Built by Maven

Metric Results

[ summary ] [ packages ] [ cycles ] [ explanations ]

The following document contains the results of a JDepend metric analysis. The various metrics are defined at the bottom of this document.

Summary

[ summary ] [ packages ] [ cycles ] [ explanations ]

Package TC CC AC Ca Ce A I D V com.github.fommil.netlib 4 3 1 0 5 25.0% 100.0% 25.0% 1 ubic.basecode.dataStructure 12 10 2 2 4 17.0% 67.0% 17.0% 1 ubic.basecode.dataStructure.graph 7 3 4 0 7 57.0% 100.0% 57.0% 1 ubic.basecode.dataStructure.matrix 24 16 8 10 14 33.0% 58.0% 8.0% 1 ubic.basecode.dataStructure.params 3 3 0 0 5 0.0% 100.0% 0.0% 1 ubic.basecode.dataStructure.tree 2 2 0 0 2 0.0% 100.0% 0.0% 1 ubic.basecode.datafilter 9 6 3 1 8 33.0% 89.0% 22.0% 1 ubic.basecode.graphics 6 6 0 0 14 0.0% 100.0% 0.0% 1 ubic.basecode.graphics.text 1 1 0 1 4 0.0% 80.0% 20.0% 1 ubic.basecode.io 2 2 0 1 6 0.0% 86.0% 14.0% 1 ubic.basecode.io.excel 5 4 1 1 6 20.0% 86.0% 6.0% 1 ubic.basecode.io.reader 8 7 1 1 12 12.0% 92.0% 5.0% 1 ubic.basecode.io.writer 2 2 0 0 8 0.0% 100.0% 0.0% 1 ubic.basecode.math 29 28 1 5 20 3.0% 80.0% 17.0% 1 ubic.basecode.math.distribution 11 9 2 1 12 18.0% 92.0% 10.0% 1 ubic.basecode.math.linalg 5 5 0 1 15 0.0% 94.0% 6.0% 1 ubic.basecode.math.linearmodels 17 11 6 1 20 35.0% 95.0% 31.0% 1 ubic.basecode.math.metaanalysis 3 2 1 0 5 33.0% 100.0% 33.0% 1 ubic.basecode.ontology.jena 33 28 5 1 31 15.000001% 97.0% 12.0% 1 ubic.basecode.ontology.model 15 1 14 4 2 93.0% 33.0% 27.000002% 1 ubic.basecode.ontology.ncbo 3 3 0 0 12 0.0% 100.0% 0.0% 1 ubic.basecode.ontology.providers 23 20 3 1 7 13.0% 88.0% 1.0% 1 ubic.basecode.ontology.search 3 2 1 2 3 33.0% 60.000004% 7.0% 1 ubic.basecode.ontology.simple 6 4 2 0 4 33.0% 100.0% 33.0% 1 ubic.basecode.util 17 16 1 5 28 6.0% 85.0% 9.0% 1 ubic.basecode.util.r 11 7 4 0 14 36.0% 100.0% 36.0% 1

Packages

[ summary ] [ packages ] [ cycles ] [ explanations ]

com.github.fommil.netlib

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 5 25.0% 100.0% 25.0% Abstract Classes Concrete Classes Used by Packages Uses Packages com.github.fommil.netlib.package-info
com.github.fommil.netlib.ARPACK
com.github.fommil.netlib.BLAS
com.github.fommil.netlib.LAPACK
None dev.ludovic.netlib.arpack
dev.ludovic.netlib.blas
dev.ludovic.netlib.lapack
java.lang
org.netlib.util

ubic.basecode.dataStructure

Afferent Couplings Efferent Couplings Abstractness Instability Distance 2 4 17.0% 67.0% 17.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.dataStructure.CountingMap$CountComparator
ubic.basecode.dataStructure.Visitable
ubic.basecode.dataStructure.BitUtil
ubic.basecode.dataStructure.CountingMap
ubic.basecode.dataStructure.CountingMap$1
ubic.basecode.dataStructure.CountingMap$AscendingCountComparator
ubic.basecode.dataStructure.CountingMap$DescendingCountComparator
ubic.basecode.dataStructure.DoubleAddingMap
ubic.basecode.dataStructure.DoublePoint
ubic.basecode.dataStructure.Link
ubic.basecode.dataStructure.Point
ubic.basecode.dataStructure.StringToStringSetMap
ubic.basecode.dataStructure.graph
ubic.basecode.dataStructure.tree
java.lang
java.text
java.util
ubic.basecode.dataStructure.matrix

