| Package | TC | CC | AC | Ca | Ce | A | I | D | V |
|---|---|---|---|---|---|---|---|---|---|
| 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 | 21 | 3.0% | 81.0% | 16.0% | 1 |
| ubic.basecode.math.distribution | 11 | 9 | 2 | 1 | 13 | 18.0% | 93.0% | 11.0% | 1 |
| ubic.basecode.math.linalg | 5 | 5 | 0 | 1 | 15 | 0.0% | 94.0% | 6.0% | 1 |
| ubic.basecode.math.linearmodels | 11 | 11 | 0 | 1 | 22 | 0.0% | 96.0% | 4.0% | 1 |
| ubic.basecode.math.metaanalysis | 3 | 2 | 1 | 0 | 5 | 33.0% | 100.0% | 33.0% | 1 |
| ubic.basecode.ontology | 3 | 3 | 0 | 2 | 14 | 0.0% | 88.0% | 12.0% | 1 |
| ubic.basecode.ontology.model | 32 | 12 | 20 | 3 | 13 | 62.0% | 81.0% | 44.0% | 1 |
| ubic.basecode.ontology.ncbo | 3 | 3 | 0 | 0 | 16 | 0.0% | 100.0% | 0.0% | 1 |
| ubic.basecode.ontology.providers | 20 | 18 | 2 | 0 | 12 | 10.0% | 100.0% | 10.0% | 1 |
| ubic.basecode.ontology.search | 8 | 8 | 0 | 1 | 24 | 0.0% | 96.0% | 4.0% | 1 |
| ubic.basecode.util | 17 | 16 | 1 | 6 | 27 | 6.0% | 82.0% | 12.0% | 1 |
| ubic.basecode.util.r | 5 | 3 | 2 | 0 | 18 | 40.0% | 100.0% | 40.0% | 1 |
| ubic.basecode.util.r.type | 5 | 4 | 1 | 2 | 5 | 20.0% | 71.0% | 9.0% | 1 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
cern.colt.list java.io java.lang java.nio java.util org.apache.commons.lang3 |
| 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 |
| 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 |
| 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 |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 5 | 21 | 3.0% | 81.0% | 16.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| ubic.basecode.math.Constants |
ubic.basecode.math.CacheKey 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.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 java.util.concurrent 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 |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 1 | 13 | 18.0% | 93.0% | 11.0% |
| 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 org.jfree.data.xy |
| 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$1 |
ubic.basecode.math.linearmodels |
cern.colt.list cern.colt.matrix cern.colt.matrix.impl cern.colt.matrix.linalg cern.jet.math java.lang java.util java.util.concurrent no.uib.cipr.matrix org.apache.commons.lang3 org.apache.commons.lang3.time org.netlib.lapack org.netlib.util org.slf4j ubic.basecode.dataStructure.matrix |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 1 | 22 | 0.0% | 96.0% | 4.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| None | ubic.basecode.math.linearmodels.DesignMatrix ubic.basecode.math.linearmodels.GenericAnovaResult ubic.basecode.math.linearmodels.GenericAnovaResult$InteractionFactor ubic.basecode.math.linearmodels.LeastSquaresFit ubic.basecode.math.linearmodels.LinearModelSummary 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.rosuda.REngine org.slf4j ubic.basecode.dataStructure.matrix ubic.basecode.math ubic.basecode.math.linalg ubic.basecode.util.r.type |
| 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 |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 2 | 14 | 0.0% | 88.0% | 12.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| None | ubic.basecode.ontology.OntologyLoader ubic.basecode.ontology.OntologyUtil ubic.basecode.ontology.OntologyUtil$1 |
ubic.basecode.ontology.model ubic.basecode.ontology.providers |
com.hp.hpl.jena.ontology com.hp.hpl.jena.rdf.model com.hp.hpl.jena.util.iterator java.io java.lang java.net java.nio.file java.util org.apache.commons.io org.apache.commons.lang3 org.apache.commons.lang3.time org.slf4j ubic.basecode.ontology.model ubic.basecode.util |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 3 | 13 | 62.0% | 81.0% | 44.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| ubic.basecode.ontology.model.AbstractOntologyResource ubic.basecode.ontology.model.AnnotationProperty ubic.basecode.ontology.model.ChainedStatement ubic.basecode.ontology.model.ChainedStatementObject ubic.basecode.ontology.model.CharacteristicStatement ubic.basecode.ontology.model.ClassStatement ubic.basecode.ontology.model.DataStatement ubic.basecode.ontology.model.DatatypeProperty ubic.basecode.ontology.model.InstanceStatement ubic.basecode.ontology.model.ObjectProperty ubic.basecode.ontology.model.OntologyCardinalityRestriction ubic.basecode.ontology.model.OntologyClassRestriction ubic.basecode.ontology.model.OntologyDatatypeRestriction ubic.basecode.ontology.model.OntologyIndividual ubic.basecode.ontology.model.OntologyProperty ubic.basecode.ontology.model.OntologyPropertyImpl ubic.basecode.ontology.model.OntologyResource ubic.basecode.ontology.model.OntologyRestriction ubic.basecode.ontology.model.OntologyRestrictionImpl ubic.basecode.ontology.model.OntologyTerm |
ubic.basecode.ontology.model.AnnotationPropertyImpl ubic.basecode.ontology.model.DatatypePropertyImpl ubic.basecode.ontology.model.ObjectPropertyImpl ubic.basecode.ontology.model.OntologyCardinalityRestriction$CardinalityType ubic.basecode.ontology.model.OntologyCardinalityRestrictionImpl ubic.basecode.ontology.model.OntologyClassRestrictionImpl ubic.basecode.ontology.model.OntologyDatatypeRestrictionImpl ubic.basecode.ontology.model.OntologyIndividualImpl ubic.basecode.ontology.model.OntologyTermImpl ubic.basecode.ontology.model.OntologyTermSimple ubic.basecode.ontology.model.PropertyFactory ubic.basecode.ontology.model.RestrictionFactory |
