Index (baseCode 1.1.23-SNAPSHOT Test API)

A B C D E F G H I J K L M N O P Q R S T U
All Classes All Packages

A

AbstractDoubleMatrixTest - Class in ubic.basecode.dataStructure.matrix: TODO Document Me
AbstractDoubleMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
AbstractOntologyTest - Class in ubic.basecode.ontology: Base class for ontology-based tests.
AbstractOntologyTest() - Constructor for class ubic.basecode.ontology.AbstractOntologyTest
AbstractRClientTest - Class in ubic.basecode.util.r
AbstractRClientTest() - Constructor for class ubic.basecode.util.r.AbstractRClientTest
AbstractTestFilter - Class in ubic.basecode.datafilter: Fixture for testing filtering of matrices.
AbstractTestFilter() - Constructor for class ubic.basecode.datafilter.AbstractTestFilter
AnnotatorClientTest - Class in ubic.basecode.ontology.ncbo
AnnotatorClientTest() - Constructor for class ubic.basecode.ontology.ncbo.AnnotatorClientTest

B

BatchIteratorTest - Class in ubic.basecode.util
BatchIteratorTest() - Constructor for class ubic.basecode.util.BatchIteratorTest
BinaryTreeTest - Class in ubic.basecode.dataStructure.tree
BinaryTreeTest() - Constructor for class ubic.basecode.dataStructure.tree.BinaryTreeTest
BitUtilTest - Class in ubic.basecode.dataStructure
BitUtilTest() - Constructor for class ubic.basecode.dataStructure.BitUtilTest

C

clearOntologyCacheDir() - Static method in class ubic.basecode.ontology.AbstractOntologyTest
CompressedNamedBitMatrixTest - Class in ubic.basecode.dataStructure.matrix
CompressedNamedBitMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
CompressedSparseDoubleMatrixTest - Class in ubic.basecode.dataStructure.matrix: T
CompressedSparseDoubleMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrixTest
ConfigUtilsTest - Class in ubic.basecode.util
ConfigUtilsTest() - Constructor for class ubic.basecode.util.ConfigUtilsTest
CorrelationStatsTest - Class in ubic.basecode.math: Most benchmarks come from R, using things like cor.test(rnorm(50), rnorm(50), method="spearman", alternative="two.sided"),
CorrelationStatsTest() - Constructor for class ubic.basecode.math.CorrelationStatsTest
CountingMapTest - Class in ubic.basecode.dataStructure
CountingMapTest() - Constructor for class ubic.basecode.dataStructure.CountingMapTest

D

DateUtilTest - Class in ubic.basecode.util
DateUtilTest() - Constructor for class ubic.basecode.util.DateUtilTest
DenseDouble3dMatrixTest - Class in ubic.basecode.dataStructure.matrix
DenseDouble3dMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
DenseDoubleMatrixTest - Class in ubic.basecode.dataStructure.matrix
DenseDoubleMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.DenseDoubleMatrixTest
DesignMatrixTest - Class in ubic.basecode.math.linearmodels
DesignMatrixTest() - Constructor for class ubic.basecode.math.linearmodels.DesignMatrixTest
DiseaseOntologyServiceTest - Class in ubic.basecode.ontology.providers
DiseaseOntologyServiceTest() - Constructor for class ubic.basecode.ontology.providers.DiseaseOntologyServiceTest
DistanceTest - Class in ubic.basecode.math
DistanceTest() - Constructor for class ubic.basecode.math.DistanceTest
DoubleAddingMapTest - Class in ubic.basecode.dataStructure
DoubleAddingMapTest() - Constructor for class ubic.basecode.dataStructure.DoubleAddingMapTest

E

ExcelUtilTest - Class in ubic.basecode.io.excel
ExcelUtilTest() - Constructor for class ubic.basecode.io.excel.ExcelUtilTest

F

f - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
FastRowAccessDoubleMatrixTest - Class in ubic.basecode.dataStructure.matrix
FastRowAccessDoubleMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrixTest
FileToolsTest - Class in ubic.basecode.util
FileToolsTest() - Constructor for class ubic.basecode.util.FileToolsTest

G

GenericOntologyServiceTest - Class in ubic.basecode.ontology.providers
GenericOntologyServiceTest() - Constructor for class ubic.basecode.ontology.providers.GenericOntologyServiceTest
getComment() - Method in class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple
getLabel() - Method in class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple
getLocalName() - Method in class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple
getTerm() - Method in class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple
getUri() - Method in class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple

H

HistogramReaderTest - Class in ubic.basecode.io.reader
HistogramReaderTest() - Constructor for class ubic.basecode.io.reader.HistogramReaderTest
HistogramSamplerTest - Class in ubic.basecode.math.distribution
HistogramSamplerTest() - Constructor for class ubic.basecode.math.distribution.HistogramSamplerTest
HistogramTest - Class in ubic.basecode.math.distribution
HistogramTest() - Constructor for class ubic.basecode.math.distribution.HistogramTest

I

initializeUberon() - Static method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
IntegerMatrixTest - Class in ubic.basecode.dataStructure.matrix
IntegerMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
isTermObsolete() - Method in class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple

J

JenaUtilsTest - Class in ubic.basecode.ontology.jena
JenaUtilsTest() - Constructor for class ubic.basecode.ontology.jena.JenaUtilsTest
JRIClientTest - Class in ubic.basecode.util.r
JRIClientTest() - Constructor for class ubic.basecode.util.r.JRIClientTest

K

KruskalWallisTest - Class in ubic.basecode.math
KruskalWallisTest() - Constructor for class ubic.basecode.math.KruskalWallisTest

L

LeastSquaresFitTest - Class in ubic.basecode.math.linearmodels
LeastSquaresFitTest() - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFitTest
LeastSquaresFitTest2 - Class in ubic.basecode.math.linearmodels
LeastSquaresFitTest2() - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFitTest2
log - Static variable in class ubic.basecode.util.r.AbstractRClientTest

M

MatrixDisplayTest - Class in ubic.basecode.graphics
MatrixDisplayTest() - Constructor for class ubic.basecode.graphics.MatrixDisplayTest
MatrixUtilTest - Class in ubic.basecode.dataStructure.matrix
MatrixUtilTest() - Constructor for class ubic.basecode.dataStructure.matrix.MatrixUtilTest
MatrixWriterTest - Class in ubic.basecode.io.writer
MatrixWriterTest() - Constructor for class ubic.basecode.io.writer.MatrixWriterTest
MeanVarianceEstimatorTest - Class in ubic.basecode.math.linearmodels
MeanVarianceEstimatorTest() - Constructor for class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
MedicOntologyServiceTest - Class in ubic.basecode.ontology.providers
MedicOntologyServiceTest() - Constructor for class ubic.basecode.ontology.providers.MedicOntologyServiceTest
MetaAnalysisTest - Class in ubic.basecode.math.metaanalysis
MetaAnalysisTest() - Constructor for class ubic.basecode.math.metaanalysis.MetaAnalysisTest
ModeratedTstatTest - Class in ubic.basecode.math.linearmodels: TODO Document Me
ModeratedTstatTest() - Constructor for class ubic.basecode.math.linearmodels.ModeratedTstatTest
MultipleTestCorrectionTest - Class in ubic.basecode.math
MultipleTestCorrectionTest() - Constructor for class ubic.basecode.math.MultipleTestCorrectionTest

