Hierarchy For All Packages

Package Hierarchies:

• pt.ist.phylolib,
• pt.ist.phylolib.cli,
• pt.ist.phylolib.command,
• pt.ist.phylolib.command.algorithm,
• pt.ist.phylolib.command.algorithm.edmonds,
• pt.ist.phylolib.command.algorithm.gcp,
• pt.ist.phylolib.command.algorithm.goeburst,
• pt.ist.phylolib.command.algorithm.nj,
• pt.ist.phylolib.command.correction,
• pt.ist.phylolib.command.distance,
• pt.ist.phylolib.command.optimization,
• pt.ist.phylolib.data,
• pt.ist.phylolib.data.dataset,
• pt.ist.phylolib.data.matrix,
• pt.ist.phylolib.data.tree,
• pt.ist.phylolib.exception,
• pt.ist.phylolib.logging,
• pt.ist.phylolib.reflection

Class Hierarchy

• java.lang.Object
  • 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)
      • pt.ist.phylolib.cli.Arguments
  • pt.ist.phylolib.command.algorithm.Algorithm (implements pt.ist.phylolib.command.ICommand<T,R>)
    • pt.ist.phylolib.command.algorithm.edmonds.Edmonds
    • pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs
      • pt.ist.phylolib.command.algorithm.gcp.CL
      • pt.ist.phylolib.command.algorithm.gcp.SL
      • pt.ist.phylolib.command.algorithm.gcp.UPGMA
      • pt.ist.phylolib.command.algorithm.gcp.UPGMC
      • pt.ist.phylolib.command.algorithm.gcp.WPGMA
      • pt.ist.phylolib.command.algorithm.gcp.WPGMC
    • pt.ist.phylolib.command.algorithm.goeburst.GoeBURST
    • pt.ist.phylolib.command.algorithm.nj.NeighbourJoining
      • pt.ist.phylolib.command.algorithm.nj.SaitouNei
      • pt.ist.phylolib.command.algorithm.nj.StudierKeppler
      • pt.ist.phylolib.command.algorithm.nj.UNJ
  • pt.ist.phylolib.data.Context
  • pt.ist.phylolib.command.correction.Correction (implements pt.ist.phylolib.command.ICommand<T,R>)
    • pt.ist.phylolib.command.correction.JukesCantor
  • pt.ist.phylolib.data.dataset.Dataset
  • pt.ist.phylolib.data.dataset.DatasetParser (implements pt.ist.phylolib.data.IReader<T>)
    • pt.ist.phylolib.data.dataset.FASTA
    • pt.ist.phylolib.data.dataset.ML
    • pt.ist.phylolib.data.dataset.SNP
  • pt.ist.phylolib.command.distance.Distance (implements pt.ist.phylolib.command.ICommand<T,R>)
    • pt.ist.phylolib.command.distance.GrapeTree
    • pt.ist.phylolib.command.distance.Hamming
    • pt.ist.phylolib.command.distance.Kimura
  • pt.ist.phylolib.data.tree.Edge
  • pt.ist.phylolib.data.File
  • pt.ist.phylolib.logging.Log
  • pt.ist.phylolib.Main
  • pt.ist.phylolib.data.matrix.Matrix
  • pt.ist.phylolib.data.matrix.MatrixParser (implements pt.ist.phylolib.data.IReader<T>, pt.ist.phylolib.data.IWriter<T>)
    • pt.ist.phylolib.data.matrix.SymmetryParser
      • pt.ist.phylolib.data.matrix.Asymmetric
      • pt.ist.phylolib.data.matrix.Symmetric
  • pt.ist.phylolib.command.algorithm.nj.NeighbourJoining.Cluster
  • pt.ist.phylolib.command.optimization.Optimization (implements pt.ist.phylolib.command.ICommand<T,R>)
    • pt.ist.phylolib.command.optimization.LBR
  • pt.ist.phylolib.cli.Options
  • pt.ist.phylolib.cli.Parameters
  • pt.ist.phylolib.data.dataset.Profile
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • pt.ist.phylolib.exception.ArgumentException
        • pt.ist.phylolib.exception.InvalidCommandException
        • pt.ist.phylolib.exception.InvalidTypeException
        • pt.ist.phylolib.exception.MissingInputException
        • pt.ist.phylolib.exception.MissingTypeException
        • pt.ist.phylolib.exception.NoCommandException
        • pt.ist.phylolib.exception.RepeatedCommandException
  • pt.ist.phylolib.data.tree.Tree
  • pt.ist.phylolib.data.tree.TreeParser (implements pt.ist.phylolib.data.IReader<T>, pt.ist.phylolib.data.IWriter<T>)
    • pt.ist.phylolib.data.tree.Newick
      • pt.ist.phylolib.data.tree.Nexus
  • pt.ist.phylolib.reflection.Types

Interface Hierarchy

• pt.ist.phylolib.command.ICommand<T,R>
• pt.ist.phylolib.command.ICommand.IGetter<T>
• pt.ist.phylolib.data.IReader<T>
• pt.ist.phylolib.data.IWriter<T>
• pt.ist.phylolib.data.matrix.Matrix.ICorrection
• pt.ist.phylolib.data.matrix.Matrix.IDistance

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • pt.ist.phylolib.cli.Command
    • pt.ist.phylolib.cli.Data
    • pt.ist.phylolib.cli.Format
    • pt.ist.phylolib.cli.Option