baseCode - JDepend Source Code Analysis

Metric Results

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

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

Summary

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

Package	TC	AC	CC	AC	EC	A	I	D
baseCode.algorithm	2	2	0	2	3	1	60%	60%
baseCode.algorithm.learning.unsupervised	1	0	1	0	7	0	100%	0%
baseCode.algorithm.learning.unsupervised.cluster	8	4	4	0	7	0.5	100%	50%
baseCode.bio	3	1	2	2	2	0.33	50%	17%
baseCode.bio.geneset	6	0	6	0	12	0	100%	0%
baseCode.common	2	2	0	3	2	1	40%	40%
baseCode.dataFilter	10	3	7	0	8	0.3	100%	30%
baseCode.dataStructure	5	0	5	4	2	0	33%	67%
baseCode.dataStructure.graph	7	4	3	3	7	0.57	70%	27%
baseCode.dataStructure.matrix	10	3	7	7	9	0.3	56%	14%
baseCode.dataStructure.tree	4	0	4	0	3	0	100%	0%
baseCode.db	1	0	1	0	3	0	100%	0%
baseCode.graphics.text	1	0	1	2	4	0	67%	33%
baseCode.gui	24	3	21	1	21	0.12	95%	8%
baseCode.gui.file	3	0	3	0	4	0	100%	0%
baseCode.gui.table	12	0	12	0	11	0	100%	0%
baseCode.io	2	0	2	0	2	0	100%	0%
baseCode.io.reader	7	1	6	2	11	0.14	85%	1%
baseCode.io.writer	1	0	1	0	4	0	100%	0%
baseCode.math	17	1	16	3	10	0.06	77%	17%
baseCode.math.distribution	7	2	5	1	8	0.29	89%	17%
baseCode.math.metaanalysis	3	1	2	0	5	0.33	100%	33%
baseCode.misc	1	0	1	0	6	0	100%	0%
baseCode.util	6	1	5	4	9	0.17	69%	14%
baseCode.xml	2	0	2	1	8	0	89%	11%

Packages

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

baseCode.algorithm

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
2	3	100%	60%	60%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
Algorithm Ranker	None	baseCode.algorithm.learning.unsupervised baseCode.algorithm.learning.unsupervised.cluster	cern.colt.list java.lang org.apache.commons.logging

baseCode.algorithm.learning.unsupervised

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	7	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	RankProp	None	baseCode.algorithm baseCode.dataStructure.matrix cern.colt.matrix cern.colt.matrix.impl com.braju.beta.format java.lang org.apache.commons.logging

baseCode.algorithm.learning.unsupervised.cluster

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	7	50%	100%	50%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
ClusteringAlgorithm DistanceFactory Distancer Similarity	AverageLinkageDistancer Cluster ClusterNode HierarchicalClusterer	None	baseCode.algorithm baseCode.common cern.colt.list cern.colt.matrix cern.colt.matrix.impl java.lang java.util

baseCode.bio

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
2	2	33%	50%	17%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
GOTermList	GOEntry GOTermProbability	baseCode.bio.geneset baseCode.xml	baseCode.dataStructure java.lang

baseCode.bio.geneset

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	12	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	ClassSizeComparator GONames GeneAnnotations GeneAnnotations$1 GeneSet GeneSetMapTools	None	baseCode.bio baseCode.dataStructure baseCode.dataStructure.graph baseCode.util baseCode.xml hep.aida hep.aida.ref java.io java.lang java.util javax.swing.table org.xml.sax

baseCode.common

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
3	2	100%	40%	40%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
Distanceable Visitable	None	baseCode.algorithm.learning.unsupervised.cluster baseCode.dataStructure.graph baseCode.dataStructure.tree	java.lang java.util

baseCode.dataFilter

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	8	30%	100%	30%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
AbstractFilter AbstractLevelFilter Filter	AffymetrixProbeNameFilter ItemLevelFilter RowAbsentFilter RowAffyNameFilter RowLevelFilter RowMissingFilter RowNameFilter	None	baseCode.dataStructure.matrix baseCode.math cern.colt.list cern.jet.stat java.lang java.lang.reflect java.util org.apache.commons.logging

baseCode.dataStructure

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
4	2	0%	33%	67%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	Link OntologyEntry Point Queue Stack	baseCode.bio baseCode.bio.geneset baseCode.dataStructure.graph baseCode.xml	java.lang java.text

baseCode.dataStructure.graph

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
3	7	57%	70%	27%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
AbstractGraph AbstractGraphNode Graph GraphNode	DirectedGraph DirectedGraphNode UndirectedGraphNode	baseCode.bio.geneset baseCode.gui baseCode.xml	baseCode.common baseCode.dataStructure java.lang java.util javax.swing javax.swing.tree org.apache.commons.logging

baseCode.dataStructure.matrix

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
7	9	30%	56%	14%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
AbstractNamedDoubleMatrix AbstractNamedMatrix NamedMatrix	DenseDoubleMatrix1D DenseDoubleMatrix2DNamed DoubleMatrix2DNamedFactory RCDoubleMatrix1D SparseDoubleMatrix2DNamed SparseRaggedDoubleMatrix2DNamed StringMatrix2DNamed	baseCode.algorithm.learning.unsupervised baseCode.dataFilter baseCode.gui baseCode.io.reader baseCode.math baseCode.misc baseCode.util	cern.colt.function cern.colt.list cern.colt.matrix cern.colt.matrix.doublealgo cern.colt.matrix.impl corejava java.lang java.text java.util

baseCode.dataStructure.tree

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	3	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	BinaryTree BinaryTreeNode Tree TreeNode	None	baseCode.common java.lang java.util