N

NetUtilsTest - Class in ubic.basecode.util
NetUtilsTest() - Constructor for class ubic.basecode.util.NetUtilsTest
NIFSTDOntologyServiceTest - Class in ubic.basecode.ontology.providers
NIFSTDOntologyServiceTest() - Constructor for class ubic.basecode.ontology.providers.NIFSTDOntologyServiceTest
NormalProbabilityComputerTest - Class in ubic.basecode.math.distribution
NormalProbabilityComputerTest() - Constructor for class ubic.basecode.math.distribution.NormalProbabilityComputerTest

O

ObiServiceTest - Class in ubic.basecode.ontology.providers
ObiServiceTest() - Constructor for class ubic.basecode.ontology.providers.ObiServiceTest
OntologyLoaderTest - Class in ubic.basecode.ontology.jena: Test loading a database-backed ontology
OntologyLoaderTest() - Constructor for class ubic.basecode.ontology.jena.OntologyLoaderTest
OntologyProvidersTest - Class in ubic.basecode.ontology.providers: Test initialization of all providers not already covered by a specific test.
OntologyProvidersTest() - Constructor for class ubic.basecode.ontology.providers.OntologyProvidersTest
OntologySearchTest - Class in ubic.basecode.ontology.jena: Most of these tests were moved over from Gemma.
OntologySearchTest() - Constructor for class ubic.basecode.ontology.jena.OntologySearchTest
OntologyTermSimple(String, String) - Constructor for class ubic.basecode.util.PrettyPrinterTest.OntologyTermSimple
OntologyTermTest - Class in ubic.basecode.ontology
OntologyTermTest() - Constructor for class ubic.basecode.ontology.OntologyTermTest

P

ParameterKeeperTest - Class in ubic.basecode.dataStructure.params
ParameterKeeperTest() - Constructor for class ubic.basecode.dataStructure.params.ParameterKeeperTest
ParamGrabberTest - Class in ubic.basecode.dataStructure.params
ParamGrabberTest() - Constructor for class ubic.basecode.dataStructure.params.ParamGrabberTest
PrecisionRecallTest - Class in ubic.basecode.math
PrecisionRecallTest() - Constructor for class ubic.basecode.math.PrecisionRecallTest
PrettyPrinterTest - Class in ubic.basecode.util
PrettyPrinterTest() - Constructor for class ubic.basecode.util.PrettyPrinterTest
PrettyPrinterTest.OntologyTermSimple - Class in ubic.basecode.util

Q

QRDecompositionTest - Class in ubic.basecode.math.linalg
QRDecompositionTest() - Constructor for class ubic.basecode.math.linalg.QRDecompositionTest

R

RandomChooserTest - Class in ubic.basecode.math
RandomChooserTest() - Constructor for class ubic.basecode.math.RandomChooserTest
RCDoubleMatrix1DTest - Class in ubic.basecode.dataStructure.matrix
RCDoubleMatrix1DTest() - Constructor for class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
RCDoubleMatrix1DTest2 - Class in ubic.basecode.dataStructure.matrix
RCDoubleMatrix1DTest2() - Constructor for class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
RServeClientTest - Class in ubic.basecode.util.r
RServeClientTest() - Constructor for class ubic.basecode.util.r.RServeClientTest

S

setup() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph: Constructor for TestDirectedGraph.
setup() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
setup() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
setup() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
setup() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
setup() - Method in class ubic.basecode.util.ConfigUtilsTest
setUp() - Method in class ubic.basecode.datafilter.AbstractTestFilter
setUp() - Method in class ubic.basecode.datafilter.TestItemLevelFilter
setUp() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
setUp() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
setUp() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
setUp() - Method in class ubic.basecode.datafilter.TestRowNameFilter
setUp() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrixTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrixTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrixTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
setUp() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
setUp() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
setUp() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
setUp() - Method in class ubic.basecode.graphics.MatrixDisplayTest
setUp() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
setUp() - Method in class ubic.basecode.io.reader.TestMapReader
setUp() - Method in class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
setUp() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
setUp() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
setUp() - Method in class ubic.basecode.io.TestByteArrayConverter
setUp() - Method in class ubic.basecode.io.writer.MatrixWriterTest
setUp() - Method in class ubic.basecode.io.writer.TestHistogramWriter
setUp() - Method in class ubic.basecode.math.DistanceTest
setUp() - Method in class ubic.basecode.math.distribution.TestWishart
setUp() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
setUp() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
setUp() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
setUp() - Method in class ubic.basecode.math.RandomChooserTest
setUp() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
setUp() - Method in class ubic.basecode.math.TestMatrixRowStats
setUp() - Method in class ubic.basecode.math.TestMatrixStats
setUp() - Method in class ubic.basecode.math.TestRank
setUp() - Method in class ubic.basecode.math.TestROC
setUp() - Method in class ubic.basecode.math.TestStats
setUp() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
setUp() - Method in class ubic.basecode.util.FileToolsTest
setUp() - Method in class ubic.basecode.util.r.JRIClientTest
setUp() - Method in class ubic.basecode.util.r.RServeClientTest
setUpOntologyCacheDir() - Static method in class ubic.basecode.ontology.AbstractOntologyTest
setUpUberon() - Static method in class ubic.basecode.ontology.jena.UberonOntologySearchTest
SingularValueDecompositionTest - Class in ubic.basecode.math
SingularValueDecompositionTest() - Constructor for class ubic.basecode.math.SingularValueDecompositionTest
SparseDoubleMatrixTest - Class in ubic.basecode.dataStructure.matrix
SparseDoubleMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
SparseRaggedDoubleMatrixTest - Class in ubic.basecode.dataStructure.matrix
SparseRaggedDoubleMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
SQLUtilsTest - Class in ubic.basecode.util
SQLUtilsTest() - Constructor for class ubic.basecode.util.SQLUtilsTest
StringDistanceTest - Class in ubic.basecode.math
StringDistanceTest() - Constructor for class ubic.basecode.math.StringDistanceTest
StringMatrixTest - Class in ubic.basecode.dataStructure.matrix
StringMatrixTest() - Constructor for class ubic.basecode.dataStructure.matrix.StringMatrixTest
StringToStringSetMapTest - Class in ubic.basecode.dataStructure
StringToStringSetMapTest() - Constructor for class ubic.basecode.dataStructure.StringToStringSetMapTest
StringUtilTest - Class in ubic.basecode.util
StringUtilTest() - Constructor for class ubic.basecode.util.StringUtilTest