ubic.basecode.dataStructure.graph

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 7 57.0% 100.0% 57.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.dataStructure.graph.AbstractGraph
ubic.basecode.dataStructure.graph.AbstractGraphNode
ubic.basecode.dataStructure.graph.Graph
ubic.basecode.dataStructure.graph.GraphNode
ubic.basecode.dataStructure.graph.DirectedGraph
ubic.basecode.dataStructure.graph.DirectedGraphNode
ubic.basecode.dataStructure.graph.UndirectedGraphNode
None java.lang
java.lang.reflect
java.util
javax.swing
javax.swing.tree
org.slf4j
ubic.basecode.dataStructure

ubic.basecode.dataStructure.matrix

Afferent Couplings Efferent Couplings Abstractness Instability Distance 10 14 33.0% 58.0% 8.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.dataStructure.matrix.AbstractMatrix
ubic.basecode.dataStructure.matrix.AbstractMatrix3D
ubic.basecode.dataStructure.matrix.DoubleMatrix
ubic.basecode.dataStructure.matrix.DoubleMatrix3D
ubic.basecode.dataStructure.matrix.Matrix2D
ubic.basecode.dataStructure.matrix.Matrix3D
ubic.basecode.dataStructure.matrix.ObjectMatrix
ubic.basecode.dataStructure.matrix.PrimitiveMatrix
ubic.basecode.dataStructure.matrix.CompressedBitMatrix
ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D
ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
ubic.basecode.dataStructure.matrix.DoubleMatrix$1
ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
ubic.basecode.dataStructure.matrix.IntegerMatrix
ubic.basecode.dataStructure.matrix.MatrixUtil
ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
ubic.basecode.dataStructure.matrix.StringMatrix
ubic.basecode.dataStructure
ubic.basecode.datafilter
ubic.basecode.graphics
ubic.basecode.io.reader
ubic.basecode.io.writer
ubic.basecode.math
ubic.basecode.math.linalg
ubic.basecode.math.linearmodels
ubic.basecode.util
ubic.basecode.util.r
cern.colt.function
cern.colt.list
cern.colt.matrix
cern.colt.matrix.impl
java.io
java.lang
java.math
java.util
java.util.function
no.uib.cipr.matrix
no.uib.cipr.matrix.sparse
org.apache.commons.collections4
org.apache.commons.lang3
ubic.basecode.math

ubic.basecode.dataStructure.params

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 5 0.0% 100.0% 0.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.dataStructure.params.ParamKeeper
ubic.basecode.dataStructure.params.ParamSpreadSheet
ubic.basecode.dataStructure.params.ParameterGrabber
None java.lang
java.lang.reflect
java.util
org.slf4j
ubic.basecode.io.excel

ubic.basecode.dataStructure.tree

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 2 0.0% 100.0% 0.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.dataStructure.tree.BinaryTree
ubic.basecode.dataStructure.tree.BinaryTreeNode
None java.lang
ubic.basecode.dataStructure

ubic.basecode.datafilter

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 8 33.0% 89.0% 22.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.datafilter.AbstractFilter
ubic.basecode.datafilter.AbstractLevelFilter
ubic.basecode.datafilter.Filter
ubic.basecode.datafilter.AffymetrixProbeNameFilter
ubic.basecode.datafilter.ItemLevelFilter
ubic.basecode.datafilter.RowAbsentFilter
ubic.basecode.datafilter.RowLevelFilter
ubic.basecode.datafilter.RowMissingFilter
ubic.basecode.datafilter.RowNameFilter
ubic.basecode.math
cern.colt.list
cern.jet.stat
java.lang
java.lang.reflect
java.util
org.slf4j
ubic.basecode.dataStructure.matrix
ubic.basecode.math

