Hierarchy For All Packages

Package Hierarchies:

PIP.Collections, PIP.Collections.Distribution, PIP.Collections.Map, PIP.Collections.Persistent, PIP.Core, PIP.Domains, PIP.Domains.Family, PIP.Domains.Interactions, PIP.Domains.Orientation, PIP.Domains.SequenceSimilarity, PIP.ExampleCode, PIP.IO, PIP.IO.Blast, PIP.IO.CreateJDODatabase, PIP.IO.CreatePeripheralData, PIP.IO.MSD, PIP.IO.StampPackage

Class Hierarchy

• java.lang.Object
  • PIP.Collections.Persistent.AbstractCollection<E> (implements java.util.Collection<E>)
    • PIP.Collections.Persistent.AbstractList<E> (implements java.util.List<E>)
      • PIP.Collections.Pair<O>
        • PIP.Collections.SymmetricPair<E>
      • PIP.Collections.Piecewise<T> (implements java.io.Serializable)
        • PIP.Domains.Domain (implements java.io.Serializable)
      • PIP.Collections.Range<E> (implements java.io.Serializable)
      • PIP.Collections.Persistent.SArrayList<T> (implements java.io.Serializable)
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • PIP.Collections.UniformSampler<E>
  • PIP.Collections.Persistent.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • PIP.Collections.MultiMap<K,V> (implements java.io.Serializable)
    • PIP.Collections.Persistent.SHashMap<K,V> (implements java.io.Serializable)
  • PIP.IO.StampPackage.Alignments
  • PIP.Core.App
  • PIP.Core.Assembly (implements PIP.Core.MSDID, java.io.Serializable)
  • PIP.Core.Atom (implements PIP.Core.MSDID, java.io.Serializable, PIP.Core.Spatial)
  • PIP.IO.Bash
  • PIP.IO.BatchCommiter
  • PIP.IO.Blast.Blaster
  • PIP.IO.Blast.BlastStats
  • PIP.Core.Chain (implements PIP.Core.MSDID, java.io.Serializable)
  • PIP.IO.CreatePeripheralData.CheckAllOrientationFilesArePresent
  • PIP.Domains.Orientation.ClassifyByOrientation
  • PIP.IO.ClearLogs
  • PIP.Collections.CollectionFactory
  • PIP.Collections.CollectionSizeComparator (implements java.util.Comparator<T>)
  • PIP.Collections.CollectionUtility
  • PIP.Collections.ComparatorUtility
  • PIP.ExampleCode.ConnectionToJDODatabase
  • PIP.ExampleCode.ConnectionTOMSDDatabase
  • PIP.IO.CreateJDODatabase.CreateDB
  • PIP.IO.CreatePeripheralData.CreatePDBFiles
  • PIP.Domains.Interactions.DistanceFactory (implements PIP.Domains.Interactions.DomainInteractionFactory)
  • PIP.Collections.Distribution.Distribution<F>
    • PIP.Collections.Distribution.Histogram<F>
  • PIP.Domains.Interactions.DomainInteraction
    • PIP.Domains.Interactions.DistanceInteraction
  • PIP.Domains.Interactions.DomainInteractionOrdered
  • PIP.Domains.Interactions.DomainInteractions
  • PIP.IO.MSD.DomainReader
    • PIP.IO.MSD.CSReaderNew
      • PIP.IO.MSD.CathReaderNew
      • PIP.IO.MSD.ScopReaderNew
  • PIP.Domains.Domains
  • PIP.Core.Element (implements java.io.Serializable)
  • PIP.Core.Elements (implements java.io.Serializable)
  • PIP.Core.Entries
  • PIP.Core.Entry (implements PIP.Core.MSDID, java.io.Serializable)
  • PIP.IO.MSD.EntryReader
  • PIP.Core.ExperimentType (implements java.io.Serializable)
  • PIP.Core.ExperimentTypes (implements java.io.Serializable)
  • PIP.Domains.Family.FamilyComparator (implements java.util.Comparator<T>)
  • PIP.Domains.Family.FamilyType
    • PIP.Domains.Family.HFType
  • PIP.IO.FixDatabases
  • PIP.IO.Blast.FormatDBFileCreator
