baseCode

##### Project Documentation

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## 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.