ubic.basecode.graphics

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 14 0.0% 100.0% 0.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.graphics.ColorMap
ubic.basecode.graphics.ColorMatrix
ubic.basecode.graphics.JGradientBar
ubic.basecode.graphics.JGradientLabel
ubic.basecode.graphics.JNumberLabel
ubic.basecode.graphics.MatrixDisplay
None cern.colt.list
java.awt
java.awt.image
java.io
java.lang
java.text
javax.imageio
javax.swing
javax.swing.border
org.apache.commons.lang3
ubic.basecode.dataStructure.matrix
ubic.basecode.graphics.text
ubic.basecode.io.reader
ubic.basecode.math

ubic.basecode.graphics.text

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 4 0.0% 80.0% 20.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.graphics.text.Util
ubic.basecode.graphics
java.awt
java.awt.font
java.awt.geom
java.lang

ubic.basecode.io

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 6 0.0% 86.0% 14.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.io.ByteArrayConverter
ubic.basecode.io.StringConverter
ubic.basecode.util
java.lang
java.lang.reflect
java.nio
java.nio.charset
java.util
org.apache.commons.lang3

ubic.basecode.io.excel

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 6 20.0% 86.0% 6.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.io.excel.SpreadSheetFilter
ubic.basecode.io.excel.CreateSpreadSheet
ubic.basecode.io.excel.ExcelUtil
ubic.basecode.io.excel.ExcelUtil$1
ubic.basecode.io.excel.SpreadSheetSchema
ubic.basecode.dataStructure.params
java.io
java.lang
java.util
org.apache.poi.hssf.usermodel
org.apache.poi.poifs.filesystem
org.apache.poi.ss.usermodel

ubic.basecode.io.reader

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 12 12.0% 92.0% 5.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.io.reader.AbstractMatrixReader
ubic.basecode.io.reader.DoubleMatrixReader
ubic.basecode.io.reader.HistogramReader
ubic.basecode.io.reader.IndexScoreDyad
ubic.basecode.io.reader.MapReader
ubic.basecode.io.reader.SparseDoubleMatrixReader
ubic.basecode.io.reader.SparseRaggedMatrixReader
ubic.basecode.io.reader.StringMatrixReader
ubic.basecode.graphics
cern.colt.list
cern.colt.map
cern.colt.matrix
hep.aida.ref
java.io
java.lang
java.text
java.util
org.apache.commons.lang3
org.slf4j
ubic.basecode.dataStructure.matrix
ubic.basecode.util

ubic.basecode.io.writer

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 8 0.0% 100.0% 0.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.io.writer.HistogramWriter
ubic.basecode.io.writer.MatrixWriter
None cern.colt.matrix
corejava
hep.aida
java.io
java.lang
java.text
java.util
ubic.basecode.dataStructure.matrix

ubic.basecode.math

Afferent Couplings Efferent Couplings Abstractness Instability Distance 5 20 3.0% 80.0% 17.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.math.Constants
ubic.basecode.math.CorrelationStats
ubic.basecode.math.DescriptiveWithMissing
ubic.basecode.math.Distance
ubic.basecode.math.KSTest
ubic.basecode.math.KeyAndValueData
ubic.basecode.math.KruskalWallis
ubic.basecode.math.MathUtil
ubic.basecode.math.MatrixNormalizer
ubic.basecode.math.MatrixRowStats
ubic.basecode.math.MatrixStats
ubic.basecode.math.MatrixStats$1
ubic.basecode.math.MatrixStats$2
ubic.basecode.math.MatrixStats$3
ubic.basecode.math.MatrixStats$4
ubic.basecode.math.MatrixStats$5
ubic.basecode.math.MultipleTestCorrection
ubic.basecode.math.PolyGamma
ubic.basecode.math.PrecisionRecall
ubic.basecode.math.ROC
ubic.basecode.math.RandomChooser
ubic.basecode.math.Rank
ubic.basecode.math.RankData
ubic.basecode.math.Smooth
ubic.basecode.math.SpecFunc$1
ubic.basecode.math.Stats
ubic.basecode.math.StringDistance
ubic.basecode.math.Wilcoxon
ubic.basecode.math.Wilcoxon$CacheKey
ubic.basecode.dataStructure.matrix
ubic.basecode.datafilter
ubic.basecode.graphics
ubic.basecode.math.linearmodels
ubic.basecode.math.metaanalysis
cern.colt.function
cern.colt.list
cern.colt.matrix
cern.colt.matrix.impl
cern.colt.matrix.linalg
cern.jet.math
cern.jet.stat
java.lang
java.math
java.util
org.apache.commons.lang3
org.apache.commons.math3.analysis.interpolation
org.apache.commons.math3.analysis.polynomials
org.apache.commons.math3.exception
org.apache.commons.math3.random
org.apache.commons.math3.special
org.slf4j
ubic.basecode.dataStructure.matrix
ubic.basecode.datafilter
ubic.basecode.math.distribution

