Hierarchy For All Packages

Package Hierarchies:

procope.data, procope.data.complexes, procope.data.networks, procope.data.petrinets, procope.data.purifications, procope.evaluation.comparison, procope.evaluation.complexquality, procope.evaluation.complexquality.go, procope.evaluation.networkperformance, procope.examples, procope.methods.clustering, procope.methods.interologs, procope.methods.interologs.blast, procope.methods.scores, procope.methods.scores.bootstrap, procope.tools, procope.tools.math, procope.tools.namemapping, procope.tools.userclasses

Class Hierarchy

• java.lang.Object
  • procope.methods.interologs.AlignmentInterologScorer (implements procope.methods.interologs.InterologScorer)
  • procope.data.petrinets.Arc
  • procope.methods.interologs.blast.BlastBBHAlignmentLengthConstraint (implements procope.methods.interologs.blast.BlastBBHConstraints)
  • procope.methods.interologs.blast.BlastHit (implements java.lang.Comparable<T>)
  • procope.methods.interologs.blast.BlastHitFileParser
  • procope.methods.interologs.blast.BlastHits (implements java.lang.Iterable<T>)
  • procope.tools.BooleanExpression
  • procope.methods.scores.bootstrap.Bootstrap
  • procope.methods.scores.bootstrap.BootstrapClustering
  • procope.methods.scores.bootstrap.BootstrapClusterings (implements java.lang.Iterable<T>)
  • procope.evaluation.comparison.BroheeSimilarity
  • procope.tools.ChartTools
  • procope.evaluation.complexquality.Colocalization
  • procope.data.networks.CombinationRules
  • procope.evaluation.complexquality.go.CommonAncestors
  • procope.data.complexes.Complex (implements java.lang.Iterable<T>, procope.data.ProteinSet)
  • procope.evaluation.networkperformance.ComplexEnrichment
  • procope.evaluation.comparison.ComplexMapping
  • procope.evaluation.comparison.ComplexMappings (implements java.lang.Iterable<T>)
  • procope.methods.scores.ComplexScoreCalculator
  • procope.data.complexes.ComplexSet (implements java.lang.Iterable<T>, procope.data.ProteinSet)
  • procope.evaluation.comparison.ComplexSetComparison
  • procope.data.complexes.ComplexSetReader
  • procope.data.complexes.ComplexSetWriter
  • procope.examples.DummyClusterer (implements procope.methods.clustering.Clusterer)
  • procope.tools.userclasses.DummyClusterer (implements procope.methods.clustering.Clusterer)
  • procope.methods.interologs.EvalueInterologScorer (implements procope.methods.interologs.InterologScorer)
  • procope.methods.interologs.FASTAParser
  • procope.evaluation.complexquality.go.GOAnnotationReader
  • procope.evaluation.complexquality.go.GOAnnotations (implements procope.data.ProteinSet)
  • procope.evaluation.complexquality.go.GONetwork
  • procope.evaluation.complexquality.go.GOTerm
  • procope.methods.clustering.HierarchicalClusterer (implements procope.methods.clustering.Clusterer)
  • procope.methods.clustering.HierarchicalClusteringTrees
  • procope.methods.clustering.HierarchicalTreeNode
  • procope.tools.math.HypergeometricDistribution
  • procope.methods.interologs.InterologsCalculator
  • procope.data.LocalizationData
  • procope.data.LocalizationDataReader
  • procope.methods.clustering.MarkovClusterer (implements procope.methods.clustering.Clusterer)
  • procope.methods.clustering.MCLEfficiencyCalculator
  • procope.methods.clustering.MCLParameters
  • procope.evaluation.comparison.NetworkComparison
  • procope.data.networks.NetworkEdge (implements java.lang.Comparable<T>)
  • procope.data.networks.NetworkGenerator
  • procope.data.networks.NetworkReader
  • procope.data.networks.NetworkWriter
