Hierarchy For All Packages

Package Hierarchies:

statalign, statalign.base, statalign.base.hmm, statalign.base.mcmc, statalign.base.thread, statalign.distance, statalign.io, statalign.io.input, statalign.io.input.plugins, statalign.mcmc, statalign.model.ext, statalign.model.ext.plugins, statalign.model.ext.plugins.structalign, statalign.model.score, statalign.model.score.plugins, statalign.model.subst, statalign.model.subst.plugins, statalign.postprocess, statalign.postprocess.gui, statalign.postprocess.gui.treeviews, statalign.postprocess.plugins, statalign.postprocess.plugins.benchmarks, statalign.postprocess.plugins.contree, statalign.postprocess.plugins.contree.hash, statalign.postprocess.plugins.contree.test, statalign.postprocess.plugins.structalign, statalign.postprocess.utils, statalign.ui, statalign.utils

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • statalign.postprocess.plugins.contree.Cluster (implements java.lang.Comparable<T>)
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • statalign.postprocess.plugins.contree.TaxaMap
  • org.apache.commons.math3.distribution.AbstractRealDistribution (implements org.apache.commons.math3.distribution.RealDistribution, java.io.Serializable)
    • statalign.utils.BetaDistribution
    • statalign.utils.GammaDistribution
    • statalign.utils.NormalDistribution
  • statalign.base.AlignColumn
  • statalign.distance.AlignmentSample
  • statalign.postprocess.plugins.benchmarks.AlignmentSample (implements java.io.Serializable)
  • statalign.base.AutomateParameters
  • statalign.postprocess.plugins.benchmarks.Benchmarks
  • statalign.mcmc.BetaPrior (implements statalign.mcmc.PriorDistribution<T>)
  • statalign.base.CircularArray<E>
  • statalign.postprocess.plugins.contree.CNetwork
  • statalign.postprocess.plugins.contree.CNetworkEdge
  • statalign.postprocess.plugins.contree.CNetworkNode
  • statalign.postprocess.plugins.contree.CNetworkPath
  • statalign.postprocess.plugins.contree.CNetworkSplit
  • statalign.postprocess.gui.ColorGradient
  • statalign.CommandLine
  • statalign.distance.ComplexPair (implements java.util.Comparator<T>)
  • 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.JPanel (implements javax.accessibility.Accessible)
          • statalign.postprocess.gui.AlignmentGUI
          • statalign.postprocess.gui.CNetworkView (implements java.awt.event.MouseWheelListener)
          • statalign.postprocess.gui.DistanceGUI
          • statalign.postprocess.gui.EntropyGUI
          • statalign.postprocess.gui.InputGUI (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
          • statalign.postprocess.gui.LogLikelihoodTraceGUI
          • statalign.postprocess.gui.PPFoldGUI
          • statalign.postprocess.gui.StructAlignTraceGUI
          • statalign.postprocess.gui.treeviews.TreeView
            • statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView
            • statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView
            • statalign.postprocess.gui.treeviews.NetworkTreeView (implements java.awt.event.MouseWheelListener)
            • statalign.postprocess.gui.treeviews.VerticalPhylogramTreeView
          • fr.orsay.lri.varna.VARNAPanel
            • statalign.postprocess.gui.StructureDetails
            • statalign.postprocess.gui.StructureGUI
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • statalign.ui.AboutDlg
            • statalign.ui.ErrorMessage (implements java.awt.event.ActionListener)
            • statalign.ui.HelpWindow (implements java.awt.event.ActionListener)
            • statalign.ui.McmcSettingsDlg (implements java.awt.event.ActionListener, java.awt.event.KeyListener)
            • statalign.ui.OutputPreferences (implements java.awt.event.ActionListener)
            • statalign.ui.RNASettingsDlg (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener, java.awt.event.KeyListener)
            • statalign.ui.TextDlg
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • statalign.ui.MainFrame (implements java.awt.event.ActionListener)
  • statalign.io.input.ConfReader
  • statalign.postprocess.plugins.contree.test.ConsensusNetworkTester
  • statalign.postprocess.plugins.contree.test.CorrectnessTester
  • statalign.postprocess.plugins.contree.CTMain
  • statalign.postprocess.plugins.contree.CTree
  • statalign.io.DataManager
  • statalign.io.input.DataReader
    • statalign.io.input.plugins.CoorReader
    • statalign.io.input.plugins.FastaReader