ubic.basecode.math.distribution

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 12 18.0% 92.0% 10.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.math.distribution.DensityGenerator
ubic.basecode.math.distribution.ProbabilityComputer
ubic.basecode.math.distribution.Dirichlet
ubic.basecode.math.distribution.Histogram
ubic.basecode.math.distribution.Histogram$1
ubic.basecode.math.distribution.Histogram$BinInfo
ubic.basecode.math.distribution.HistogramSampler
ubic.basecode.math.distribution.NormalProbabilityComputer
ubic.basecode.math.distribution.UniformDensityComputer
ubic.basecode.math.distribution.UniformProbabilityComputer
ubic.basecode.math.distribution.Wishart
ubic.basecode.math
cern.colt.list
cern.colt.matrix
cern.colt.matrix.impl
cern.colt.matrix.linalg
cern.jet.random
cern.jet.random.engine
cern.jet.stat
hep.aida
hep.aida.ref
java.io
java.lang
java.text

ubic.basecode.math.linalg

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 15 0.0% 94.0% 6.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.math.linalg.Blas
ubic.basecode.math.linalg.Dqrsl
ubic.basecode.math.linalg.QRDecomposition
ubic.basecode.math.linalg.SingularValueDecomposition
ubic.basecode.math.linalg.SingularValueDecomposition$1
ubic.basecode.math.linearmodels
cern.colt.list
cern.colt.matrix
cern.colt.matrix.impl
cern.colt.matrix.linalg
cern.jet.math
java.lang
java.util
java.util.concurrent
no.uib.cipr.matrix
org.apache.commons.lang3
org.apache.commons.lang3.time
org.netlib.lapack
org.netlib.util
org.slf4j
ubic.basecode.dataStructure.matrix

ubic.basecode.math.linearmodels

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 20 35.0% 95.0% 31.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.math.linearmodels.AnovaResult
ubic.basecode.math.linearmodels.GenericAnovaResult
ubic.basecode.math.linearmodels.LinearModelSummary
ubic.basecode.math.linearmodels.OneWayAnovaResult
ubic.basecode.math.linearmodels.TwoWayAnovaResult
ubic.basecode.math.linearmodels.package-info
ubic.basecode.math.linearmodels.AnovaEffect
ubic.basecode.math.linearmodels.DesignMatrix
ubic.basecode.math.linearmodels.LeastSquaresFit
ubic.basecode.math.linearmodels.LinearModelSummaryImpl
ubic.basecode.math.linearmodels.LinearModelSummaryUtils
ubic.basecode.math.linearmodels.MeanVarianceEstimator
ubic.basecode.math.linearmodels.MeanVarianceEstimator$1
ubic.basecode.math.linearmodels.ModeratedTstat
ubic.basecode.math.linearmodels.ModeratedTstat$1
ubic.basecode.math.linearmodels.ModeratedTstat$2
ubic.basecode.math.linearmodels.ModeratedTstat$3
ubic.basecode.util.r
cern.colt.bitvector
cern.colt.function
cern.colt.list
cern.colt.matrix
cern.colt.matrix.impl
cern.colt.matrix.linalg
cern.jet.math
cern.jet.stat
java.io
java.lang
java.util
org.apache.commons.lang3
org.apache.commons.lang3.time
org.apache.commons.math3.distribution
org.apache.commons.math3.exception
org.apache.commons.math3.special
org.slf4j
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.math.linalg

