • phylonet.bits.BitVectorTestCase
  • phylonet.network.model.bni.BniNetNode<T> (implements phylonet.network.model.NetNode<T>)
  • phylonet.network.model.bni.BniNetwork<T> (implements java.lang.Cloneable, phylonet.network.model.Network<T>)
  • phylonet.coalescent.Bootstrap
  • phylonet.tree.util.Clustering
  • phylonet.coalescent.ClusteringInference
  • phylonet.network.io.ClustersReader<T>
  • phylonet.cmdline.tool.CmdLineTool
    • phylonet.cmdline.tool.BootstrapCmdLineTool
    • phylonet.cmdline.tool.CharnetCmdLineTool
    • phylonet.cmdline.tool.CmpnetsCmdLineTool
    • phylonet.cmdline.tool.CompatCmdLineTool
    • phylonet.cmdline.tool.CountCoalCmdLineTool
    • phylonet.cmdline.tool.DeepCoalCountCmdLineTool
    • phylonet.cmdline.tool.GenCplexCmdLineTool
    • phylonet.cmdline.tool.GenstCmdLineTool
    • phylonet.cmdline.tool.GTDistrInNetworkCmdLineTool
    • phylonet.cmdline.tool.GTRefineAndRootCmdLineTool
    • phylonet.cmdline.tool.InferStCmdLineTool
    • phylonet.cmdline.tool.LcaCmdLineTool
    • phylonet.cmdline.tool.MastCmdLineTool
    • phylonet.cmdline.tool.NetparsCmdLineTool
    • phylonet.cmdline.tool.RecompCmdLineTool
    • phylonet.cmdline.tool.RfCmdLineTool
    • phylonet.cmdline.tool.RiataHgtCmdLineTool
    • phylonet.cmdline.tool.SimGTInNetworkCmdLineTool
  • phylonet.coalescent.CoalescentCounter
  • phylonet.coalescent.CoalescentCounterTestCase
  • phylonet.tree.util.Collapse
  • phylonet.tree.util.Collapse.CollapseDescriptor
  • phylonet.tree.util.CollapseTestCase
  • phylonet.cmdline.CommandLineApp
  • phylonet.cmdline.CommandLineAppTestCase
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.AbstractButton (implements java.awt.ItemSelectable, javax.swing.SwingConstants)
          • javax.swing.JButton (implements javax.accessibility.Accessible)
            • phylonet.app.tool.component.BrowseButton
        • javax.swing.JComboBox (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
          • phylonet.app.tool.component.PhyloComboBox
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • phylonet.app.view.datum.DatumThumbnailView
          • phylonet.app.tool.component.ExtendableComboBoxList
          • phylonet.app.tool.component.ExtendableNodeSetsList
          • phylonet.app.tool.inferst.subpanel.InferenceMethodParametersSubpanel
            • phylonet.app.tool.inferst.subpanel.GlassMatrixSubpanel
            • phylonet.app.tool.inferst.subpanel.GlassTreeSubpanel
            • phylonet.app.tool.inferst.subpanel.MajoritySubpanel
            • phylonet.app.tool.inferst.subpanel.MdcDpRootedTimeSubpanel
            • phylonet.app.tool.inferst.subpanel.MdcDpSubpanel
            • phylonet.app.tool.inferst.subpanel.MdcIlpSubpanel
            • phylonet.app.tool.inferst.subpanel.MdcIlpTimeSubpanel
            • phylonet.app.tool.inferst.subpanel.NoParametersSubpanel
          • phylonet.tree.view.swing.NewickViewer
          • phylonet.riatahgt.viewer.TreeCanvas
        • javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • javax.swing.JTextArea
            • phylonet.app.tool.component.PhyloTextArea
          • javax.swing.JTextField (implements javax.swing.SwingConstants)
            • phylonet.app.tool.component.PhyloTextField
        • phylonet.tree.view.swing.TreeView
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • phylonet.app.tool.AParamsDialog
              • phylonet.app.tool.charnet.CharnetParamsDialog
              • phylonet.app.tool.cmpnets.CmpnetsParamsDialog