T

tearDown() - Method in class ubic.basecode.datafilter.AbstractTestFilter
tearDown() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
tearDown() - Method in class ubic.basecode.datafilter.TestRowNameFilter
tearDown() - Method in class ubic.basecode.graphics.MatrixDisplayTest
tearDown() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
tearDown() - Method in class ubic.basecode.io.reader.TestMapReader
tearDown() - Method in class ubic.basecode.io.TestByteArrayConverter
tearDown() - Method in class ubic.basecode.util.ConfigUtilsTest
tearDown() - Method in class ubic.basecode.util.FileToolsTest
tearDown() - Method in class ubic.basecode.util.r.JRIClientTest
tearDown() - Method in class ubic.basecode.util.r.RServeClientTest
tempDir - Static variable in class ubic.basecode.ontology.AbstractOntologyTest
test() - Method in class ubic.basecode.dataStructure.DoubleAddingMapTest
test() - Method in class ubic.basecode.dataStructure.params.ParameterKeeperTest
test() - Method in class ubic.basecode.dataStructure.params.ParamGrabberTest
test() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
test() - Method in class ubic.basecode.ontology.providers.MedicOntologyServiceTest
test() - Method in class ubic.basecode.ontology.providers.NIFSTDOntologyServiceTest
test1() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
test2() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest: This matrix is singular.
test2NoPivoting() - Method in class ubic.basecode.math.linalg.QRDecompositionTest: Test ability to reproduce standard QR
test3() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
testA() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
testAddChild() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testAddChildFail() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testAddDataExtension() - Method in class ubic.basecode.util.FileToolsTest
testAddImageExtension() - Method in class ubic.basecode.util.FileToolsTest
testAddParent() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testAddParentFail() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testAddrow() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testAExact() - Method in class ubic.basecode.math.TestWilcoxon
testAnovaA() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAnovaB() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAnovaC() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAnovaD() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAnovaE() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAnovaF() - Method in class ubic.basecode.util.r.AbstractRClientTest: One way @
testAroc() - Method in class ubic.basecode.math.TestROC
testArocPvalue() - Method in class ubic.basecode.math.TestROC
testArray - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testAssign() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
testAssignAndRetrieveMatrix() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAssignAndRetrieveMatrixB() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAssignAndRetrieveMatrixC() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAssignAndRetrieveMatrixD() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAssignAr() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
testAssignDoubleFunction() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
testAssignStringList() - Method in class ubic.basecode.util.r.AbstractRClientTest
testAutoCorrelation() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testAveragePrecision() - Method in class ubic.basecode.math.PrecisionRecallTest
testAveragePrecisionB() - Method in class ubic.basecode.math.PrecisionRecallTest
testAveragePrecisionBNotInOrder() - Method in class ubic.basecode.math.PrecisionRecallTest
testAveragePrecisionNotInOrder() - Method in class ubic.basecode.math.PrecisionRecallTest
testAveragePrecisionWithTie() - Method in class ubic.basecode.math.PrecisionRecallTest: Should give the same result as test B, because precision is the same at each step despite the tie.
testB() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
testB() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
testBadFileName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testBadMatch() - Method in class ubic.basecode.math.StringDistanceTest
testBatches() - Method in class ubic.basecode.util.BatchIteratorTest: Test method for ca.elmonline.util.BatchIterator#batches(java.util.Collection, int).
testBatchIterator() - Method in class ubic.basecode.util.BatchIteratorTest: Test method for ca.elmonline.util.BatchIterator#BatchIterator(java.util.Collection, int).
testBenjaminiHochberg() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
testBenjaminiHochbergCut() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
testBenjaminiHochbergM() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
testBenjaminiYekuteliCut() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
testBGaussian() - Method in class ubic.basecode.math.TestWilcoxon
testBig() - Method in class ubic.basecode.math.TestROC: Bug 3620
testBig() - Method in class ubic.basecode.math.TestWilcoxon
testBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testBitMatrix() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testBlobToString() - Method in class ubic.basecode.util.SQLUtilsTest
testBonferroniCut() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
testBooleansToByteArray() - Method in class ubic.basecode.io.TestByteArrayConverter
testBooleansToLongArray() - Method in class ubic.basecode.io.TestByteArrayConverter
TestByteArrayConverter - Class in ubic.basecode.io
TestByteArrayConverter() - Constructor for class ubic.basecode.io.TestByteArrayConverter
testByteArrayToBooleans() - Method in class ubic.basecode.io.TestByteArrayConverter
testByteArrayToDoubleConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
testByteArrayToDoubleMatrix() - Method in class ubic.basecode.io.TestByteArrayConverter
testByteArrayToDoubles() - Method in class ubic.basecode.io.TestByteArrayConverter
testByteArrayToLongs() - Method in class ubic.basecode.io.TestByteArrayConverter
testByteArrayToTabbedString() - Method in class ubic.basecode.io.TestByteArrayConverter
testC() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
testCacheOntologyToDisk() - Method in class ubic.basecode.ontology.jena.OntologyLoaderTest
testCdf() - Method in class ubic.basecode.math.TestStats
testCGaussian() - Method in class ubic.basecode.math.TestWilcoxon
testChangeExtension() - Method in class ubic.basecode.util.FileToolsTest
testCheckForFile() - Method in class ubic.basecode.util.NetUtilsTest
testCheckPathIsReadableFile() - Method in class ubic.basecode.util.FileToolsTest
testCheckPathIsReadableFileNot() - Method in class ubic.basecode.util.FileToolsTest
testChooseRandomDeck() - Method in class ubic.basecode.math.RandomChooserTest
testChooserandomInt() - Method in class ubic.basecode.math.RandomChooserTest: Test method for RandomChooser.chooserandom(int, int).
testChooserandomInts() - Method in class ubic.basecode.math.RandomChooserTest
testChooserandomWrep() - Method in class ubic.basecode.math.RandomChooserTest: Test method for RandomChooser.chooserandomWrep(int, int)} .
testCleanFileName() - Method in class ubic.basecode.util.FileToolsTest
testCleanFileNameErr() - Method in class ubic.basecode.util.FileToolsTest
testClear() - Method in class ubic.basecode.dataStructure.BitUtilTest
testColSumsWithMissing() - Method in class ubic.basecode.math.TestMatrixStats
testColumns() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testColumns() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testColumns() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.columns().
testColumns() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testCommonPrefix() - Method in class ubic.basecode.util.StringUtilTest
testCommonPrefixNone() - Method in class ubic.basecode.util.StringUtilTest
testCommonSuffix() - Method in class ubic.basecode.util.StringUtilTest
testCommonSuffixNone() - Method in class ubic.basecode.util.StringUtilTest
testConcurrentModificationException() - Method in class ubic.basecode.util.BatchIteratorTest
testConstructFromArray() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrixTest
testConstructFromArray() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrixTest
testConvertLog() - Method in class ubic.basecode.math.TestMatrixStats
testConvertToLog2Cpm() - Method in class ubic.basecode.math.TestMatrixStats
testCopy() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testCopy() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testCopyFile() - Method in class ubic.basecode.util.FileToolsTest
testCopyFileFailOnDirectoryInput() - Method in class ubic.basecode.util.FileToolsTest
testCopyFileFailOnDirectoryOutput() - Method in class ubic.basecode.util.FileToolsTest
testCorrel() - Method in class ubic.basecode.math.CorrelationStatsTest
testCorrelAsByte() - Method in class ubic.basecode.math.CorrelationStatsTest
testCorrelationA() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testCorrelationB() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
TestCorrelationEffectMetaAnalysis - Class in ubic.basecode.math.metaanalysis: Tests based on Cooper and Hedges.
TestCorrelationEffectMetaAnalysis() - Constructor for class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testCorrelationForPvalue() - Method in class ubic.basecode.math.CorrelationStatsTest
testCorrelationMatrix() - Method in class ubic.basecode.math.TestMatrixStats
testCorrelationMatrixThreshold() - Method in class ubic.basecode.math.TestMatrixStats
testCorrelationOfStandardizedDoubleArrayDoubleArray() - Method in class ubic.basecode.math.DistanceTest
testCorrelationOfStandardizedDoubleArrayListDoubleArrayList() - Method in class ubic.basecode.math.DistanceTest
testCorrelTooSmall() - Method in class ubic.basecode.math.CorrelationStatsTest
testCount() - Method in class ubic.basecode.dataStructure.BitUtilTest
testCount() - Method in class ubic.basecode.dataStructure.CountingMapTest: Test method for ca.elmonline.util.CountingMap#count(java.lang.Object).
testCountsPerMillionWithMissing() - Method in class ubic.basecode.math.TestMatrixStats
testCov2Cor() - Method in class ubic.basecode.math.TestMatrixStats
testCovariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testCsvSplitA() - Method in class ubic.basecode.util.TestStringUtil
testCsvSplitB() - Method in class ubic.basecode.util.TestStringUtil
testCsvSplitC() - Method in class ubic.basecode.util.TestStringUtil
testCsvSplitD() - Method in class ubic.basecode.util.TestStringUtil
testCsvSplitE() - Method in class ubic.basecode.util.TestStringUtil
testCsvSplitF() - Method in class ubic.basecode.util.TestStringUtil
testCumHyperGeometric() - Method in class ubic.basecode.math.TestSpecFunc
testCumHyperGeometricB() - Method in class ubic.basecode.math.TestSpecFunc
testCumHyperGeometricUT() - Method in class ubic.basecode.math.TestSpecFunc
testCumulate() - Method in class ubic.basecode.math.TestStats
testCumulateRight() - Method in class ubic.basecode.math.TestStats
testCv() - Method in class ubic.basecode.math.TestStats
testdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
testdata - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testdata - Variable in class ubic.basecode.math.TestMatrixRowStats
testDataFrameA() - Method in class ubic.basecode.util.r.AbstractRClientTest
testdBinom() - Method in class ubic.basecode.math.TestSpecFunc
testDeleteDir() - Method in class ubic.basecode.util.FileToolsTest: Tests trying to delete a directory without first deleting the files.
testDeleteFilesAndDir() - Method in class ubic.basecode.util.FileToolsTest: Tests deleting files in a directory tree, then the directories.