ubic.basecode.math.metaanalysis

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 5 33.0% 100.0% 33.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.math.metaanalysis.MetaAnalysis
ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
None cern.colt.list
cern.jet.stat
java.io
java.lang
ubic.basecode.math

ubic.basecode.ontology.jena

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 31 15.000001% 97.0% 12.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.ontology.jena.AbstractOntologyResource
ubic.basecode.ontology.jena.OntologyPropertyImpl
ubic.basecode.ontology.jena.OntologyRestrictionImpl
ubic.basecode.ontology.jena.SearchIndex
ubic.basecode.ontology.jena.package-info
ubic.basecode.ontology.jena.AbstractOntologyService$1
ubic.basecode.ontology.jena.AbstractOntologyService$State
ubic.basecode.ontology.jena.AnnotationPropertyImpl
ubic.basecode.ontology.jena.AnnotationPropertyImpl$1
ubic.basecode.ontology.jena.BnodeFilter
ubic.basecode.ontology.jena.ClasspathOntologyService
ubic.basecode.ontology.jena.DatatypePropertyImpl
ubic.basecode.ontology.jena.IAO
ubic.basecode.ontology.jena.OBO
ubic.basecode.ontology.jena.ObjectPropertyImpl
ubic.basecode.ontology.jena.OntologyCardinalityRestrictionImpl
ubic.basecode.ontology.jena.OntologyClassRestrictionImpl
ubic.basecode.ontology.jena.OntologyDatatypeRestrictionImpl
ubic.basecode.ontology.jena.OntologyIndexer$IndexableProperty
ubic.basecode.ontology.jena.OntologyIndexer$LuceneSearchIndex
ubic.basecode.ontology.jena.OntologyIndividualImpl
ubic.basecode.ontology.jena.OntologyLoader
ubic.basecode.ontology.jena.OntologyLoader$1
ubic.basecode.ontology.jena.OntologyModelImpl
ubic.basecode.ontology.jena.PredicateFilter
ubic.basecode.ontology.jena.PropertyFactory
ubic.basecode.ontology.jena.RO
ubic.basecode.ontology.jena.RestrictionFactory
ubic.basecode.ontology.jena.RestrictionWithOnPropertyFilter
ubic.basecode.ontology.jena.RestrictionWithValuesFromFilter
ubic.basecode.ontology.jena.SearchIndex$JenaSearchResult
ubic.basecode.ontology.jena.TdbOntologyService
ubic.basecode.ontology.jena.UrlOntologyService
ubic.basecode.ontology.providers
com.hp.hpl.jena.enhanced
com.hp.hpl.jena.ontology
com.hp.hpl.jena.ontology.impl
com.hp.hpl.jena.query
com.hp.hpl.jena.rdf.model
com.hp.hpl.jena.shared
com.hp.hpl.jena.tdb
com.hp.hpl.jena.util.iterator
com.hp.hpl.jena.vocabulary
java.io
java.lang
java.net
java.nio.channels
java.nio.file
java.util
java.util.function
java.util.zip
org.apache.commons.io
org.apache.commons.lang3
org.apache.commons.lang3.time
org.apache.lucene.analysis
org.apache.lucene.document
org.apache.lucene.index
org.apache.lucene.queryParser
org.apache.lucene.search
org.apache.lucene.util
org.slf4j
ubic.basecode.ontology.model
ubic.basecode.ontology.providers
ubic.basecode.ontology.search
ubic.basecode.util

ubic.basecode.ontology.model

Afferent Couplings Efferent Couplings Abstractness Instability Distance 4 2 93.0% 33.0% 27.000002% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.ontology.model.AnnotationProperty
ubic.basecode.ontology.model.DatatypeProperty
ubic.basecode.ontology.model.ObjectProperty
ubic.basecode.ontology.model.OntologyCardinalityRestriction
ubic.basecode.ontology.model.OntologyClassRestriction
ubic.basecode.ontology.model.OntologyDatatypeRestriction
ubic.basecode.ontology.model.OntologyIndividual
ubic.basecode.ontology.model.OntologyModel
ubic.basecode.ontology.model.OntologyProperty
ubic.basecode.ontology.model.OntologyResource
ubic.basecode.ontology.model.OntologyRestriction
ubic.basecode.ontology.model.OntologyStatement
ubic.basecode.ontology.model.OntologyTerm
ubic.basecode.ontology.model.package-info
ubic.basecode.ontology.model.OntologyCardinalityRestriction$CardinalityType
ubic.basecode.ontology.jena
ubic.basecode.ontology.providers
ubic.basecode.ontology.search
ubic.basecode.ontology.simple
java.lang
java.util