              • phylonet.app.tool.countcoal.CountCoalParamsDialog
              • phylonet.app.tool.inferst.InferSTParamsDialog
              • phylonet.app.tool.lca.LCAParamsDialog
              • phylonet.app.tool.mast.MASTParamsDialog
              • phylonet.app.tool.netpars.NetparsParamsDialog
              • phylonet.app.tool.recomp.RECOMPParamsDialog
              • phylonet.app.tool.rf.RFParamsDialog
              • phylonet.app.tool.riatahgt.RiataHGTParamsDialog
            • phylonet.app.tool.AResultsDialog
              • phylonet.app.tool.charnet.CharnetResultsDialog
                • phylonet.app.tool.charnet.CharnetClusterResultsDialog
                • phylonet.app.tool.charnet.CharnetTreeResultsDialog
                • phylonet.app.tool.charnet.CharnetTripartitionResultsDialog
              • phylonet.app.tool.cmpnets.CmpnetsResultsDialog
              • phylonet.app.tool.countcoal.CountCoalResultsDialog
              • phylonet.app.tool.inferst.InferStResultsDialog
              • phylonet.app.tool.lca.LCAResultsDialog
              • phylonet.app.tool.mast.MASTResultsDialog
              • phylonet.app.tool.netpars.NetparsResultsDialog
              • phylonet.app.tool.recomp.RECOMPResultsDialog
              • phylonet.app.tool.rf.RFResultsDialog
              • phylonet.app.tool.riatahgt.RiataHGTResultsDialog
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • phylonet.app.view.datum.ADatumView
              • phylonet.app.view.datum.BatchDatumView
              • phylonet.app.view.datum.HGTDatumView
              • phylonet.app.view.datum.NetworkDatumView
              • phylonet.app.view.datum.SequenceAlignmentDatumView
              • phylonet.app.view.datum.TreeDatumView
            • phylonet.app.view.PhyloNetAppView
            • phylonet.riatahgt.viewer.RiataViewerFrame
  • phylonet.consensus.ConsensusTestCase
  • phylonet.tree.util.Consolidate
  • phylonet.tree.util.Consolidate.ConsolidateDescriptor
  • phylonet.coalescent.DeepCoalescencesCounter
  • phylonet.coalescent.DemocraticVoteInference
  • phylonet.network.model.bni.DfsSearch<T> (implements java.lang.Iterable<T>)
  • phylonet.app.util.Dialogs
  • phylonet.app.util.DialogsTestCase
  • phylonet.algorithms.shortestpath.Dijkstra
  • phylonet.algorithms.shortestpath.DijkstraTestCase
  • phylonet.graph.io.EdgeListReader
  • phylonet.riatahgt.EventBootstrap
  • phylonet.riatahgt.ExMultipleMastsTestCase
  • phylonet.network.io.ExNewickReader<T>
  • phylonet.network.io.ExNewickReaderTestCase
  • phylonet.network.io.ExNewickWriter<T>
  • phylonet.riatahgt.ExRiataMultipleHgtTestCase
  • phylonet.sequence.io.FastaReader (implements java.lang.Iterable<T>)
  • phylonet.sequence.io.FastaReader.FastaRecord
  • phylonet.mct.GaneshkumarWarnowMCT
  • phylonet.mct.GaneshkumarWarnowMCTTestCase
  • phylonet.coalescent.GeneTreeRefinement
  • phylonet.coalescent.GLASSInference
  • phylonet.network.gtdistribution.GTDistributionInNetwork
  • phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSP
  • phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSPTestCase
  • phylonet.riatahgt.HgtEvent (implements java.io.Serializable)
  • phylonet.network.io.HgtReader<T>
  • phylonet.riatahgt.HgtScenario (implements java.io.Serializable)
  • phylonet.algorithms.bipartitemaching.HungarianBipartiteMatcher
  • phylonet.algorithms.bipartitemaching.HungarianTestCase
  • phylonet.ilp.IlpGenerator
  • phylonet.ilp.IlpGeneratorTestCase
  • phylonet.util.ImmutableCollectionWrapper (implements phylonet.util.ImmutableCollection)