ubic.basecode.ontology ubic.basecode.ontology.providers ubic.basecode.ontology.search |
com.hp.hpl.jena.enhanced com.hp.hpl.jena.graph com.hp.hpl.jena.ontology com.hp.hpl.jena.ontology.impl com.hp.hpl.jena.rdf.model com.hp.hpl.jena.rdf.model.impl com.hp.hpl.jena.util.iterator java.io java.lang java.util org.apache.commons.lang3 org.slf4j ubic.basecode.ontology |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 0 | 16 | 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.apache.http org.apache.http.client org.apache.http.client.methods org.apache.http.impl.client org.slf4j org.w3c.dom org.xml.sax ubic.basecode.util |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 0 | 12 | 10.0% | 100.0% | 10.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService ubic.basecode.ontology.providers.AbstractOntologyService |
ubic.basecode.ontology.providers.AbstractOntologyService$OntologyInitializationThread 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 |
None | com.hp.hpl.jena.ontology java.io java.lang java.util java.util.concurrent.atomic org.apache.commons.lang3 org.apache.commons.lang3.time org.slf4j ubic.basecode.ontology ubic.basecode.ontology.model ubic.basecode.ontology.search ubic.basecode.util |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 1 | 24 | 0.0% | 96.0% | 4.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| None | ubic.basecode.ontology.search.IndexerSelector ubic.basecode.ontology.search.OntologyIndexer ubic.basecode.ontology.search.OntologySearch ubic.basecode.ontology.search.OntologySearchException ubic.basecode.ontology.search.OntologySearchJenaException ubic.basecode.ontology.search.RetryWithoutWildcardFailedException ubic.basecode.ontology.search.SearchIndex ubic.basecode.ontology.search.SearchIndex$1 |
ubic.basecode.ontology.providers |
com.hp.hpl.jena.ontology com.hp.hpl.jena.rdf.model com.hp.hpl.jena.shared com.hp.hpl.jena.util.iterator com.hp.hpl.jena.vocabulary java.io java.lang java.util java.util.regex org.apache.commons.lang3 org.apache.commons.lang3.time org.apache.commons.text org.apache.jena.larq org.apache.lucene.analysis org.apache.lucene.analysis.en org.apache.lucene.analysis.standard org.apache.lucene.index org.apache.lucene.queryParser org.apache.lucene.search org.apache.lucene.store org.apache.lucene.util org.slf4j ubic.basecode.ontology.model ubic.basecode.util |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 6 | 27 | 6.0% | 82.0% | 12.0% |
| 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 ubic.basecode.ontology.ncbo ubic.basecode.ontology.providers ubic.basecode.ontology.search ubic.basecode.util.r |
cern.colt.list cern.colt.matrix com.opencsv com.opencsv.exceptions java.awt java.beans java.io java.lang java.lang.reflect java.math java.net 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.ex org.apache.commons.configuration2.io 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 |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 0 | 18 | 40.0% | 100.0% | 40.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| ubic.basecode.util.r.AbstractRClient ubic.basecode.util.r.RClient |
ubic.basecode.util.r.JRIClient ubic.basecode.util.r.RConnectionFactory ubic.basecode.util.r.RServeClient |
None | java.io java.lang java.net java.util org.apache.commons.collections4 org.apache.commons.collections4.functors org.apache.commons.configuration2 org.apache.commons.configuration2.ex org.apache.commons.configuration2.io org.apache.commons.lang3 org.rosuda.REngine org.rosuda.REngine.JRI org.rosuda.REngine.Rserve org.slf4j ubic.basecode.dataStructure.matrix ubic.basecode.math.linearmodels ubic.basecode.util ubic.basecode.util.r.type |
| Afferent Couplings | Efferent Couplings | Abstractness | Instability | Distance |
|---|---|---|---|---|
| 2 | 5 | 20.0% | 71.0% | 9.0% |
| Abstract Classes | Concrete Classes | Used by Packages | Uses Packages |
|---|---|---|---|
| ubic.basecode.util.r.type.AnovaResult |
ubic.basecode.util.r.type.AnovaEffect ubic.basecode.util.r.type.HTest ubic.basecode.util.r.type.OneWayAnovaResult ubic.basecode.util.r.type.TwoWayAnovaResult |
ubic.basecode.math.linearmodels ubic.basecode.util.r |
java.io java.lang java.util org.apache.commons.lang3 org.rosuda.REngine |
| 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.dataStructure.matrix ubic.basecode.math ubic.basecode.dataStructure.matrix |
| ubic.basecode.graphics | ubic.basecode.dataStructure.matrix ubic.basecode.math ubic.basecode.dataStructure.matrix |
| ubic.basecode.io.reader | ubic.basecode.util 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.dataStructure.matrix ubic.basecode.math ubic.basecode.dataStructure.matrix |
| ubic.basecode.math.metaanalysis | ubic.basecode.math ubic.basecode.dataStructure.matrix ubic.basecode.math |
| ubic.basecode.ontology | ubic.basecode.util ubic.basecode.dataStructure.matrix ubic.basecode.math ubic.basecode.dataStructure.matrix |
| ubic.basecode.ontology.model | ubic.basecode.ontology 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.ontology.search | 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.dataStructure.matrix ubic.basecode.math ubic.basecode.dataStructure.matrix |
| 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. |