ubic.basecode.ontology.ncbo

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 12 0.0% 100.0% 0.0% Abstract Classes Concrete Classes Used by Packages Uses Packages None ubic.basecode.ontology.ncbo.AnnotatorClient
ubic.basecode.ontology.ncbo.AnnotatorResponse
ubic.basecode.ontology.ncbo.OmimAnnotatorClient
None java.io
java.lang
java.net
java.util
java.util.regex
javax.xml.parsers
org.apache.commons.lang3
org.apache.commons.lang3.exception
org.slf4j
org.w3c.dom
org.xml.sax
ubic.basecode.util

ubic.basecode.ontology.providers

Afferent Couplings Efferent Couplings Abstractness Instability Distance 1 7 13.0% 88.0% 1.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService
ubic.basecode.ontology.providers.OntologyService
ubic.basecode.ontology.providers.package-info
ubic.basecode.ontology.providers.AbstractDelegatingOntologyService
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.OntologyService$InferenceMode
ubic.basecode.ontology.providers.OntologyService$LanguageLevel
ubic.basecode.ontology.providers.SequenceOntologyService
ubic.basecode.ontology.providers.UberonOntologyService
ubic.basecode.ontology.providers.UnitsOntologyService
ubic.basecode.ontology.jena
java.io
java.lang
java.util
ubic.basecode.ontology.jena
ubic.basecode.ontology.model
ubic.basecode.ontology.search
ubic.basecode.util

ubic.basecode.ontology.search

Afferent Couplings Efferent Couplings Abstractness Instability Distance 2 3 33.0% 60.000004% 7.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.ontology.search.package-info
ubic.basecode.ontology.search.OntologySearchException
ubic.basecode.ontology.search.OntologySearchResult
ubic.basecode.ontology.jena
ubic.basecode.ontology.providers
java.lang
java.util
ubic.basecode.ontology.model

ubic.basecode.ontology.simple

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 4 33.0% 100.0% 33.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.ontology.simple.AbstractOntologyResourceSimple
ubic.basecode.ontology.simple.package-info
ubic.basecode.ontology.simple.OntologyIndividualSimple
ubic.basecode.ontology.simple.OntologyPropertySimple
ubic.basecode.ontology.simple.OntologyStatementSimple
ubic.basecode.ontology.simple.OntologyTermSimple
None java.io
java.lang
java.util
ubic.basecode.ontology.model

ubic.basecode.util

Afferent Couplings Efferent Couplings Abstractness Instability Distance 5 28 6.0% 85.0% 9.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.util.StatusViewer
ubic.basecode.util.BatchIterator
ubic.basecode.util.BrowserLauncher
ubic.basecode.util.ConfigUtils
ubic.basecode.util.Configuration
ubic.basecode.util.DateUtil
ubic.basecode.util.FileTools
ubic.basecode.util.FileTools$1
ubic.basecode.util.FileTools$2
ubic.basecode.util.GenericStreamConsumer
ubic.basecode.util.NetUtils
ubic.basecode.util.PrettyPrinter
ubic.basecode.util.RegressionTesting
ubic.basecode.util.SQLUtils
ubic.basecode.util.StatusDebugLogger
ubic.basecode.util.StatusStderr
ubic.basecode.util.StringUtil
ubic.basecode.io.reader
ubic.basecode.ontology.jena
ubic.basecode.ontology.ncbo
ubic.basecode.ontology.providers
ubic.basecode.util.r
cern.colt.list
cern.colt.matrix
java.awt
java.beans
java.io
java.lang
java.lang.reflect
java.math
java.net
java.nio.charset
java.sql
java.text
java.util
java.util.regex
java.util.zip
org.apache.commons.configuration2
org.apache.commons.configuration2.builder
org.apache.commons.configuration2.convert
org.apache.commons.configuration2.ex
org.apache.commons.configuration2.io
org.apache.commons.csv
org.apache.commons.io
org.apache.commons.lang3
org.apache.commons.lang3.time
org.apache.commons.net.ftp
org.slf4j
ubic.basecode.dataStructure.matrix
ubic.basecode.io