  • phylonet.util.ImmutableSetWrapper (implements phylonet.util.ImmutableSet)
  • phylonet.rpt.Iterating
  • phylonet.util.LIDAMath
  • phylonet.coalescent.MajorityConsensusInference
  • phylonet.mast.MastWrapper
  • phylonet.mast.MastWrapperTestCase
  • phylonet.maxclique.MaxClique
  • phylonet.maxclique.MaxCliqueNonParameterizedTestCase
  • phylonet.maxclique.MaxCliqueParameterizedTestCase
  • phylonet.heaps.MaxDoubleHeap
  • phylonet.heaps.MaxHeap<N,D> (implements java.lang.Iterable<T>)
    • phylonet.heaps.BinaryMaxHeap<N,D>
  • phylonet.heaps.MaxIntHeap
  • phylonet.coalescent.MDCInference_DP
  • phylonet.coalescent.MDCInference_ILP
  • phylonet.coalescent.MDCURInference
  • phylonet.coalescent.MDCURInference_DP
  • phylonet.coalescent.MDCURInference_ILP
  • phylonet.coalescent.MDCWithTime
  • phylonet.heaps.MinFibonacciHeap.FibonacciHeapEntry
  • phylonet.heaps.MinFibonacciHeapTestCase
  • phylonet.heaps.MinHeap<N,D> (implements java.lang.Iterable<T>)
    • phylonet.heaps.BinaryMinHeap<N,D>
    • phylonet.heaps.MinFibonacciHeap<N,D>
  • phylonet.nj.NeighborJoining
  • phylonet.network.util.NetNodes
  • phylonet.network.characterization.NetworkCluster<T>
  • phylonet.network.characterization.NetworkEdge<T>
  • phylonet.network.util.Networks
  • phylonet.network.characterization.NetworkTree<T>
  • phylonet.network.characterization.NetworkTreeEnumerator<T> (implements java.lang.Iterable<T>)
  • phylonet.network.characterization.NetworkTripartition<T>
  • phylonet.tree.io.NewickReader
  • phylonet.tree.io.NewickReaderTestCase
  • phylonet.tree.io.NewickWriter
  • phylonet.nj.NJTestCase
  • phylonet.lca.NodeListReader
  • phylonet.fitchpars.ParsimonyCalculator
  • phylonet.fitchpars.ParsimonyCalculatorTestCase
  • phylonet.graph.model.PathImpl (implements phylonet.graph.model.Path)
    • phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSP.HMSPath
  • phylonet.recomp.comparator.PAUPWindowComparator (implements phylonet.recomp.WindowComparator)
    • phylonet.recomp.comparator.PAUPAvgMaxComparator
    • phylonet.recomp.comparator.PAUPAvgMinComparator
    • phylonet.recomp.comparator.PAUPIntersectionComparator
    • phylonet.recomp.comparator.PAUPParsDiffComparator
  • phylonet.app.util.PhyloLogger
  • phylonet.app.PhyloNetApp
  • phylonet.app.controller.PhyloNetAppController
  • phylonet.app.model.PhyloNetAppModel
  • phylonet.PhyloTestCase
  • phylonet.sequence.io.PlainXReader (implements java.lang.Iterable<T>)
  • phylonet.sequence.io.PlainXReader.PlainXRecord
  • phylonet.tree.util.PostTraversal<D> (implements java.lang.Iterable<T>)
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.BufferedReader
      • java.io.LineNumberReader
        • phylonet.rpt.io.LineReader (implements java.lang.Iterable<T>)
  • phylonet.recomp.RECOMP
  • phylonet.tree.util.Resolve
  • phylonet.riatahgt.RiataHgt (implements java.io.Serializable)
  • phylonet.riatahgt.RiataHGTTestCase
  • phylonet.riatahgt.viewer.RiataViewerFrameTestCase
  • phylonet.lca.SchieberVishkinLCA
  • phylonet.lca.SchieberVishkinLCATestCase
  • phylonet.sequence.model.SequenceAlignment (implements java.io.Serializable)
  • phylonet.sequence.model.SequenceAlignmentTestCase
  • phylonet.graph.model.sgi.SGIEdge<ND,ED> (implements phylonet.graph.model.MutableEdge)
  • phylonet.graph.model.sgi.SGIGraph<ND,ED> (implements phylonet.graph.model.MutableGraph)
  • phylonet.graph.model.sgi.SGINode<ND,ED> (implements phylonet.graph.model.MutableNode)
  • phylonet.simulator.SimGTInNetwork