  • procope.tools.math.PearsonCoefficient (implements procope.tools.math.CorrelationCoefficient)
  • procope.data.petrinets.PetriNetCreator
  • procope.data.petrinets.Place
  • procope.evaluation.comparison.Point
  • procope.tools.namemapping.ProteinManager
  • procope.data.networks.ProteinNetwork (implements java.lang.Iterable<T>, procope.data.ProteinSet)
  • procope.examples.ProtManager
  • procope.methods.scores.bootstrap.PurificationBootstrapSamples
  • procope.data.purifications.PurificationData (implements java.lang.Iterable<T>, procope.data.ProteinSet)
  • procope.data.purifications.PurificationDataReader
  • procope.data.purifications.PurificationDataWriter
  • procope.data.purifications.PurificationExperiment (implements procope.data.ProteinSet)
  • java.util.Random (implements java.io.Serializable)
    • procope.tools.math.MTRandom
  • procope.evaluation.networkperformance.ROC
  • procope.evaluation.networkperformance.ROCCurve (implements java.lang.Iterable<T>)
  • procope.evaluation.networkperformance.ROCCurveHandler
  • procope.evaluation.networkperformance.ROCPoint
  • procope.methods.scores.ScoresCalculator (implements procope.data.ProteinSet)
    • procope.methods.scores.DiceCoefficients
    • procope.examples.DummyScores
    • procope.evaluation.complexquality.go.FunctionalSimilarities
      • procope.evaluation.complexquality.go.FunctionalSimilaritiesSchlicker
    • procope.methods.scores.HartCalculator
    • procope.methods.scores.PECalculator
    • procope.methods.scores.SocioAffinityCalculator
  • procope.tools.SequenceAligner
  • procope.methods.interologs.Sequences
  • procope.tools.SparseMatrixInt
  • procope.tools.math.SpearmanCoefficient (implements procope.tools.math.CorrelationCoefficient)
  • procope.data.StringToIntMapper
  • procope.tools.namemapping.Synonyms
  • procope.evaluation.complexquality.go.TermSimilaritiesSchlicker (implements procope.evaluation.complexquality.go.TermSimilarities)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • procope.tools.InvalidExpressionException
      • java.lang.RuntimeException
        • procope.tools.ProCopeException
      • org.xml.sax.SAXException
        • procope.tools.userclasses.UserClassSpecException
  • procope.tools.Tools
  • procope.data.petrinets.ToPNetGenerator
  • procope.data.petrinets.Transition
  • procope.examples.UseCase1
  • procope.examples.UseCase2
  • procope.examples.UseCase3
  • procope.examples.UseCase4
  • procope.tools.userclasses.UserClusterer
  • procope.tools.userclasses.UserParameter
  • procope.tools.userclasses.UserScoresCalculator
  • procope.data.petrinets.XGMMLGenerator
  • procope.data.XGMMLWriter

Interface Hierarchy

• procope.methods.interologs.blast.BlastBBHConstraints
• procope.methods.clustering.Clusterer
• procope.tools.math.CorrelationCoefficient
• procope.methods.interologs.InterologScorer
• procope.data.networks.NetworkSearchCallback
• procope.data.ProteinSet
• procope.evaluation.complexquality.go.TermSimilarities

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • procope.data.networks.CombinationRules.CombinationType
    • procope.data.networks.CombinationRules.WeightMergePolicy
    • procope.evaluation.complexquality.go.GONetwork.Relationships
    • procope.evaluation.complexquality.go.GONetwork.Namespace
    • procope.evaluation.complexquality.go.TermSimilaritiesSchlicker.TermSimilarityMeasure
    • procope.evaluation.complexquality.go.FunctionalSimilaritiesSchlicker.FunctionalSimilarityMeasure
    • procope.methods.clustering.HierarchicalLinkage
    • procope.methods.interologs.AlignmentInterologScorer.AlignmentScoring
    • procope.tools.userclasses.UserDataType