testDeleteLeaf1() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testDeleteLeafFail() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testDeleteLeafNotLeaf() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testDensity() - Method in class ubic.basecode.math.distribution.UniformDensityComputerTest: Test method for UniformDensityComputer.density(double).
TestDescriptiveWithMissing - Class in ubic.basecode.math
TestDescriptiveWithMissing() - Constructor for class ubic.basecode.math.TestDescriptiveWithMissing
TestDirectedGraph - Class in ubic.basecode.dataStructure.graph
TestDirectedGraph() - Constructor for class ubic.basecode.dataStructure.graph.TestDirectedGraph
testDoubleArrayToByteArrayConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
testDoubleArrayToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
testDoubleArrayToDelimitedStringConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
testDoubleArrayTwoDoubleArrayEval() - Method in class ubic.basecode.util.r.AbstractRClientTest
TestDoubleMatrixReader - Class in ubic.basecode.io.reader
TestDoubleMatrixReader() - Constructor for class ubic.basecode.io.reader.TestDoubleMatrixReader
testDoubleStandardize() - Method in class ubic.basecode.math.TestMatrixStats
testDoubleTwoDoubleArrayEval() - Method in class ubic.basecode.util.r.AbstractRClientTest
testDownloadFile() - Method in class ubic.basecode.util.NetUtilsTest
testDropColumn() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testDuplicateRows() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest: Duplicate row
testDurbinWatson() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testDurbinWatsonShort() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testDurbinWatsonTwo() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testDVolume() - Method in class ubic.basecode.math.TestWilcoxon
testEditDistanceA() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceB() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceC() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceD() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceE() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceF() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceG() - Method in class ubic.basecode.math.StringDistanceTest
testEditDistanceH() - Method in class ubic.basecode.math.StringDistanceTest
testEstrogen() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Tests limma-like functionality.
testEuclDistance() - Method in class ubic.basecode.math.DistanceTest
testEVolume() - Method in class ubic.basecode.math.TestWilcoxon
testExec() - Method in class ubic.basecode.util.r.AbstractRClientTest
testExecDoubleArray() - Method in class ubic.basecode.util.r.AbstractRClientTest
testExecError() - Method in class ubic.basecode.util.r.AbstractRClientTest
testExpandedSize() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
testExpandedValues() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
testFactorAssign() - Method in class ubic.basecode.util.r.AbstractRClientTest
testFdist() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
testFillRange() - Method in class ubic.basecode.math.TestMathUtil
testFillRangeDown() - Method in class ubic.basecode.math.TestMathUtil
testFillRangeNo() - Method in class ubic.basecode.math.TestMathUtil
testFilter() - Method in class ubic.basecode.datafilter.TestItemLevelFilter
testFilter() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilter() - Method in class ubic.basecode.datafilter.TestRowAffyNameFilter
testFilter() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilter() - Method in class ubic.basecode.datafilter.TestRowNameFilter
testFilterBadFraction() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterExclude() - Method in class ubic.basecode.datafilter.TestRowNameFilter
testFilterFraction() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterFraction() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterFractionInvalid() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterFractionInvalid() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterFractionInvalid2() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterFractionMaxRemoveHighAndLow() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterFractionMaxRemoveHighAndLowBothFraction() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterFractionMaxRemoveHighAndLowBothLevels() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterFractionMaxRemoveNeg() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterFractionMaxRemoveNegHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterKeepMarginal() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testfilterlist - Variable in class ubic.basecode.datafilter.TestRowNameFilter
testFilterMax() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxFraction() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxFractionAll() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxFractionHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxFractionNone() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxFractionNoneRemoveNeg() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMaxTooHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMean() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMeanHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMedian() - Method in class ubic.basecode.datafilter.TestRowLevelFilter: mm<-read.table("testdata.txt", header=T, row.names=1) length(which(apply(mm, 1, median) > 100))
testFilterMedianHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter: mm<-read.table("testdata.txt", header=T, row.names=1) length(which(apply(mm, 1, median) < 1000))
testFilterMin() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterMinHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterNoFilter() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
testFilterNoFiltering() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterNullFlags() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterPresentCountInvalid() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterPresentCountInvalid() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterString() - Method in class ubic.basecode.datafilter.TestRowNameFilter
testFilterStringExclude() - Method in class ubic.basecode.datafilter.TestRowNameFilter
testFilterStringMatrix() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterStringMatrix() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterWithMissing() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterWithMissing() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterWithMissingLessStringent() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
testFilterWithMissingLessStringent() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFilterWithMissingLowMaxFraction() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testFindExecutable() - Method in class ubic.basecode.util.r.AbstractRClientTest
testFindTerm() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testFisherCombinePvalues() - Method in class ubic.basecode.math.metaanalysis.MetaAnalysisTest
testFisherCombinePvaluesB() - Method in class ubic.basecode.math.metaanalysis.MetaAnalysisTest
testFtpFileSize() - Method in class ubic.basecode.util.NetUtilsTest
testFtpFileSizeDoesntExist() - Method in class ubic.basecode.util.NetUtilsTest
testFVolume() - Method in class ubic.basecode.math.TestWilcoxon
testGenericOntologyServiceMem() - Method in class ubic.basecode.ontology.providers.GenericOntologyServiceTest
testGeometricMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testget() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
testGet() - Method in class ubic.basecode.dataStructure.BitUtilTest
testGet() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGet() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testGet() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGet() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.get(int, int).
testGet2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.get(int, int).
testGetApproximateQuantile() - Method in class ubic.basecode.math.distribution.HistogramTest: Test method for Histogram.getApproximateQuantile(int).
testGetBiggestBinSize() - Method in class ubic.basecode.math.distribution.HistogramTest: Test method for Histogram.getBiggestBinSize().
testGetByKeys() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DoubleMatrix.getByKeys(Object, Object).
testGetByKeys() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetByKeys() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for DoubleMatrix.getByKeys(Object, Object).
testGetChildren() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testGetChildren() - Method in class ubic.basecode.ontology.OntologyTermTest
testGetChildrenFromMultipleTerms() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testGetChildrenFromMultipleTermsWithSearch() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testGetChildrenHasPart() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testGetChildrenHasProperPart() - Method in class ubic.basecode.ontology.OntologyTermTest: FIXME this uses NIF, which we are no longer using actively - not a big deal since this just tests mechanics
testGetColByName() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getColByName(java.lang.Object).
testGetColByName() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for ubic.basecode.dataStructure.matrix.SparseDoubleMatrix#getColByName(java.lang.Object).
testGetColByNameFail() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetColByNameNull() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testgetcolobj() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getColObj(int).
testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
testGetColObj2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getColObj(int).
testGetColRange() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetColRange() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testGetColRange() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testGetColumn() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getColumn(int).
testGetColumn() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetColumn() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getColumn(int).
testGetCompressedFile() - Method in class ubic.basecode.util.FileToolsTest
testGetCompressedFileZip() - Method in class ubic.basecode.util.FileToolsTest
testGetConfigBuilderFile() - Method in class ubic.basecode.util.ConfigUtilsTest
testGetConfigBuilderFileNew() - Method in class ubic.basecode.util.ConfigUtilsTest
testGetConfigBuilderString() - Method in class ubic.basecode.util.ConfigUtilsTest
testGetConfigBuilderStringNew() - Method in class ubic.basecode.util.ConfigUtilsTest
testGetConfigBuilderURL() - Method in class ubic.basecode.util.ConfigUtilsTest
testGetConfigBuilderURLNew() - Method in class ubic.basecode.util.ConfigUtilsTest
testGetEntry() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetExtension() - Method in class ubic.basecode.util.FileToolsTest
testGetInputStreamFromPlainOrCompressedFile() - Method in class ubic.basecode.util.FileToolsTest
testGetLeft() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest: Test method for ubic.basecode.dataStructure.tree.BinaryTree#getLeft().
testGetLines() - Method in class ubic.basecode.util.FileToolsTest
testGetObject() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getObject(int, int).
testGetObject() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetObject() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getObject(int, int).
testGetOutOfBounds() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testGetParents() - Method in class ubic.basecode.ontology.OntologyTermTest
testGetParentsFromMultipleTerms() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testGetParentsHasPart() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testGetParentsHasProperPart() - Method in class ubic.basecode.ontology.OntologyTermTest