baseCode.db

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	3	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	Handle	None	java.lang java.sql java.util

baseCode.graphics.text

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
2	4	0%	67%	33%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	Util	baseCode.gui baseCode.gui.table	java.awt java.awt.font java.awt.geom java.lang

baseCode.gui

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
1	21	12%	95%	8%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
AppDialog Wizard WizardStep	AppDialog$HelpEditorPane AppDialog$LinkFollower AppDialog_actionButton_actionAdapter AppDialog_cancelButton_actionAdapter AppDialog_helpButton_actionAdapter AppDialog_mouselistener_actionAdapter ColorMap ColorMatrix GuiUtil JGradientBar JGradientLabel JLinkLabel JMatrixDisplay JNumberLabel JWebBrowser StatusJlabel TreePanel Wizard_backButton_actionAdapter Wizard_cancelButton_actionAdapter Wizard_finishButton_actionAdapter Wizard_nextButton_actionAdapter	baseCode.gui.table	baseCode.dataStructure.graph baseCode.dataStructure.matrix baseCode.graphics.text baseCode.io.reader baseCode.math baseCode.util cern.colt.list java.awt java.awt.event java.awt.image java.io java.lang java.net java.text java.util javax.imageio javax.swing javax.swing.event javax.swing.text javax.swing.tree org.apache.commons.logging

baseCode.gui.file

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	4	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	DataFileFilter ImageFileFilter XMLFileFilter	None	baseCode.util java.io java.lang javax.swing.filechooser

baseCode.gui.table

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	11	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	JBarGraphCellRenderer JMatrixCellRenderer JVerticalHeaderRenderer TableSorter TableSorter$1 TableSorter$2 TableSorter$Arrow TableSorter$Directive TableSorter$MouseHandler TableSorter$Row TableSorter$SortableHeaderRenderer TableSorter$TableModelHandler	None	baseCode.graphics.text baseCode.gui java.awt java.awt.event java.lang java.text java.util javax.swing javax.swing.border javax.swing.event javax.swing.table

baseCode.io

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	2	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	ByteArrayConverter StringConverter	None	java.io java.lang

baseCode.io.reader

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
2	11	14%	85%	1%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
AbstractNamedMatrixReader	DoubleMatrixReader IndexScoreDyad MapReader SparseDoubleMatrixReader SparseRaggedDouble2DNamedMatrixReader StringMatrixReader	baseCode.gui baseCode.misc	baseCode.dataStructure.matrix baseCode.util cern.colt.list cern.colt.map cern.colt.matrix com.braju.beta.format com.braju.beta.lang java.io java.lang java.util org.apache.commons.logging

baseCode.io.writer

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	4	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	HistogramWriter	None	corejava hep.aida java.io java.lang

baseCode.math

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
3	10	6%	77%	17%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
Constants	CorrelationStats DescriptiveWithMissing Distance KSTest MatrixRowStats MatrixStats MatrixStats$1 MatrixStats$2 MultipleTestCorrection ROC RandomChooser Rank SpecFunc Stats keyAndValueData rankData	baseCode.dataFilter baseCode.gui baseCode.math.metaanalysis	baseCode.dataStructure.matrix baseCode.math.distribution cern.colt.function cern.colt.list cern.colt.matrix cern.colt.matrix.impl cern.jet.math cern.jet.stat java.lang java.util

baseCode.math.distribution

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
1	8	29%	89%	17%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
DensityGenerator ProbabilityComputer	Dirichlet NormalProbabilityComputer UniformDensityComputer UniformProbabilityComputer Wishart	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 java.lang

baseCode.math.metaanalysis

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	5	33%	100%	33%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
MetaAnalysis	CorrelationEffectMetaAnalysis MeanDifferenceMetaAnalysis	None	baseCode.math cern.colt.list cern.jet.stat java.io java.lang

baseCode.misc

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
0	6	0%	100%	0%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	GroupMap	None	baseCode.dataStructure.matrix baseCode.io.reader java.io java.lang java.util org.apache.commons.logging

baseCode.util

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
4	9	17%	69%	14%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
StatusViewer	BrowserLauncher FileTools RegressionTesting StatusDebugLogger StatusStderr	baseCode.bio.geneset baseCode.gui baseCode.gui.file baseCode.io.reader	baseCode.dataStructure.matrix cern.colt.list cern.colt.matrix cern.colt.matrix.impl java.io java.lang java.lang.reflect java.util org.apache.commons.logging

baseCode.xml

Afferent Couplings	Efferent Couplings	Abstractness	Instability	Distance
1	8	0%	89%	11%

Abstract Classes	Concrete Classes	Used by Packages	Uses Packages
None	GOHandler GOParser	baseCode.bio.geneset	baseCode.bio baseCode.dataStructure baseCode.dataStructure.graph java.io java.lang java.util org.xml.sax org.xml.sax.helpers

Cycles

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

There are no cyclic dependencies.

Explanations

[ 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.

Project Documentation

Metric Results

Summary

Packages

baseCode.algorithm

baseCode.algorithm.learning.unsupervised

baseCode.algorithm.learning.unsupervised.cluster

baseCode.bio

baseCode.bio.geneset

baseCode.common

baseCode.dataFilter

baseCode.dataStructure

baseCode.dataStructure.graph

baseCode.dataStructure.matrix

baseCode.dataStructure.tree

baseCode.db

baseCode.graphics.text

baseCode.gui

baseCode.gui.file

baseCode.gui.table

baseCode.io

baseCode.io.reader

baseCode.io.writer

baseCode.math

baseCode.math.distribution

baseCode.math.metaanalysis

baseCode.misc

baseCode.util

baseCode.xml

Cycles

Explanations