Hierarchy For All Packages

Package Hierarchies:

• ubic.basecode.datafilter,
• ubic.basecode.dataStructure,
• ubic.basecode.dataStructure.graph,
• ubic.basecode.dataStructure.matrix,
• ubic.basecode.dataStructure.params,
• ubic.basecode.dataStructure.tree,
• ubic.basecode.graphics,
• ubic.basecode.graphics.text,
• ubic.basecode.io,
• ubic.basecode.io.excel,
• ubic.basecode.io.reader,
• ubic.basecode.io.writer,
• ubic.basecode.math,
• ubic.basecode.math.distribution,
• ubic.basecode.math.linalg,
• ubic.basecode.math.linearmodels,
• ubic.basecode.math.metaanalysis,
• ubic.basecode.ontology,
• ubic.basecode.ontology.jena,
• ubic.basecode.ontology.model,
• ubic.basecode.ontology.ncbo,
• ubic.basecode.ontology.providers,
• ubic.basecode.ontology.search,
• ubic.basecode.util,
• ubic.basecode.util.r,
• ubic.basecode.util.r.type

Class Hierarchy

• java.lang.Object
  • ubic.basecode.datafilter.AbstractFilter<M,R,C,V> (implements ubic.basecode.datafilter.Filter<M,R,C,V>)
    • ubic.basecode.datafilter.AbstractLevelFilter<R,C>
      • ubic.basecode.datafilter.ItemLevelFilter<R,C>
      • ubic.basecode.datafilter.RowLevelFilter<R,C>
    • ubic.basecode.datafilter.AffymetrixProbeNameFilter<M,R,C,V>
    • ubic.basecode.datafilter.RowAbsentFilter<M,R,C,V>
    • ubic.basecode.datafilter.RowMissingFilter<M,R,C,V>
    • ubic.basecode.datafilter.RowNameFilter<M,R,C,V>
  • ubic.basecode.dataStructure.graph.AbstractGraph<R,K,V> (implements ubic.basecode.dataStructure.graph.Graph<R,K,V>)
    • ubic.basecode.dataStructure.graph.DirectedGraph<K,V>
  • 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)
      • ubic.basecode.dataStructure.DoubleAddingMap<K>
      • ubic.basecode.dataStructure.StringToStringSetMap
  • ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,V> (implements ubic.basecode.dataStructure.matrix.Matrix2D<R,C,V>, java.io.Serializable)
    • ubic.basecode.dataStructure.matrix.CompressedBitMatrix<R,C> (implements ubic.basecode.dataStructure.matrix.ObjectMatrix<R,C,V>)
    • ubic.basecode.dataStructure.matrix.DoubleMatrix<R,C> (implements ubic.basecode.dataStructure.matrix.PrimitiveMatrix<R,C,V>)
      • ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix<R,C>
      • ubic.basecode.dataStructure.matrix.DenseDoubleMatrix<R,C>
      • ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix<R,C>
      • ubic.basecode.dataStructure.matrix.SparseDoubleMatrix<R,C>
      • ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix<R,C>
    • ubic.basecode.dataStructure.matrix.IntegerMatrix<R,C> (implements ubic.basecode.dataStructure.matrix.PrimitiveMatrix<R,C,V>)
    • ubic.basecode.dataStructure.matrix.ObjectMatrixImpl<R,C,V> (implements ubic.basecode.dataStructure.matrix.ObjectMatrix<R,C,V>)
    • ubic.basecode.dataStructure.matrix.StringMatrix<R,C> (implements ubic.basecode.dataStructure.matrix.ObjectMatrix<R,C,V>)
  • ubic.basecode.dataStructure.matrix.AbstractMatrix3D<R,C,S,V> (implements ubic.basecode.dataStructure.matrix.Matrix3D<R,C,S,V>)
    • ubic.basecode.dataStructure.matrix.DenseObject3DMatrix<R,C,S>
    • ubic.basecode.dataStructure.matrix.DoubleMatrix3D<R,C,S>
      • ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix<R,C,S>
  • ubic.basecode.io.reader.AbstractMatrixReader<M,V>
    • ubic.basecode.io.reader.DoubleMatrixReader
      • ubic.basecode.io.reader.SparseDoubleMatrixReader
      • ubic.basecode.io.reader.SparseRaggedMatrixReader
    • ubic.basecode.io.reader.StringMatrixReader
  • ubic.basecode.ontology.jena.AbstractOntologyService (implements ubic.basecode.ontology.providers.OntologyService)
    • ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService
      • ubic.basecode.ontology.providers.CellLineOntologyService
      • ubic.basecode.ontology.providers.CellTypeOntologyService
      • ubic.basecode.ontology.providers.ChebiOntologyService
      • ubic.basecode.ontology.providers.DiseaseOntologyService
      • ubic.basecode.ontology.providers.ExperimentalFactorOntologyService
      • ubic.basecode.ontology.providers.FMAOntologyService
      • ubic.basecode.ontology.providers.GenericOntologyService
      • ubic.basecode.ontology.providers.HumanDevelopmentOntologyService
      • ubic.basecode.ontology.providers.HumanPhenotypeOntologyService
      • ubic.basecode.ontology.providers.MammalianPhenotypeOntologyService
      • ubic.basecode.ontology.providers.MedicOntologyService
      • ubic.basecode.ontology.providers.MouseDevelopmentOntologyService
      • ubic.basecode.ontology.providers.NIFSTDOntologyService
      • ubic.basecode.ontology.providers.ObiService
      • ubic.basecode.ontology.providers.SequenceOntologyService
      • ubic.basecode.ontology.providers.UberonOntologyService
      • ubic.basecode.ontology.providers.UnitsOntologyService
  • ubic.basecode.util.r.AbstractRClient (implements ubic.basecode.util.r.RClient)
    • ubic.basecode.util.r.JRIClient
    • ubic.basecode.util.r.RServeClient
  • ubic.basecode.ontology.ncbo.AnnotatorClient
  • ubic.basecode.ontology.ncbo.AnnotatorResponse (implements java.lang.Comparable<T>)
  • ubic.basecode.util.r.type.AnovaEffect (implements java.io.Serializable)
  • ubic.basecode.util.r.type.AnovaResult
    • ubic.basecode.math.linearmodels.GenericAnovaResult (implements java.io.Serializable)