testgetRelative5yearsago() - Method in class ubic.basecode.util.DateUtilTest
testgetRelative5yearsFromnow() - Method in class ubic.basecode.util.DateUtilTest
testgetRelativeDateDayago() - Method in class ubic.basecode.util.DateUtilTest
testgetRelativeTomorrow() - Method in class ubic.basecode.util.DateUtilTest
testGetRight() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest: Test method for ubic.basecode.dataStructure.tree.BinaryTree#getRight().
testGetRoot() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest: Test method for BinaryTree.getRoot().
testGetRow() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetRow() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetRow() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getRow(int).
testGetRow() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testGetRow2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getRow(int).
testGetRowArrayList() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetRowArrayList() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getRowArrayList(int).
testGetRowArrayList() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testGetRowArrayList2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getRowArrayList(int).
testGetRowBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testGetRowByName() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getRowByName(java.lang.Object).
testGetRowByName() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getRowByName(java.lang.Object).
testGetRowByNameFail() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetRowByNameNull() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetRowMatrix1D() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testgetrowobj() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
testGetRowObj() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetRowObj() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testGetRowObj() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.getRowObj(int).
testGetRowObj2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.getRowObj(int).
testGetRowRange() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testGetRowRange() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testGetRowRange() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testGetSet() - Method in class ubic.basecode.io.excel.ExcelUtilTest
testGetSheetFromFile() - Method in class ubic.basecode.io.excel.ExcelUtilTest
testgetStringListFromFile() - Method in class ubic.basecode.util.FileToolsTest
testGetWithoutExtension() - Method in class ubic.basecode.util.FileToolsTest
testGetWithoutExtensionB() - Method in class ubic.basecode.util.FileToolsTest
testGetWithoutExtensionC() - Method in class ubic.basecode.util.FileToolsTest
testHammingDistance() - Method in class ubic.basecode.math.StringDistanceTest
testHasChanged() - Method in class ubic.basecode.ontology.jena.OntologyLoaderTest
testHasImageExtension() - Method in class ubic.basecode.util.FileToolsTest
testHasXMLExtension() - Method in class ubic.basecode.util.FileToolsTest
testHistogramReaderIs() - Method in class ubic.basecode.io.reader.HistogramReaderTest
testHistogramReaderString() - Method in class ubic.basecode.io.reader.HistogramReaderTest
TestHistogramWriter - Class in ubic.basecode.io.writer
TestHistogramWriter() - Constructor for class ubic.basecode.io.writer.TestHistogramWriter
testHypergeometric() - Method in class ubic.basecode.math.TestSpecFunc
testIncrement() - Method in class ubic.basecode.dataStructure.CountingMapTest: Test method for ca.elmonline.util.CountingMap#increment(java.lang.Object).
testIncrementalUpdate() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testIncrementalUpdateSums() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testIncrementalWeightedUpdate() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testIndexing() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
testInferenceCapabilities() - Method in class ubic.basecode.ontology.jena.JenaUtilsTest
testInitializeAllProviders() - Method in class ubic.basecode.ontology.providers.OntologyProvidersTest
testInitializeInBackgroundThread() - Method in class ubic.basecode.ontology.providers.GenericOntologyServiceTest
testInsertLeft() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest: Test method for BinaryTree.insertLeft(ubic.basecode.dataStructure.tree.BinaryTreeNode, java.lang.Object) .
testInsertRight() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest: Test method for BinaryTree.insertRight(ubic.basecode.dataStructure.tree.BinaryTreeNode, java.lang.Object) .
testInteractionAndRelevel() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
testInteractionC() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
testInterpolate() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest: Tests two things: 1.
testIntsToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
testInvalidVariance() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest
testInverseFisherTransform() - Method in class ubic.basecode.math.CorrelationStatsTest
testIsEmpty() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest: Test method for BinaryTree.isEmpty().
testIsGZipped() - Method in class ubic.basecode.util.FileToolsTest
testIsLeaf() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
testIsMissing() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testIsMissing() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testIsMissing() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.isMissing(int, int).
testIsMissing2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.isMissing(int, int).
testIsValidFraction() - Method in class ubic.basecode.math.TestStats
testIsValidFraction2() - Method in class ubic.basecode.math.TestStats
testIsZipped() - Method in class ubic.basecode.util.FileToolsTest
TestItemLevelFilter - Class in ubic.basecode.datafilter
TestItemLevelFilter() - Constructor for class ubic.basecode.datafilter.TestItemLevelFilter
TestKSTest - Class in ubic.basecode.math
TestKSTest() - Constructor for class ubic.basecode.math.TestKSTest
testKSTestOneSample() - Method in class ubic.basecode.math.TestKSTest
testKSTestTwoSample() - Method in class ubic.basecode.math.TestKSTest
testKurtosis() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testKurtosisList() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testKW() - Method in class ubic.basecode.math.KruskalWallisTest
testLag1() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testLimma() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
testLimmaA() - Method in class ubic.basecode.util.r.AbstractRClientTest: Also exercises dataFrameEval
testLimmaMissing() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
testLinearModelA() - Method in class ubic.basecode.util.r.AbstractRClientTest: Like a two-sample t-test where the intercept is also of interest.
testLinearModelB() - Method in class ubic.basecode.util.r.AbstractRClientTest: With a continuous covariate as well a categorical one.
testLinearModelC() - Method in class ubic.basecode.util.r.AbstractRClientTest
testLinearModelD() - Method in class ubic.basecode.util.r.AbstractRClientTest: Basically a one-way anova with 4 levels in the factor.
testListDirectoryFiles() - Method in class ubic.basecode.util.FileToolsTest
testListEvalA() - Method in class ubic.basecode.util.r.AbstractRClientTest
testListEvalB() - Method in class ubic.basecode.util.r.AbstractRClientTest
testLoadAndSearch() - Method in class ubic.basecode.ontology.providers.ObiServiceTest
testLoadConfigFile() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadConfigFileNew() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadConfigString() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadConfigStringNew() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadConfigStringNewName() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadConfigURL() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadConfigURLNew() - Method in class ubic.basecode.util.ConfigUtilsTest
testLoadLibrary() - Method in class ubic.basecode.util.r.AbstractRClientTest
testLoadModelWithImports() - Method in class ubic.basecode.ontology.providers.DiseaseOntologyServiceTest
testLoadScript() - Method in class ubic.basecode.util.r.AbstractRClientTest
testLogTransform() - Method in class ubic.basecode.math.TestMatrixStats
testLSFOneContinuousWithMissing3() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testLSFThreeLevelsOnecontinous2() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testLSFThreeLevelsOneContinuousWithMissing3() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testLSFTwoLevels() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testLSFTwoLevels2() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Many missing values; Two factors, two levels + interaction.
testLSFTwoLevels3() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testLSFTwoLevelsOneContinuous() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testM - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testMad() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMakeRnames() - Method in class ubic.basecode.util.StringUtilTest
testManhattanDistance() - Method in class ubic.basecode.math.DistanceTest
TestMapReader - Class in ubic.basecode.io.reader
TestMapReader() - Constructor for class ubic.basecode.io.reader.TestMapReader
TestMathUtil - Class in ubic.basecode.math
TestMathUtil() - Constructor for class ubic.basecode.math.TestMathUtil
testMatrix() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
testMatrix2() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
TestMatrixNormalizer - Class in ubic.basecode.math
TestMatrixNormalizer() - Constructor for class ubic.basecode.math.TestMatrixNormalizer
TestMatrixRowStats - Class in ubic.basecode.math
TestMatrixRowStats() - Constructor for class ubic.basecode.math.TestMatrixRowStats
TestMatrixStats - Class in ubic.basecode.math
TestMatrixStats() - Constructor for class ubic.basecode.math.TestMatrixStats
testMatrixWeightedMeanVariance() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest2: Weighted regression test - Based on a few genes from GSE9376, but samples scrambled
testMatrixWeightedRegress() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Weighted least squares test for 2D matrices
testMax() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMax() - Method in class ubic.basecode.math.TestMathUtil
testMax() - Method in class ubic.basecode.math.TestMatrixStats
testMaxFractionRemovedInvalid() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
testMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMeanAboveQuantile() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMeanAboveQuantile() - Method in class ubic.basecode.math.TestStats
TestMeanDifferenceMetaAnalysis - Class in ubic.basecode.math.metaanalysis
TestMeanDifferenceMetaAnalysis() - Constructor for class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testMeanDoubleAr() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMeanDoubleArB() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMeanEff() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMeans() - Method in class ubic.basecode.math.TestMatrixRowStats
testMeans2() - Method in class ubic.basecode.math.TestMatrixRowStats
testMeanVarianceNoDesignWithColsRowAllMissing() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest: Data has missing values, no Design matrix provided so plot a generic mean-variance plot
testMeanVarianceNoDesignWithMissing() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest: Data has missing values, no Design matrix provided so plot a generic mean-variance plot (no voom)
testMedian() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMin() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testMin() - Method in class ubic.basecode.math.TestMatrixStats
testmissingdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
testNan() - Method in class ubic.basecode.math.TestMatrixStats
testNextDoubleMatrix() - Method in class ubic.basecode.math.distribution.TestWishart
testNextSample() - Method in class ubic.basecode.math.distribution.HistogramSamplerTest: Test method for HistogramSampler.nextSample().
testNHBE() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Tests limma-like functionality Multiple levels per factor, unbalanced design
testNormalizeDoubleArrayList() - Method in class ubic.basecode.math.TestStats
testNormalizeDoubleArrayListdouble() - Method in class ubic.basecode.math.TestStats
testNumberOfDistinctValues() - Method in class ubic.basecode.math.TestStats
testNumberOfDistinctValuesNonNA() - Method in class ubic.basecode.math.TestStats
testObjectToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
testOmitBadPredicates() - Method in class ubic.basecode.ontology.jena.OntologySearchTest: See bug 2920
testOmitBadPredicates2() - Method in class ubic.basecode.ontology.jena.OntologySearchTest: See bug 3269
testOmitDefinition() - Method in class ubic.basecode.ontology.jena.UberonOntologySearchTest
testOmitDefinitions() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
testOmitDefinitions2() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
testOmitDefinitions3() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
testOmitDefinitions4() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
testOneWayAnova() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Has a lot of missing values.
testOptimizedCorrelation() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testOrder() - Method in class ubic.basecode.math.TestRank
testOrderB() - Method in class ubic.basecode.math.TestRank
testOutOfBounds() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testOutOfBounds2() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testOverlap() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testPersistence() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
testPrintBeans() - Method in class ubic.basecode.util.PrettyPrinterTest
testProbabilityDouble() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest: Test method for NormalProbabilityComputer.probability(double).
testProbabilityDoubleBoolean() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest: Test method for NormalProbabilityComputer.probability(double, boolean).
testProbabilityDoubleBooleanLower() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest
testProduct() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testPvalue() - Method in class ubic.basecode.math.CorrelationStatsTest
testQuantile() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testQuantile() - Method in class ubic.basecode.math.TestStats
testQuantile75() - Method in class ubic.basecode.math.TestStats
testQuantileInverse() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testQuantileNormalize() - Method in class ubic.basecode.math.TestMatrixNormalizer: mm<-read.table("testdata.txt", header=T, row.names=1) library(preprocessCore) rr<-normalize.quantiles(as.matrix(mm)) rr[3,5] [1] 29860.93 > rr[13,5] [1] 466.7833 > rr[3,12] [1] 31620.79 > rr[4,10] [1] 1071.525 > rr[6,7] [1] 288.925 >
testQuantileNormalizeWithMissing() - Method in class ubic.basecode.math.TestMatrixNormalizer: Note that we do this differnetly than the Bioconductor implementation.
testQuantiles() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testRandomSubset() - Method in class ubic.basecode.math.RandomChooserTest
testRange() - Method in class ubic.basecode.math.TestStats
testRange() - Method in class ubic.basecode.util.DateUtilTest
testRangeBad() - Method in class ubic.basecode.util.DateUtilTest
TestRank - Class in ubic.basecode.math
TestRank() - Constructor for class ubic.basecode.math.TestRank
testRankInterpolated() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testRankTransformDoubleArrayList() - Method in class ubic.basecode.math.TestRank
testRankTransformDoubleArrayListDesc() - Method in class ubic.basecode.math.TestRank
testRankTransformMap() - Method in class ubic.basecode.math.TestRank
testRankTransformMapDesc() - Method in class ubic.basecode.math.TestRank
testRankWithTies() - Method in class ubic.basecode.math.TestRank
testRankWithTiesB() - Method in class ubic.basecode.math.TestRank
testRankWithTiesC() - Method in class ubic.basecode.math.TestRank
testRankWithTiesD() - Method in class ubic.basecode.math.TestRank
testRankWithTiesE() - Method in class ubic.basecode.math.TestRank
testRbfNormalize() - Method in class ubic.basecode.math.TestMatrixStats
testRead() - Method in class ubic.basecode.io.reader.TestMapReader
testReadBad() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadBlankCorner() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadChooseRows() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadChooseRowsBadfileName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadChooseRowsSkipcols() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStream() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
testReadInputStreamColumnCount() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamColumnCount() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
testReadInputStreamGotColName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamGotColName() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
testReadInputStreamGotColNameSkipColumn() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamGotRowName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamGotRowName() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
testReadInputStreamMissing() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamMissingBad() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamMissingSpaces() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamRowCount() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testReadInputStreamRowCount() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
testReadJW() - Method in class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
testReadNoHeader() - Method in class ubic.basecode.io.reader.TestMapReader
testReadNoHeaderFile() - Method in class ubic.basecode.io.reader.TestMapReader
testReadStream() - Method in class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
testReadStreamAdjList() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
testReadStreamAdjListBig() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
testRejectNonEnglish() - Method in class ubic.basecode.ontology.OntologyTermTest
testRemoveMissing1() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testRemoveMissing2() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testRepeat() - Method in class ubic.basecode.math.RandomChooserTest: Check correctness of the sampling algorithm for choosing subsets of size 2.
testRepeatSubset() - Method in class ubic.basecode.math.RandomChooserTest: Check correctness of the sampling algorithm for choosing subsets of size 2.
testResourcetoPath() - Method in class ubic.basecode.util.FileToolsTest
TestROC - Class in ubic.basecode.math
TestROC() - Constructor for class ubic.basecode.math.TestROC
TestRowAbsentFilter - Class in ubic.basecode.datafilter: See the file test/data/matrix-testing.xls for the validation.
TestRowAbsentFilter() - Constructor for class ubic.basecode.datafilter.TestRowAbsentFilter
TestRowAffyNameFilter - Class in ubic.basecode.datafilter
TestRowAffyNameFilter() - Constructor for class ubic.basecode.datafilter.TestRowAffyNameFilter
TestRowLevelFilter - Class in ubic.basecode.datafilter
TestRowLevelFilter() - Constructor for class ubic.basecode.datafilter.TestRowLevelFilter
TestRowMissingFilter - Class in ubic.basecode.datafilter: See the file test/data/matrix-testing.xls for the validation.
TestRowMissingFilter() - Constructor for class ubic.basecode.datafilter.TestRowMissingFilter
TestRowNameFilter - Class in ubic.basecode.datafilter
TestRowNameFilter() - Constructor for class ubic.basecode.datafilter.TestRowNameFilter
testRows() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testRows() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testRows() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.rows().
testRows() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testRows2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.rows().
testRunFixedE() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunFixedQ() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunFixedVar() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunFixedZ() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunRandomBSV() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunRandomE() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunRandomVar() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunRandomZ() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
testRunUFEffect() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunUFVar() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunUFZscore() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunURBSV() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunZFEffect() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunZFVar() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunZFZscore() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunZRBSV() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testRunZRQval() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
testSampleKurtosis() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSampleSkew() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSampleStandardDeviation() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSampleVariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSaveImage() - Method in class ubic.basecode.graphics.MatrixDisplayTest
testSaveImageStandardize() - Method in class ubic.basecode.graphics.MatrixDisplayTest
testScaledDesign() - Method in class ubic.basecode.math.linalg.QRDecompositionTest: Case where the Design matrix values include values other than 1's and 0's.
testScore() - Method in class ubic.basecode.ontology.jena.UberonOntologySearchTest
testSeen() - Method in class ubic.basecode.dataStructure.CountingMapTest: Test method for ca.elmonline.util.CountingMap#seen(java.lang.Object).
testSeenValues() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
testSelectColumns() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testSelectColumnsAndRows() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testSelectColumnsAndRowsBad() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testSelectRows() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
testSelfSquare() - Method in class ubic.basecode.math.TestMatrixStats
testSet() - Method in class ubic.basecode.dataStructure.BitUtilTest
testSet() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSet() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testSet() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for ubic.basecode.dataStructure.matrix.SparseDoubleMatrix#set(int, int, double).
testSet2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for ubic.basecode.dataStructure.matrix.DenseDoubleMatrix#set(int, int, double).
testSetByKeys() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testSetFormula() - Method in class ubic.basecode.io.excel.ExcelUtilTest
testSetIntIntDouble() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSetIntIntObject() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSetObj() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testSingular() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testSingular2() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
testSingular2() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Originally causes failures during summarization step.
testSingularValueDecomposition() - Method in class ubic.basecode.math.SingularValueDecompositionTest