ubic.basecode.util.r

Afferent Couplings Efferent Couplings Abstractness Instability Distance 0 14 36.0% 100.0% 36.0% Abstract Classes Concrete Classes Used by Packages Uses Packages ubic.basecode.util.r.AbstractAnovaResult
ubic.basecode.util.r.AbstractRClient
ubic.basecode.util.r.RClient
ubic.basecode.util.r.package-info
ubic.basecode.util.r.HTest
ubic.basecode.util.r.JRIClient
ubic.basecode.util.r.LinearModelSummaryImpl
ubic.basecode.util.r.OneWayAnovaResultImpl
ubic.basecode.util.r.RConnectionFactory
ubic.basecode.util.r.RServeClient
ubic.basecode.util.r.TwoWayAnovaResultImpl
None java.io
java.lang
java.util
org.apache.commons.collections4
org.apache.commons.collections4.functors
org.apache.commons.lang3
org.apache.commons.math3.distribution
org.rosuda.REngine
org.rosuda.REngine.JRI
org.rosuda.REngine.Rserve
org.slf4j
ubic.basecode.dataStructure.matrix
ubic.basecode.math.linearmodels
ubic.basecode.util

Cycles

[ summary ] [ packages ] [ cycles ] [ explanations ]

Package Package Dependencies ubic.basecode.dataStructure ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.dataStructure.graph ubic.basecode.dataStructure
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.dataStructure.matrix ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.dataStructure.tree ubic.basecode.dataStructure
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.datafilter ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.graphics ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.io.reader ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.io.writer ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.math ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.math.linalg ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.math.linearmodels ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.math.metaanalysis ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.ontology.jena ubic.basecode.ontology.providers
ubic.basecode.util
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.ontology.ncbo ubic.basecode.util
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.ontology.providers ubic.basecode.util
ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.util ubic.basecode.dataStructure.matrix
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.util.r ubic.basecode.math.linearmodels
ubic.basecode.math
ubic.basecode.dataStructure.matrix
ubic.basecode.math

Explanation

[ summary ] [ packages ] [ cycles ] [ explanations ]

The following explanations are for quick reference and are lifted directly from the original JDepend documentation.

Term Description Number of Classes The number of concrete and abstract classes (and interfaces) in the package is an indicator of the extensibility of the package. Afferent Couplings The number of other packages that depend upon classes within the package is an indicator of the package's responsibility. Efferent Couplings The number of other packages that the classes in the package depend upon is an indicator of the package's independence. Abstractness The ratio of the number of abstract classes (and interfaces) in the analyzed package to the total number of classes in the analyzed package. The range for this metric is 0 to 1, with A=0 indicating a completely concrete package and A=1 indicating a completely abstract package. Instability The ratio of efferent coupling (Ce) to total coupling (Ce / (Ce + Ca)). This metric is an indicator of the package's resilience to change. The range for this metric is 0 to 1, with I=0 indicating a completely stable package and I=1 indicating a completely instable package. Distance The perpendicular distance of a package from the idealized line A + I = 1. This metric is an indicator of the package's balance between abstractness and stability. A package squarely on the main sequence is optimally balanced with respect to its abstractness and stability. Ideal packages are either completely abstract and stable (x=0, y=1) or completely concrete and instable (x=1, y=0). The range for this metric is 0 to 1, with D=0 indicating a package that is coincident with the main sequence and D=1 indicating a package that is as far from the main sequence as possible. Cycles Packages participating in a package dependency cycle are in a deadly embrace with respect to reusability and their release cycle. Package dependency cycles can be easily identified by reviewing the textual reports of dependency cycles. Once these dependency cycles have been identified with JDepend, they can be broken by employing various object-oriented techniques.