  • PIP.Collections.General
  • PIP.IO.CreatePeripheralData.GenerateOrientationFiles
  • PIP.ExampleCode.HelpfulFunctions
  • PIP.Domains.Family.HierarchicalFamily (implements PIP.Domains.Family.Family)
    • PIP.Domains.Family.Cath
    • PIP.Domains.Family.Scop
    • PIP.Domains.Family.Subfamily
  • PIP.Domains.HighestResolutionDomainComp (implements java.util.Comparator<T>)
  • PIP.Domains.HighestResolutionInteractionComp (implements java.util.Comparator<T>)
  • PIP.Collections.Distribution.HistogramUtility
  • PIP.IO.CreatePeripheralData.IdListCreator
  • PIP.Collections.IntegerComparator (implements java.util.Comparator<T>)
  • PIP.Domains.Interactions.InteractionSourceType
  • PIP.Domains.Interactions.InteractionSurface
  • PIP.IO.IOUtility
  • PIP.IO.StampPackage.IRMSDCalc
  • PIP.ExampleCode.IteratingThroughDataBasedOnDomainInteractions
  • PIP.ExampleCode.IteratingThroughDataBasedOnDomains
  • PIP.ExampleCode.IteratingThroughDataBasedOnEntryHeirarchy
  • PIP.IO.JDBCUtility
  • PIP.IO.JoinResults
  • PIP.Collections.Map.MapKeyComparator<K,V> (implements java.util.Comparator<T>)
  • PIP.Collections.Map.MapValueComparator<K,V> (implements java.util.Comparator<T>)
  • PIP.Core.MathUtility
  • PIP.IO.StampPackage.MatrixFactory
  • PIP.Domains.Interactions.NumberInteractingAtomsMeasure (implements PIP.Domains.Interactions.Measure)
  • PIP.Domains.Interactions.NumberInteractingResiduesMeasure (implements PIP.Domains.Interactions.Measure)
  • PIP.Domains.Interactions.NumberOfUniqueDomainInteractionsComparator (implements java.util.Comparator<T>)
  • PIP.Domains.Orientation.OrientatedDomInt
  • PIP.Domains.Orientation.OrientationSimilarInteractions
  • PIP.Collections.PairsIterator<E> (implements java.util.Iterator<E>)
  • PIP.IO.Blast.ParseBlastOutput
  • PIP.IO.PBFactory
  • PIP.IO.CreatePeripheralData.PDBFile
    • PIP.IO.CreatePeripheralData.PDBFileChainBased
    • PIP.IO.CreatePeripheralData.PDBFileDomainBased
  • PIP.IO.CreateJDODatabase.PersistDatabase
  • PIP.IO.CreateJDODatabase.PersistDomainInteractions
  • PIP.IO.CreateJDODatabase.PersistEntries
  • PIP.IO.CreateJDODatabase.PersistOritentationInteractions
  • PIP.IO.CreateJDODatabase.PersistPeripheral
  • PIP.Domains.Family.Pfam (implements PIP.Domains.Family.Family)
  • PIP.IO.MSD.PfamReader
  • PIP.IO.PymolScript
  • PIP.Core.Residue (implements PIP.Core.MSDID, java.io.Serializable, PIP.Core.Spatial)
  • PIP.Core.ResidueName (implements java.io.Serializable)
  • PIP.Core.ResidueNames (implements java.io.Serializable)
  • PIP.IO.StampPackage.RMSDComponents
  • PIP.IO.StampPackage.RunStamp
  • PIP.Collections.SArrayListFactory (implements org.apache.commons.collections.Factory)
  • PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs
  • PIP.IO.StampPackage.StampComparison
  • PIP.IO.StampPackage.Stamper
  • PIP.Domains.Family.SubfamilyComparator (implements java.util.Comparator<T>)
  • PIP.IO.StampPackage.Transform
  • PIP.IO.StampPackage.Transformations
  • PIP.Collections.UniformSamplerIterator<E> (implements java.util.Iterator<E>)

Interface Hierarchy

• PIP.Domains.Interactions.DomainInteractionFactory
• PIP.Domains.Interactions.Measure
• PIP.Core.MSDID
• java.io.Serializable
  • PIP.Domains.Family.Family
• PIP.Core.Spatial