testSize() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSize() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testSize() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testSkew() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSmallNumbers() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
testSortByColumnAbsoluteValue() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSortedKeyList() - Method in class ubic.basecode.dataStructure.CountingMapTest: Test method for ca.elmonline.util.CountingMap#sortedEntrySet(java.lang.Object).
testSortedKeyListBoolean() - Method in class ubic.basecode.dataStructure.CountingMapTest: Test method for ca.elmonline.util.CountingMap#sortedEntrySet(boolean).
TestSparseDoubleMatrixReader - Class in ubic.basecode.io.reader
TestSparseDoubleMatrixReader() - Constructor for class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
TestSparseRaggedDouble2DNamedMatrixReader - Class in ubic.basecode.io.reader
TestSparseRaggedDouble2DNamedMatrixReader() - Constructor for class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
testSpearmanOneList1() - Method in class ubic.basecode.math.DistanceTest
testSpearmanOneList2() - Method in class ubic.basecode.math.DistanceTest
testSpearmanOneList3() - Method in class ubic.basecode.math.DistanceTest
testSpearmanOneList4() - Method in class ubic.basecode.math.DistanceTest
testSpearmanPvalueA() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueA2() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueB() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueD() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueD2() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueE() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueEh() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueEm() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueF() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueG() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueG2() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanPvalueTDist() - Method in class ubic.basecode.math.CorrelationStatsTest
testSpearmanRankCorrelation() - Method in class ubic.basecode.math.DistanceTest
testSpearmanRankCorrelation2() - Method in class ubic.basecode.math.DistanceTest
testSpearmanRankCorrelation3() - Method in class ubic.basecode.math.DistanceTest
testSpearmanRankCorrelationNaN() - Method in class ubic.basecode.math.DistanceTest
TestSpecFunc - Class in ubic.basecode.math
TestSpecFunc() - Constructor for class ubic.basecode.math.TestSpecFunc
testSqueezeVar() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
testSqueezeVarB() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest: Test based on GSE112792; see test-squeezevar.R
testSqueezeVarWMissing() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
testStandardDeviations() - Method in class ubic.basecode.math.TestMatrixRowStats
testStandardize() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testStandardize() - Method in class ubic.basecode.math.TestMatrixStats
testStandardizeNoVariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
TestStats - Class in ubic.basecode.math
TestStats() - Constructor for class ubic.basecode.math.TestStats
testStemming() - Method in class ubic.basecode.ontology.jena.OntologySearchTest
TestStringConverter - Class in ubic.basecode.io: $Id$
TestStringConverter() - Constructor for class ubic.basecode.io.TestStringConverter
teststringdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
testStringFilter() - Method in class ubic.basecode.datafilter.TestRowAffyNameFilter
testStringListEval() - Method in class ubic.basecode.util.r.AbstractRClientTest
testStringListEvalB() - Method in class ubic.basecode.util.r.AbstractRClientTest
TestStringMatrixReader - Class in ubic.basecode.io.reader
TestStringMatrixReader() - Constructor for class ubic.basecode.io.reader.TestStringMatrixReader
teststringmissingdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
testStringToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
testStringToDoubleArrayConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
TestStringUtil - Class in ubic.basecode.util
TestStringUtil() - Constructor for class ubic.basecode.util.TestStringUtil
testSubset() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
testSubsetCols() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testSubsetColumns() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSubsetColumns() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
testSubsetRows() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testSubsetRows() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testSubsetRows() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testSubsetRowsFail() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
testSum() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSumArray() - Method in class ubic.basecode.math.TestMathUtil
testSummation() - Method in class ubic.basecode.dataStructure.CountingMapTest
testSumOfInversions() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSumOfPowerDeviationsA() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSumOfPowers() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSumOfSquaredDeviations() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSumOfSquares() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testSumOfSquaresDoubleMatrixNamed() - Method in class ubic.basecode.math.TestMatrixRowStats
testSumOfSquaresDoubleMatrixNamedDoubleArrayList() - Method in class ubic.basecode.math.TestMatrixRowStats
testSums() - Method in class ubic.basecode.math.TestMatrixRowStats
testTestDir() - Method in class ubic.basecode.util.FileToolsTest
testTestFileFile() - Method in class ubic.basecode.util.FileToolsTest
testTestFileString() - Method in class ubic.basecode.util.FileToolsTest
testThreeWaySingular() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testToArray() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testToArray() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testToBool() - Method in class ubic.basecode.dataStructure.BitUtilTest
testToInteger() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
testTopoSort() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testtostring() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
testToString() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testToString() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DoubleMatrix.toString().
testToString() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for DoubleMatrix.toString().
testToString() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
testTotalBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
testTouch() - Method in class ubic.basecode.util.FileToolsTest
testTreeView() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
testTrigammaInverse() - Method in class ubic.basecode.math.TestSpecFunc
testTrigammaInverseB() - Method in class ubic.basecode.math.TestSpecFunc: handling of missing and out of range values
testTrimmedMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testTTest() - Method in class ubic.basecode.util.r.AbstractRClientTest
testTTestFail() - Method in class ubic.basecode.util.r.AbstractRClientTest
testTwoStringHashKey() - Method in class ubic.basecode.util.TestStringUtil
testTwoStringHashKeyB() - Method in class ubic.basecode.util.TestStringUtil
testTwoWayAnovaUnfittable() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Sanity check.
testTwoWayAnovaWithInteractions() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: Check for problem reported by TF -- Gemma gives slightly different result.
testTwoWayTwoLevelsOneContinousInteractionC() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest: No missing values; Two-way ANOVA with interaction, PLUS a continuous covariate.
testUberon() - Method in class ubic.basecode.ontology.providers.UberonOntologyServiceTest
testUnGzipFile() - Method in class ubic.basecode.util.FileToolsTest
testUnzipFile() - Method in class ubic.basecode.util.FileToolsTest
testVariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testVectorRegress() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testVectorWeightedRegress() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testVectorWeightedRegressWithMissing() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
testViewColumn() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testViewColumn() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
testViewRow() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
testViewRow() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest: Test method for SparseDoubleMatrix.viewRow(int).
testViewRow2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest: Test method for DenseDoubleMatrix.viewRow(int).
testVoom() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest: Test calculation of weights for LeastSquaresFitting.
testWeightedHammingA() - Method in class ubic.basecode.math.StringDistanceTest
testWeightedHammingB() - Method in class ubic.basecode.math.StringDistanceTest
testWeightedHammingC() - Method in class ubic.basecode.math.StringDistanceTest
testWeightedMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
testWeightedSuffixHammingA() - Method in class ubic.basecode.math.StringDistanceTest
testWeightedSuffixHammingB() - Method in class ubic.basecode.math.StringDistanceTest
testWeightedSuffixHammingC() - Method in class ubic.basecode.math.StringDistanceTest
testWhereIs() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
TestWilcoxon - Class in ubic.basecode.math: Gold standard (?) is the exactRankTests (http://cran.r-project.org/src/contrib/Descriptions/exactRankTests.html) or on Catmap.
TestWilcoxon() - Constructor for class ubic.basecode.math.TestWilcoxon
testWilcoxonPExactA() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPExactB() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPExactC() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPExactD() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPGauss() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPGaussB() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPVolume() - Method in class ubic.basecode.math.TestWilcoxon
testWilxcoxonPWithTies() - Method in class ubic.basecode.math.TestWilcoxon
testWinsorizedMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
TestWishart - Class in ubic.basecode.math.distribution
TestWishart() - Constructor for class ubic.basecode.math.distribution.TestWishart
testWithNaNs() - Method in class ubic.basecode.math.TestRank
testWithNaNs2() - Method in class ubic.basecode.math.TestRank
testWithNaNs3() - Method in class ubic.basecode.math.TestRank
testWithoutOntologyCacheDir() - Method in class ubic.basecode.ontology.providers.GenericOntologyServiceTest
testWrite3DMatrix() - Method in class ubic.basecode.io.writer.MatrixWriterTest
testWriteMatrix() - Method in class ubic.basecode.io.writer.MatrixWriterTest: Test method for ubic.basecode.io.writer.MatrixWriter#writeMatrix(ubic.basecode.dataStructure.matrix.NamedMatrix, boolean) .
testWriteMatrixB() - Method in class ubic.basecode.io.writer.MatrixWriterTest
testWriteOutAsPNG() - Method in class ubic.basecode.graphics.MatrixDisplayTest
testWriteOutAsPNG2() - Method in class ubic.basecode.graphics.MatrixDisplayTest
testWriter() - Method in class ubic.basecode.io.writer.TestHistogramWriter
testZDotProductDoubleMatrix1D() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
testZDotProductDoubleMatrix1DHarder() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
testZDotProductDoubleMatrix1DHarderReverse() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
testZDotProductDoubleMatrix1DReverse() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
testZSum() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest: Test method for RCDoubleMatrix1D.zSum().

