Hierarchy For All Packages

Package Hierarchies:

• org.biopax.paxtools.pattern,
• org.biopax.paxtools.pattern.constraint,
• org.biopax.paxtools.pattern.example,
• org.biopax.paxtools.pattern.miner,
• org.biopax.paxtools.pattern.util

Class Hierarchy

• java.lang.Object
  • org.biopax.paxtools.pattern.util.AdjacencyMatrix
  • org.biopax.paxtools.pattern.util.Blacklist
  • org.biopax.paxtools.pattern.miner.BlacklistGenerator
  • org.biopax.paxtools.pattern.miner.BlacklistGenerator2
  • org.biopax.paxtools.pattern.miner.BlacklistGenerator3
  • org.biopax.paxtools.pattern.util.ChemicalNameNormalizer
  • org.biopax.paxtools.pattern.miner.CommonIDFetcher (implements org.biopax.paxtools.pattern.miner.IDFetcher)
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.biopax.paxtools.pattern.miner.Dialog (implements java.awt.event.ActionListener, java.awt.event.KeyListener)
  • org.biopax.paxtools.pattern.constraint.ConBox
  • org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher (implements org.biopax.paxtools.pattern.miner.IDFetcher)
  • org.biopax.paxtools.pattern.constraint.ConstraintAdapter (implements org.biopax.paxtools.pattern.Constraint)
    • org.biopax.paxtools.pattern.constraint.ActivityConstraint
    • org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint
    • org.biopax.paxtools.pattern.constraint.ConstraintChain
    • org.biopax.paxtools.pattern.constraint.ControlsNotParticipant
    • org.biopax.paxtools.pattern.constraint.ConversionSide
    • org.biopax.paxtools.pattern.constraint.Empty
    • org.biopax.paxtools.pattern.constraint.Equality
    • org.biopax.paxtools.pattern.constraint.Field
      • org.biopax.paxtools.pattern.constraint.FieldOfMultiple
    • org.biopax.paxtools.pattern.constraint.HasAnID
    • org.biopax.paxtools.pattern.constraint.IDConstraint
    • org.biopax.paxtools.pattern.constraint.InterToPartER
    • org.biopax.paxtools.pattern.constraint.LinkedPE
    • org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint
    • org.biopax.paxtools.pattern.constraint.NonUbique
    • org.biopax.paxtools.pattern.constraint.NOT
    • org.biopax.paxtools.pattern.constraint.OR
      • org.biopax.paxtools.pattern.constraint.AND
      • org.biopax.paxtools.pattern.constraint.MultiPathConstraint
      • org.biopax.paxtools.pattern.constraint.XOR
    • org.biopax.paxtools.pattern.constraint.Participant
    • org.biopax.paxtools.pattern.constraint.ParticipatesInConv
    • org.biopax.paxtools.pattern.constraint.PathConstraint
    • org.biopax.paxtools.pattern.constraint.PEChainsIntersect
    • org.biopax.paxtools.pattern.constraint.RelatedControl
    • org.biopax.paxtools.pattern.constraint.SelfOrThis
    • org.biopax.paxtools.pattern.constraint.Size
    • org.biopax.paxtools.pattern.constraint.Type
  • org.biopax.paxtools.pattern.miner.CustomFormat (implements org.biopax.paxtools.pattern.miner.SIFToText)
  • org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
  • org.biopax.paxtools.pattern.util.DifferentialModificationUtil
  • org.biopax.paxtools.pattern.miner.ExtendedSIFWriter
  • org.biopax.paxtools.pattern.util.HGNC
  • org.biopax.paxtools.pattern.MappedConst (implements org.biopax.paxtools.pattern.Constraint)
  • org.biopax.paxtools.pattern.Match (implements java.lang.Cloneable)
  • org.biopax.paxtools.pattern.miner.MinerAdapter (implements org.biopax.paxtools.pattern.miner.Miner)
    • org.biopax.paxtools.pattern.miner.AbstractSIFMiner (implements org.biopax.paxtools.pattern.miner.SIFMiner)
      • org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
      • org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
      • org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
      • org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
        • org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner
      • org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
      • org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
        • org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
      • org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
        • org.biopax.paxtools.pattern.miner.ControlsPhosphorylationMiner
        • org.biopax.paxtools.pattern.miner.ControlsTransportMiner
        • org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
        • org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
        • org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
      • org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
      • org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
      • org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
      • org.biopax.paxtools.pattern.miner.InComplexWithMiner
      • org.biopax.paxtools.pattern.miner.InteractsWithMiner
      • org.biopax.paxtools.pattern.miner.NeighborOfMiner
      • org.biopax.paxtools.pattern.miner.ReactsWithMiner
      • org.biopax.paxtools.pattern.miner.UsedToProduceMiner
    • org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner
    • org.biopax.paxtools.pattern.miner.DirectedRelationMiner
    • org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner
    • org.biopax.paxtools.pattern.miner.UbiquitousIDMiner
  • org.biopax.paxtools.pattern.miner.OutputColumn
  • org.biopax.paxtools.pattern.Pattern
  • org.biopax.paxtools.pattern.PatternBox
  • org.biopax.paxtools.pattern.util.PhysicalEntityChain
  • org.biopax.paxtools.pattern.Searcher
  • org.biopax.paxtools.pattern.miner.SIFInteraction (implements java.lang.Comparable<T>)
  • org.biopax.paxtools.pattern.miner.SIFSearcher
  • org.biopax.paxtools.pattern.miner.SimpleIDFetcher (implements org.biopax.paxtools.pattern.miner.IDFetcher)

Interface Hierarchy

• org.biopax.paxtools.pattern.Constraint
• org.biopax.paxtools.pattern.miner.IDFetcher
• org.biopax.paxtools.pattern.miner.Miner
  • org.biopax.paxtools.pattern.miner.SIFMiner
• org.biopax.paxtools.pattern.util.ProgressWatcher
• org.biopax.paxtools.pattern.miner.SIFToText
• org.biopax.paxtools.pattern.miner.SIFType

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biopax.paxtools.pattern.constraint.InterToPartER.Direction
    • org.biopax.paxtools.pattern.constraint.Field.Operation
    • org.biopax.paxtools.pattern.constraint.Size.Type
    • org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type
    • org.biopax.paxtools.pattern.constraint.ConversionSide.Type
    • org.biopax.paxtools.pattern.constraint.LinkedPE.Type
    • org.biopax.paxtools.pattern.miner.SIFEnum (implements org.biopax.paxtools.pattern.miner.SIFType)
    • org.biopax.paxtools.pattern.miner.OutputColumn.Type
    • org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity
    • org.biopax.paxtools.pattern.util.RelType