baseCode

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## Summary

[ summary] [ package list] [ test cases]

Tests | Errors | Failures | Success rate | Time(s)
--- | --- | --- | --- | ---
179 | 0 | 0 | 100.00% | 43.57

Note: failuresare anticipated and checked for with assertions while errorsare unanticipated.

## Package List

[ summary] [ package list] [ test cases]

Package | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
baseCode.dataFilter | 50 | 0 | 0 | 100.00% | 4.07
baseCode.dataStructure.graph | 3 | 0 | 0 | 100.00% | 0.40
baseCode.dataStructure | 9 | 0 | 0 | 100.00% | 0.83
baseCode.dataStructure.matrix | 11 | 0 | 0 | 100.00% | 1.02
baseCode.io.reader | 17 | 0 | 0 | 100.00% | 5.08
baseCode.io | 8 | 0 | 0 | 100.00% | 25.14
baseCode.io.writer | 1 | 0 | 0 | 100.00% | 0.43
baseCode.math.distribution | 1 | 0 | 0 | 100.00% | 0.48
baseCode.math | 61 | 0 | 0 | 100.00% | 4.32
baseCode.math.metaanalysis | 17 | 0 | 0 | 100.00% | 1.03
baseCode.xml | 1 | 0 | 0 | 100.00% | 0.76

Note: package statistics are not computed recursively, they only sum up all of its testsuites numbers.

### baseCode.dataFilter

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestItemLevelFilter | 1 | 0 | 0 | 100.00% | 0.585
| TestRowAbsentFilter | 9 | 0 | 0 | 100.00% | 0.720
| TestRowAffyNameFilter | 2 | 0 | 0 | 100.00% | 0.604
| TestRowLevelFilter | 23 | 0 | 0 | 100.00% | 0.826
| TestRowMissingFilter | 11 | 0 | 0 | 100.00% | 0.712
| TestRowNameFilter | 4 | 0 | 0 | 100.00% | 0.626

### baseCode.dataStructure.graph

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestDirectedGraph | 3 | 0 | 0 | 100.00% | 0.405

### baseCode.dataStructure

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestQueue | 4 | 0 | 0 | 100.00% | 0.414
| TestStack | 5 | 0 | 0 | 100.00% | 0.412

### baseCode.dataStructure.matrix

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestRCDoubleMatrix1D | 6 | 0 | 0 | 100.00% | 0.452
| TestSparseRaggedDoubleMatrix2DNamed | 5 | 0 | 0 | 100.00% | 0.571

### baseCode.io.reader

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestDoubleMatrixReader | 6 | 0 | 0 | 100.00% | 0.584
| TestMapReader | 2 | 0 | 0 | 100.00% | 0.414
| TestSparseDoubleMatrixReader | 2 | 0 | 0 | 100.00% | 0.603
| TestSparseRaggedDouble2DNamedMatrixReader | 3 | 0 | 0 | 100.00% | 2.959
| TestStringMatrixReader | 4 | 0 | 0 | 100.00% | 0.521

### baseCode.io

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestByteArrayConverter | 6 | 0 | 0 | 100.00% | 24.732
| TestStringConverter | 2 | 0 | 0 | 100.00% | 0.409

### baseCode.io.writer

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestHistogramWriter | 1 | 0 | 0 | 100.00% | 0.427

### baseCode.math.distribution

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestWishart | 1 | 0 | 0 | 100.00% | 0.484

### baseCode.math

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestCorrelationStats | 9 | 0 | 0 | 100.00% | 0.407
| TestDescriptiveWithMissing | 20 | 0 | 0 | 100.00% | 0.444
| TestKSTest | 2 | 0 | 0 | 100.00% | 0.437
| TestMatrixRowStats | 5 | 0 | 0 | 100.00% | 0.599
| TestMatrixStats | 4 | 0 | 0 | 100.00% | 0.643
| TestROC | 2 | 0 | 0 | 100.00% | 0.430
| TestRank | 3 | 0 | 0 | 100.00% | 0.452
| TestSpecFunc | 4 | 0 | 0 | 100.00% | 0.425
| TestStats | 12 | 0 | 0 | 100.00% | 0.485

### baseCode.math.metaanalysis

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestCorrelationEffectMetaAnalysis | 9 | 0 | 0 | 100.00% | 0.542
| TestMeanDifferenceMetaAnalysis | 8 | 0 | 0 | 100.00% | 0.484