    • statalign.io.input.plugins.NewickReader
    • statalign.io.input.plugins.PDBReader
  • statalign.postprocess.plugins.benchmarks.Dataset (implements java.io.Serializable)
  • statalign.postprocess.utils.DisplayString
  • statalign.distance.Distance
  • statalign.postprocess.plugins.contree.test.EdgeLengthTester
  • statalign.postprocess.utils.EntropyContainer
  • statalign.postprocess.plugins.benchmarks.ExperimentalData
  • statalign.io.input.FileTokenReader
  • statalign.model.ext.plugins.structalign.Funcs
  • statalign.mcmc.GammaPrior (implements statalign.mcmc.PriorDistribution<T>)
  • statalign.postprocess.plugins.contree.hash.HashEntry
  • statalign.postprocess.plugins.contree.hash.HashTable
  • statalign.postprocess.plugins.contree.hash.HashUtils
  • statalign.base.hmm.Hmm
    • statalign.base.hmm.Hmm2
      • statalign.base.hmm.HmmTkf92
    • statalign.base.hmm.HmmSilent
      • statalign.base.hmm.HmmNonParam
  • statalign.mcmc.HyperbolicPrior (implements statalign.mcmc.PriorDistribution<T>)
  • statalign.base.InputData
  • statalign.io.input.InputReader
  • statalign.mcmc.InverseGammaPrior (implements statalign.mcmc.PriorDistribution<T>)
  • java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • statalign.ui.ScrollAdapter
  • statalign.model.ext.plugins.structalign.LinearLink (implements statalign.utils.LinkFunction<T>)
  • statalign.mcmc.LinearPrior (implements statalign.mcmc.PriorDistribution<T>)
  • statalign.postprocess.utils.LogLikelihoodTraceContainer
  • statalign.mcmc.LogNormalPrior (implements statalign.mcmc.PriorDistribution<T>)
  • statalign.base.MainManager
  • statalign.postprocess.utils.Mapping
  • statalign.mcmc.McmcModule
    • statalign.base.mcmc.CoreMcmcModule
    • statalign.model.ext.ModelExtension
      • statalign.model.ext.plugins.PPFold
      • statalign.model.ext.plugins.RNAAliFold
      • statalign.model.ext.plugins.StructAlign (implements java.awt.event.ActionListener)
  • statalign.mcmc.McmcMove
    • statalign.base.mcmc.AlignmentMove
    • statalign.model.ext.plugins.structalign.AlignmentMove
    • statalign.mcmc.ContinuousPositiveParameterMove
      • statalign.base.mcmc.AllEdgeMove
      • statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove
        • statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove
      • statalign.base.mcmc.EdgeMove
      • statalign.base.mcmc.IndelMove
        • statalign.base.mcmc.LambdaMove
        • statalign.base.mcmc.MuMove
        • statalign.base.mcmc.PhiMove
        • statalign.base.mcmc.RhoMove
        • statalign.base.mcmc.RMove
        • statalign.base.mcmc.ThetaMove
    • statalign.base.mcmc.LOCALTopologyMove
    • statalign.mcmc.McmcCombinationMove
    • statalign.model.ext.plugins.structalign.RotationOrTranslationMove
      • statalign.model.ext.plugins.structalign.LibraryMove
      • statalign.model.ext.plugins.structalign.RotationMove
      • statalign.model.ext.plugins.structalign.TranslationMove
    • statalign.base.mcmc.SilentIndelMove
    • statalign.base.mcmc.SubstMove
    • statalign.base.mcmc.TopologyMove
  • statalign.base.MCMCPars
  • statalign.base.McmcStep
  • statalign.model.ext.ModelExtManager
  • statalign.MPIUtils
  • statalign.model.ext.plugins.structalign.MultiNormCholesky
  • statalign.postprocess.utils.NewickParser
  • statalign.model.subst.plugins.NucleotideModelUtils
  • statalign.distance.Pair<L,R>
  • statalign.distance.PairCompare (implements java.util.Comparator<T>)
  • statalign.postprocess.PluginParameters
  • statalign.postprocess.Postprocess
    • statalign.postprocess.plugins.ConsensusNetwork
    • statalign.postprocess.plugins.CurrentAlignment
    • statalign.postprocess.plugins.Entropy
    • statalign.base.Input
    • statalign.postprocess.plugins.LogLikelihoodTrace
    • statalign.postprocess.plugins.MpdAlignment
    • statalign.postprocess.plugins.PPFold
    • statalign.postprocess.plugins.structalign.RmsdTrace
    • statalign.postprocess.plugins.structalign.StructTrace
    • statalign.postprocess.plugins.Structure
    • statalign.postprocess.TreeVisualizer
      • statalign.postprocess.plugins.ConsensusTreeVisualizer
      • statalign.postprocess.plugins.CurrentTreeVisualizer
    • statalign.postprocess.plugins.VisualDistance
  • statalign.postprocess.PostprocessManager
  • statalign.mcmc.ProposalDistribution<T>
    • statalign.mcmc.GammaProposal
    • statalign.mcmc.GaussianProposal
    • statalign.mcmc.LogisticProposal