  • phylonet.algorithms.pairalignment.SmithWaterman
  • phylonet.algorithms.pairalignment.SmithWaterman.Match
  • phylonet.coalescent.Solution
  • phylonet.mast.SteelWarnowMAST
    • phylonet.riatahgt.ExMultipleMasts
  • phylonet.mast.SteelWarnowMASTTestCase
  • phylonet.tree.model.sti.STINode<D> (implements phylonet.tree.model.TMutableNode)
  • phylonet.tree.model.sti.STITree<D> (implements phylonet.tree.model.MutableTree)
  • phylonet.tree.model.sti.STITreeBipartition
  • phylonet.tree.model.sti.STITreeCluster
    • phylonet.tree.model.sti.STITreeClusterWD<D>
  • phylonet.symmdiff.SymmetricDifference
  • phylonet.symmdiff.SymmetricDifferenceTestCase
  • phylonet.coalescent.TaxaDistanceMatrix
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • phylonet.network.io.ExNewickException
      • phylonet.tree.io.ParseException
      • java.lang.RuntimeException
        • phylonet.app.tool.InvalidParameterException
        • phylonet.cmdline.tool.ToolException
        • phylonet.cmdline.tool.ToolInitializationException
      • phylonet.sequence.model.SequenceException
  • phylonet.compatibility.TreeCompatibility
  • phylonet.consensus.TreeConsensusCalculator
  • phylonet.tree.util.Trees
  • phylonet.network.io.TreesReader
  • phylonet.tree.util.TreesTestCase
  • phylonet.network.io.TripartitionsReader

Interface Hierarchy

• phylonet.app.model.DataCriterion
• phylonet.graph.model.Graph
  • phylonet.graph.model.MutableGraph
• phylonet.graph.model.GraphComponent
  • phylonet.graph.model.Edge
    • phylonet.graph.model.MutableEdge
  • phylonet.graph.model.MutableEdge
  • phylonet.graph.model.MutableNode
  • phylonet.graph.model.Node
    • phylonet.graph.model.MutableNode
• phylonet.graph.model.GraphListener
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • phylonet.util.ImmutableCollection
      • phylonet.util.ImmutableSet (also extends java.util.Set<E>)
    • phylonet.util.ImmutableSet (also extends phylonet.util.ImmutableCollection, java.util.Set<E>)
    • java.util.Set<E>
      • phylonet.util.ImmutableSet (also extends phylonet.util.ImmutableCollection)
  • phylonet.util.ImmutableCollection
    • phylonet.util.ImmutableSet (also extends java.util.Set<E>)
  • phylonet.util.ImmutableSet (also extends phylonet.util.ImmutableCollection, java.util.Set<E>)
  • java.util.Set<E>
    • phylonet.util.ImmutableSet (also extends phylonet.util.ImmutableCollection)
• phylonet.graph.model.Path
• phylonet.rpt.Printable
  • phylonet.tree.model.MutableTree
  • phylonet.tree.model.TMutableNode
  • phylonet.tree.model.TNode (also extends java.io.Serializable)
    • phylonet.tree.model.TMutableNode
  • phylonet.tree.model.Tree (also extends java.io.Serializable)
    • phylonet.tree.model.MutableTree
• java.io.Serializable
  • phylonet.tree.model.MutableTree
  • phylonet.network.model.NetNode<T>
  • phylonet.network.model.Network<T>
  • phylonet.tree.model.TMutableNode
  • phylonet.tree.model.TNode (also extends phylonet.rpt.Printable)
    • phylonet.tree.model.TMutableNode
  • phylonet.tree.model.Tree (also extends phylonet.rpt.Printable)
    • phylonet.tree.model.MutableTree
• phylonet.recomp.WindowComparator

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • phylonet.network.characterization.NetworkCharacterizationMeasure
    • phylonet.tree.view.swing.TreeView.TreeStyle
    • phylonet.app.tool.inferst.InferenceMethod
    • phylonet.recomp.comparator.PAUPWindowComparator.DistanceMeasure
    • phylonet.app.tool.recomp.RECOMPParamsDialog.ComparisonFunction