Hierarchy For All Packages

Package Hierarchies:

edu.uconn.mcb.lineageevolver, edu.uconn.mcb.lineageevolver.config, edu.uconn.mcb.lineageevolver.graph, edu.uconn.mcb.lineageevolver.misc, edu.uconn.mcb.lineageevolver.parsing

Class Hierarchy

• class java.lang.Object
  • class edu.uconn.mcb.lineageevolver.AATranslator
  • class edu.uconn.mcb.lineageevolver.ASRVByteAAGene (implements edu.uconn.mcb.lineageevolver.Gene)
  • class edu.uconn.mcb.lineageevolver.ByteAminoAcid (implements edu.uconn.mcb.lineageevolver.AminoAcid, edu.uconn.mcb.lineageevolver.Substitutable)
  • class edu.uconn.mcb.lineageevolver.config.Configuration (implements java.io.Serializable)
  • class edu.uconn.mcb.lineageevolver.graph.EdgeListEdge (implements edu.uconn.mcb.lineageevolver.graph.GraphEdge)
  • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph (implements edu.uconn.mcb.lineageevolver.graph.DirectedGraph)
    • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology (implements edu.uconn.mcb.lineageevolver.graph.GraphTopology)
  • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData
  • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.Event (implements java.lang.Comparable, edu.uconn.mcb.lineageevolver.graph.GraphTopologyEvent)
    • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.GenomeEvent
      • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.SubstitutionEvent
    • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.LineageEvent
      • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.ForkEvent
  • class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.NodeData
  • class edu.uconn.mcb.lineageevolver.graph.EdgeListNode (implements edu.uconn.mcb.lineageevolver.graph.GraphNode)
  • class edu.uconn.mcb.lineageevolver.parsing.FASTAParser
  • class edu.uconn.mcb.lineageevolver.Genome (implements java.lang.Cloneable, edu.uconn.mcb.lineageevolver.misc.Visitable)
  • class edu.uconn.mcb.lineageevolver.GenomeVisitor (implements edu.uconn.mcb.lineageevolver.misc.Visitor)
    • class edu.uconn.mcb.lineageevolver.GeneDuplicator
    • class edu.uconn.mcb.lineageevolver.GeneKiller
    • class edu.uconn.mcb.lineageevolver.GenomeEvolver
    • class edu.uconn.mcb.lineageevolver.GenomeRearranger
  • class edu.uconn.mcb.lineageevolver.JTT (implements edu.uconn.mcb.lineageevolver.SubstitutionMatrix)
  • class edu.uconn.mcb.lineageevolver.parsing.LECParser
  • class edu.uconn.mcb.lineageevolver.Lineage (implements edu.uconn.mcb.lineageevolver.misc.Visitable)
  • class edu.uconn.mcb.lineageevolver.LineageVisitor (implements edu.uconn.mcb.lineageevolver.misc.Visitor)
    • class edu.uconn.mcb.lineageevolver.LineageFork
  • class edu.uconn.mcb.lineageevolver.RandomSelection
  • class edu.uconn.mcb.lineageevolver.Recombiner
    • class edu.uconn.mcb.lineageevolver.DiagonalRecombiner
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class java.lang.RuntimeException
        • class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid
          • class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidByte
          • class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidChar
          • class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidInt
        • class edu.uconn.mcb.lineageevolver.Genome.NoHGTProcessed
        • class edu.uconn.mcb.lineageevolver.Lineage.HGTDenied
        • class edu.uconn.mcb.lineageevolver.Recombiner.NoRecombineRegion

Interface Hierarchy

• interface java.lang.Cloneable
  • interface edu.uconn.mcb.lineageevolver.AminoAcid (also extends edu.uconn.mcb.lineageevolver.Substitutable)
  • interface edu.uconn.mcb.lineageevolver.Gene
• interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph
  • interface edu.uconn.mcb.lineageevolver.graph.GraphTopology
• interface edu.uconn.mcb.lineageevolver.graph.GraphEdge
• interface edu.uconn.mcb.lineageevolver.graph.GraphNode
• interface edu.uconn.mcb.lineageevolver.graph.GraphTopologyEvent
• interface edu.uconn.mcb.lineageevolver.Substitutable
  • interface edu.uconn.mcb.lineageevolver.AminoAcid (also extends java.lang.Cloneable)
• interface edu.uconn.mcb.lineageevolver.SubstitutionMatrix
• interface edu.uconn.mcb.lineageevolver.misc.Visitable
• interface edu.uconn.mcb.lineageevolver.misc.Visitor
  • interface edu.uconn.mcb.lineageevolver.misc.StrResultVisitor