### baseCode.xml

Class | Tests | Errors | Failures | Success Rate | Time
--- | --- | --- | --- | --- | ---
| TestGOParser | 1 | 0 | 0 | 100.00% | 0.759

## Test Cases

[ summary] [ package list] [ test cases]

### TestItemLevelFilter

| testFilter | 0.19

### TestRowAbsentFilter

| testFilter | 0.20
| testFilterWithMissing | 0.02
| testFilterWithMissingLessStringent | 0.02
| testFilterStringMatrix | 0.02
| testFilterKeepMarginal | 0.02
| testFilterFraction | 0.01
| testFilterFractionInvalid | 0.01
| testFilterPresentCountInvalid | 0.01
| testFilterNullFlags | 0.01

### TestRowAffyNameFilter

| testFilter | 0.18
| testStringFilter | 0.02

### TestRowLevelFilter

| testFilterMax | 0.19
| testFilterMaxTooHigh | 0.02
| testFilterMin | 0.02
| testFilterMean | 0.02
| testFilterMedian | 0.01
| testFilterMaxFraction | 0.01
| testFilterMaxFractionAll | 0.01
| testFilterMaxFractionNone | 0.01
| testFilterMaxFractionNoneRemoveNeg | 0.01
| testFilterFractionMaxRemoveNeg | 0.01
| testFilterBadFraction | 0.01
| testFilterNoFilter | 0.01
| testFilterMaxHigh | 0.01
| testFilterMinHigh | 0.01
| testFilterMeanHigh | 0.01
| testFilterMedianHigh | 0.01
| testFilterMaxFractionHigh | 0.01
| testFilterFractionMaxRemoveNegHigh | 0.01
| testFilterFractionMaxRemoveHighAndLow | 0.01
| testFilterFractionMaxRemoveHighAndLowBothFraction | 0.01
| testFilterFractionMaxRemoveHighAndLowBothLevels | 0.01
| testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove | 0.01
| testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow | 0.01

### TestRowMissingFilter

| testFilter | 0.19
| testFilterNoFiltering | 0.02
| testFilterWithMissing | 0.02
| testFilterWithMissingLowMaxFraction | 0.01
| testFilterWithMissingLessStringent | 0.02
| testFilterStringMatrix | 0.01
| testFilterFraction | 0.01
| testFilterFractionInvalid | 0.01
| testFilterFractionInvalid2 | 0.01
| testMaxFractionRemovedInvalid | 0.01
| testFilterPresentCountInvalid | 0.01

### TestRowNameFilter

| testFilter | 0.18
| testFilterExclude | 0.02
| testFilterString | 0.02
| testFilterStringExclude | 0.01

### TestDirectedGraph

| testToString | 0.01
| testTopoSort | 0.00
| testGetChildren | 0.00

### TestQueue

| testEnqueue | 0.01
| testDequeue | 0.00
| testEmptyDequeue | 0.00
| testFullEnqueue | 0.00

### TestStack

| testPop | 0.01
| testPush | 0.00
| testTop | 0.00
| testEmptyPop | 0.00
| testFullPush | 0.00

### TestRCDoubleMatrix1D

| testForEachNonZero | 0.05
| testZDotProductDoubleMatrix1D | 0.00
| testZDotProductDoubleMatrix1DReverse | 0.00
| testZDotProductDoubleMatrix1DHarder | 0.00
| testZDotProductDoubleMatrix1DHarderReverse | 0.00
| testAssignDoubleFunction | 0.00

### TestSparseRaggedDoubleMatrix2DNamed

| testRows | 0.15
| testColumns | 0.00
| testGetRowArrayList | 0.01
| testGetRowMatrix1D | 0.01
| testGetRow | 0.00

### TestDoubleMatrixReader

| testReadInputStreamMissing | 0.13
| testReadInputStreamMissingBad | 0.00
| testReadInputStreamRowCount | 0.02
| testReadInputStreamColumnCount | 0.00
| testReadInputStreamGotRowName | 0.00
| testReadInputStreamGotColName | 0.01