    • statalign.mcmc.MultiplicativeProposal
    • statalign.mcmc.UniformProposal
  • statalign.io.ProteinSkeletons (implements statalign.io.DataType)
  • statalign.model.ext.plugins.structalign.QuadraticLink (implements statalign.utils.LinkFunction<T>)
  • statalign.io.RawSequences (implements statalign.io.DataType)
  • statalign.utils.Reversed<T> (implements java.lang.Iterable<T>)
  • statalign.postprocess.utils.RNAalifold
  • statalign.postprocess.plugins.RNAalifoldResult (implements java.io.Serializable)
  • statalign.postprocess.utils.RNAFoldingTools
  • statalign.postprocess.utils.RNAFoldingTools.MultiThreadedPosteriorDecoding
  • statalign.model.ext.plugins.structalign.RotationProposal
  • statalign.utils.SimpleStats
  • statalign.StatAlign
  • statalign.StatAlignParallel
  • statalign.postprocess.plugins.benchmarks.StatAlignResult
  • statalign.base.State
  • statalign.base.thread.Stoppable
    • statalign.base.Mcmc
    • statalign.base.Tree (implements statalign.io.DataType)
    • statalign.base.TreeAlgo
  • statalign.model.ext.plugins.structalign.StructAlignMoveParams
  • statalign.model.ext.plugins.structalign.StructAlignParameterInterface
  • statalign.model.ext.plugins.structalign.StructAlignParameterInterface.EpsilonInterface (implements statalign.mcmc.ParameterInterface)
  • statalign.model.ext.plugins.structalign.StructAlignParameterInterface.NuInterface (implements statalign.mcmc.ParameterInterface)
  • statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2HInterface (implements statalign.mcmc.ParameterInterface)
  • statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2Interface (implements statalign.mcmc.ParameterInterface)
  • statalign.model.ext.plugins.structalign.StructAlignParameterInterface.TauInterface (implements statalign.mcmc.ParameterInterface)
  • statalign.postprocess.plugins.structalign.StructAlignTraceParameters
  • statalign.postprocess.plugins.structalign.StructAlignTraceParameters.PlottableParameter
  • statalign.model.subst.SubstitutionModel
    • statalign.model.subst.plugins.AminoAcidModel
      • statalign.model.subst.plugins.Blosum
      • statalign.model.subst.plugins.CpRev
      • statalign.model.subst.plugins.Dayhoff
      • statalign.model.subst.plugins.Jones
      • statalign.model.subst.plugins.MtMam
      • statalign.model.subst.plugins.MtREV
      • statalign.model.subst.plugins.RtREV
      • statalign.model.subst.plugins.Vt
      • statalign.model.subst.plugins.Wag
    • statalign.model.subst.plugins.NucleotideModel
      • statalign.model.subst.plugins.Felsenstein81
      • statalign.model.subst.plugins.Felsenstein84
      • statalign.model.subst.plugins.HKY85
      • statalign.model.subst.plugins.JukesCantor
      • statalign.model.subst.plugins.Kimura3
      • statalign.model.subst.plugins.ReversibleNucleotide
      • statalign.model.subst.plugins.Tamura92
      • statalign.model.subst.plugins.TamuraNei
  • statalign.model.score.SubstitutionScore
    • statalign.model.score.plugins.Blosum62
    • statalign.model.score.plugins.DNAScore
  • statalign.model.ext.plugins.structalign.Subtree
  • statalign.postprocess.plugins.contree.test.TestNetwork
  • java.lang.Thread (implements java.lang.Runnable)
    • statalign.base.thread.StoppableThread
      • statalign.base.thread.MainThread
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • statalign.model.subst.RecognitionError
    • java.lang.Exception
      • java.io.IOException
        • statalign.io.input.IllegalFormatException
        • statalign.io.input.plugins.NewickReader.FormatException
      • java.lang.RuntimeException
        • statalign.postprocess.utils.NewickParserException
      • statalign.base.thread.StoppedException
  • statalign.postprocess.Track
  • statalign.model.ext.plugins.structalign.Transformation
  • statalign.postprocess.plugins.TreeNode
  • statalign.mcmc.UniformPrior (implements statalign.mcmc.PriorDistribution<T>)
  • statalign.postprocess.plugins.contree.Utils
  • statalign.base.Utils
  • statalign.base.Vertex
  • statalign.model.ext.plugins.structalign.vonMises
  • statalign.model.ext.plugins.structalign.vonMisesFisher

Interface Hierarchy

• statalign.io.DataType
• statalign.utils.LinkFunction<T>
• statalign.mcmc.ParameterInterface
• statalign.mcmc.PriorDistribution<T>

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • statalign.utils.Libraries
    • statalign.io.input.plugins.NewickReader.FormatExceptType