    • ubic.basecode.util.r.type.OneWayAnovaResult
    • ubic.basecode.util.r.type.TwoWayAnovaResult
  • ubic.basecode.util.BatchIterator<E> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  • ubic.basecode.dataStructure.tree.BinaryTree<T>
  • ubic.basecode.dataStructure.BitUtil
  • ubic.basecode.math.linalg.Blas
  • ubic.basecode.util.BrowserLauncher
  • ubic.basecode.io.ByteArrayConverter
  • ubic.basecode.graphics.ColorMap
  • ubic.basecode.graphics.ColorMatrix<A,B> (implements java.lang.Cloneable)
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • ubic.basecode.graphics.JGradientBar
          • ubic.basecode.graphics.MatrixDisplay<R,C>
  • ubic.basecode.util.Configuration
  • ubic.basecode.util.ConfigUtils
  • ubic.basecode.math.Constants
  • ubic.basecode.math.CorrelationStats
  • ubic.basecode.dataStructure.CountingMap<K> (implements java.util.Map<K,V>)
  • ubic.basecode.io.excel.CreateSpreadSheet
    • ubic.basecode.dataStructure.params.ParamSpreadSheet
  • ubic.basecode.util.DateUtil
  • cern.jet.stat.Descriptive
    • ubic.basecode.math.DescriptiveWithMissing
  • ubic.basecode.math.linearmodels.DesignMatrix
  • ubic.basecode.math.distribution.Dirichlet
  • ubic.basecode.math.Distance
  • ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
  • ubic.basecode.dataStructure.DoublePoint
  • ubic.basecode.math.linalg.Dqrsl
  • ubic.basecode.io.excel.ExcelUtil
  • ubic.basecode.util.FileTools
  • ubic.basecode.math.distribution.Histogram
  • ubic.basecode.io.reader.HistogramReader
  • ubic.basecode.math.distribution.HistogramSampler
  • ubic.basecode.io.writer.HistogramWriter
  • ubic.basecode.util.r.type.HTest
  • ubic.basecode.math.KruskalWallis
  • ubic.basecode.math.KSTest
  • ubic.basecode.math.linearmodels.LeastSquaresFit
  • ubic.basecode.math.linearmodels.LinearModelSummary (implements java.io.Serializable)
  • ubic.basecode.io.reader.MapReader
  • ubic.basecode.math.MathUtil
  • ubic.basecode.math.MatrixNormalizer<R,C>
  • ubic.basecode.math.MatrixRowStats
  • ubic.basecode.math.MatrixStats
  • ubic.basecode.dataStructure.matrix.MatrixUtil
  • ubic.basecode.io.writer.MatrixWriter<R,C>
  • ubic.basecode.math.linearmodels.MeanVarianceEstimator
  • ubic.basecode.math.metaanalysis.MetaAnalysis
    • ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
    • ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
  • ubic.basecode.math.linearmodels.ModeratedTstat
  • ubic.basecode.math.MultipleTestCorrection
  • ubic.basecode.util.NetUtils
  • ubic.basecode.math.distribution.NormalProbabilityComputer (implements ubic.basecode.math.distribution.ProbabilityComputer)
  • ubic.basecode.ontology.ncbo.OmimAnnotatorClient
  • ubic.basecode.ontology.search.OntologySearch
  • ubic.basecode.ontology.model.OntologyTermSimple (implements ubic.basecode.ontology.model.OntologyTerm, java.io.Serializable)
  • ubic.basecode.dataStructure.params.ParameterGrabber
  • ubic.basecode.dataStructure.params.ParamKeeper
  • cern.colt.PersistentObject (implements java.lang.Cloneable, java.io.Serializable)
    • cern.colt.matrix.impl.AbstractMatrix
      • cern.colt.matrix.impl.AbstractMatrix1D
        • cern.colt.matrix.DoubleMatrix1D
          • cern.colt.matrix.impl.DenseDoubleMatrix1D
            • ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D
          • ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
  • ubic.basecode.dataStructure.Point
    • ubic.basecode.dataStructure.Link (implements java.lang.Comparable<T>)
  • ubic.basecode.math.PrecisionRecall
  • ubic.basecode.util.PrettyPrinter
  • ubic.basecode.math.linalg.QRDecomposition
  • ubic.basecode.math.RandomChooser
  • ubic.basecode.math.Rank
  • ubic.basecode.util.r.RConnectionFactory
  • ubic.basecode.util.RegressionTesting
  • ubic.basecode.math.ROC
  • ubic.basecode.math.linalg.SingularValueDecomposition<R,C>
  • ubic.basecode.math.Smooth
  • ubic.basecode.math.SpecFunc
  • ubic.basecode.io.excel.SpreadSheetSchema
  • ubic.basecode.util.SQLUtils
  • ubic.basecode.math.Stats
  • ubic.basecode.util.StatusDebugLogger (implements ubic.basecode.util.StatusViewer)
  • ubic.basecode.util.StatusStderr (implements ubic.basecode.util.StatusViewer)
  • ubic.basecode.io.StringConverter
  • ubic.basecode.math.StringDistance
  • ubic.basecode.util.StringUtil
  • java.lang.Thread (implements java.lang.Runnable)
    • ubic.basecode.util.GenericStreamConsumer
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • ubic.basecode.ontology.search.OntologySearchException
  • ubic.basecode.math.distribution.UniformDensityComputer (implements ubic.basecode.math.distribution.DensityGenerator)
  • ubic.basecode.math.distribution.UniformProbabilityComputer (implements ubic.basecode.math.distribution.ProbabilityComputer)
  • ubic.basecode.graphics.text.Util
  • ubic.basecode.dataStructure.Visitable
    • ubic.basecode.dataStructure.graph.AbstractGraphNode<K,V> (implements ubic.basecode.dataStructure.graph.GraphNode<K,V>)
      • ubic.basecode.dataStructure.graph.DirectedGraphNode<K,V> (implements java.lang.Comparable<T>)
      • ubic.basecode.dataStructure.graph.UndirectedGraphNode<K,V> (implements java.lang.Comparable<T>)
    • ubic.basecode.dataStructure.tree.BinaryTreeNode<T>
  • ubic.basecode.math.Wilcoxon
  • ubic.basecode.math.distribution.Wishart