### TestMapReader

| testRead | 0.02
| testReadNoHeader | 0.00

### TestSparseDoubleMatrixReader

| testReadStream | 0.15
| testReadJW | 0.06

### TestSparseRaggedDouble2DNamedMatrixReader

| testReadInputStream | 0.16
| testReadStreamAdjList | 0.01
| testReadStreamAdjListBig | 2.39

### TestStringMatrixReader

| testReadInputStreamRowCount | 0.10
| testReadInputStreamColumnCount | 0.01
| testReadInputStreamGotRowName | 0.01
| testReadInputStreamGotColName | 0.00

### TestByteArrayConverter

| testDoubleArrayToBytes | 2.94
| testByteArrayToDoubles | 2.61
| testByteArrayToDoubleConversionSpeed | 3.61
| testStringToDoubleArrayConversionSpeed | 6.14
| testDoubleArrayToByteArrayConversionSpeed | 3.16
| testDoubleArrayToDelimitedStringConversionSpeed | 5.87

### TestStringConverter

| testStringToBytes | 0.01
| testStringToDoubles | 0.00

### TestHistogramWriter

| testWriter | 0.02

### TestWishart

| testNextDoubleMatrix | 0.08

### TestCorrelationStats

| testPvalue | 0.00
| testCorrelAsByte | 0.00
| testFisherTransform | 0.00
| testPvalueAsByte | 0.00
| testByteToPvalue | 0.00
| testByteToCorrel | 0.00
| testCorrelationTstat | 0.00
| testCompare | 0.00
| testCorrelationForPvalue | 0.00

### TestDescriptiveWithMissing

| testCorrelationA | 0.03
| testCorrelationB | 0.00
| testCovariance | 0.00
| testDurbinWatson | 0.00
| testDurbinWatsonTwo | 0.00
| testDurbinWatsonShort | 0.00
| testGeometricMean | 0.00
| testMean | 0.00
| testMin | 0.00
| testMax | 0.00
| testMedian | 0.00
| testProduct | 0.00
| testSampleKurtosis | 0.00
| testQuantile | 0.00
| testSum | 0.00
| testSumOfSquares | 0.00
| testSampleVariance | 0.00
| testStandardize | 0.01
| testTrimmedMean | 0.00
| testVariance | 0.00

### TestKSTest

| testKSTestTwoSample | 0.04
| testKSTestOneSample | 0.00

### TestMatrixRowStats

| testSumOfSquaresDenseDoubleMatrix2DNamed | 0.16
| testSumOfSquaresDenseDoubleMatrix2DNamedDoubleArrayList | 0.01
| testMeans | 0.00
| testSums | 0.01
| testStandardDeviations | 0.01

### TestMatrixStats

| testMin | 0.14
| testMax | 0.02
| testCorrelationMatrix | 0.04
| testRbfNormalize | 0.05

### TestROC

| testAroc | 0.03
| testArocN | 0.00

### TestRank

| testRankTransformDoubleArrayList | 0.04
| testRankTransformMap | 0.00
| testRankTransformBadMap | 0.00

### TestSpecFunc

| testHypergeometric | 0.01
| testCumHyperGeometric | 0.00
| testCumHyperGeometricUT | 0.00
| testdBinom | 0.00

### TestStats

| testIsValidFraction | 0.03
| testIsValidFraction2 | 0.00
| testCv | 0.01
| testCumulate | 0.01
| testCumulateRight | 0.00
| testCdf | 0.00
| testNormalizeDoubleArrayListdouble | 0.00
| testNormalizeDoubleArrayList | 0.00
| testMeanAboveQuantile | 0.00
| testRange | 0.00
| testQuantile | 0.00
| testQuantile75 | 0.00

### TestCorrelationEffectMetaAnalysis

| testRunZFVar | 0.09
| testRunZFEffect | 0.00
| testRunZFZscore | 0.00
| testRunUFVar | 0.00
| testRunUFEffect | 0.00
| testRunUFZscore | 0.00
| testRunZRQval | 0.00
| testRunZRBSV | 0.00
| testRunURBSV | 0.00

### TestMeanDifferenceMetaAnalysis

| testRunFixedVar | 0.04
| testRunFixedE | 0.00
| testRunFixedQ | 0.00
| testRunFixedZ | 0.00
| testRunRandomVar | 0.00
| testRunRandomE | 0.00
| testRunRandomBSV | 0.00
| testRunRandomZ | 0.00

### TestGOParser

| testGOParser | 0.31