baseCode

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## PMD Results

The following document contains the results of PMD.

## Summary

Files | Errors
--- | ---
12 | 23

## Files

Files | Violations
--- | ---
baseCode/algorithm/learning/unsupervised/cluster/HierarchicalClusterer.java | 1
baseCode/bio/geneset/GeneSetMapTools.java | 2
baseCode/dataStructure/matrix/NamedMatrix.java | 1
baseCode/dataStructure/matrix/SparseRaggedDoubleMatrix2DNamed.java | 1
baseCode/gui/table/JMatrixCellRenderer.java | 2
baseCode/io/ByteArrayConverter.java | 6
baseCode/io/StringConverter.java | 1
baseCode/io/reader/SparseDoubleMatrixReader.java | 4
baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java | 2
baseCode/math/KSTest.java | 1
baseCode/math/distribution/Dirichlet.java | 1
baseCode/util/BrowserLauncher.java | 1

### baseCode/algorithm/learning/unsupervised/cluster/HierarchicalClusterer.java

Violation | Line
--- | ---
Avoid unused local variables such as 'ald' | 73

### baseCode/bio/geneset/GeneSetMapTools.java

Violation | Line
--- | ---
Avoid unused formal parameters such as 'bigClassPenalty' | 341
Avoid empty 'if' statements | 366

### baseCode/dataStructure/matrix/NamedMatrix.java

Violation | Line
--- | ---
Avoid unused imports such as 'Vector' | 5

### baseCode/dataStructure/matrix/SparseRaggedDoubleMatrix2DNamed.java

Violation | Line
--- | ---
Avoid unused local variables such as 'result' | 129

### baseCode/gui/table/JMatrixCellRenderer.java

Violation | Line
--- | ---
Avoid empty 'if' statements | 43
Avoid empty 'if' statements | 47

### baseCode/io/ByteArrayConverter.java

Violation | Line
--- | ---
Avoid empty catch blocks | 62
Avoid empty catch blocks | 91
Avoid empty catch blocks | 118
Avoid empty catch blocks | 147
Avoid empty catch blocks | 178
Avoid empty catch blocks | 217

### baseCode/io/StringConverter.java

Violation | Line
--- | ---
Avoid unused local variables such as 's' | 59

### baseCode/io/reader/SparseDoubleMatrixReader.java

Violation | Line
--- | ---
Avoid unnecessary temporaries when converting primitives to Strings | 120
Avoid unnecessary temporaries when converting primitives to Strings | 121
Avoid empty 'if' statements | 200
Avoid empty 'if' statements | 213

### baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java

Violation | Line
--- | ---
Avoid unnecessary temporaries when converting primitives to Strings | 304
Avoid unnecessary temporaries when converting primitives to Strings | 352

### baseCode/math/KSTest.java

Violation | Line
--- | ---
Avoid unused local variables such as 'n' | 26

### baseCode/math/distribution/Dirichlet.java

Violation | Line
--- | ---
Avoid unused private fields such as 'a' | 21

### baseCode/util/BrowserLauncher.java

Violation | Line
--- | ---
Avoid unused private fields such as 'JDirect_MacOSX' | 124