Interface Hierarchy

• ubic.basecode.ontology.model.ChainedStatementObject
• ubic.basecode.ontology.model.CharacteristicStatement
  • ubic.basecode.ontology.model.ChainedStatement
  • ubic.basecode.ontology.model.ClassStatement
  • ubic.basecode.ontology.model.DataStatement
  • ubic.basecode.ontology.model.InstanceStatement
• java.lang.Comparable<T>
  • ubic.basecode.ontology.model.OntologyResource
    • ubic.basecode.ontology.model.AnnotationProperty
    • ubic.basecode.ontology.model.OntologyIndividual
    • ubic.basecode.ontology.model.OntologyProperty
      • ubic.basecode.ontology.model.DatatypeProperty
      • ubic.basecode.ontology.model.ObjectProperty
    • ubic.basecode.ontology.model.OntologyTerm
      • ubic.basecode.ontology.model.OntologyRestriction
        • ubic.basecode.ontology.model.OntologyCardinalityRestriction
        • ubic.basecode.ontology.model.OntologyClassRestriction
        • ubic.basecode.ontology.model.OntologyDatatypeRestriction
• ubic.basecode.math.distribution.DensityGenerator
• ubic.basecode.datafilter.Filter<M,R,C,V>
• ubic.basecode.dataStructure.graph.Graph<R,K,V>
• ubic.basecode.dataStructure.graph.GraphNode<K,V>
• ubic.basecode.dataStructure.matrix.Matrix2D<R,C,V>
  • ubic.basecode.dataStructure.matrix.ObjectMatrix<R,C,V>
  • ubic.basecode.dataStructure.matrix.PrimitiveMatrix<R,C,V>
• ubic.basecode.dataStructure.matrix.Matrix3D<R,C,S,V>
• ubic.basecode.ontology.model.OntologyModel
• ubic.basecode.ontology.providers.OntologyService
• ubic.basecode.math.distribution.ProbabilityComputer
• ubic.basecode.util.r.RClient
• ubic.basecode.io.excel.SpreadSheetFilter
• ubic.basecode.util.StatusViewer

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.basecode.ontology.model.OntologyCardinalityRestriction.CardinalityType
    • ubic.basecode.ontology.providers.OntologyService.InferenceMode
    • ubic.basecode.ontology.providers.OntologyService.LanguageLevel