U

UberonOntologySearchTest - Class in ubic.basecode.ontology.jena
UberonOntologySearchTest() - Constructor for class ubic.basecode.ontology.jena.UberonOntologySearchTest
UberonOntologyServiceTest - Class in ubic.basecode.ontology.providers
UberonOntologyServiceTest() - Constructor for class ubic.basecode.ontology.providers.UberonOntologyServiceTest
ubic.basecode.datafilter - package ubic.basecode.datafilter
ubic.basecode.dataStructure - package ubic.basecode.dataStructure
ubic.basecode.dataStructure.graph - package ubic.basecode.dataStructure.graph
ubic.basecode.dataStructure.matrix - package ubic.basecode.dataStructure.matrix
ubic.basecode.dataStructure.params - package ubic.basecode.dataStructure.params
ubic.basecode.dataStructure.tree - package ubic.basecode.dataStructure.tree
ubic.basecode.graphics - package ubic.basecode.graphics
ubic.basecode.io - package ubic.basecode.io
ubic.basecode.io.excel - package ubic.basecode.io.excel
ubic.basecode.io.reader - package ubic.basecode.io.reader
ubic.basecode.io.writer - package ubic.basecode.io.writer
ubic.basecode.math - package ubic.basecode.math
ubic.basecode.math.distribution - package ubic.basecode.math.distribution
ubic.basecode.math.linalg - package ubic.basecode.math.linalg
ubic.basecode.math.linearmodels - package ubic.basecode.math.linearmodels
ubic.basecode.math.metaanalysis - package ubic.basecode.math.metaanalysis
ubic.basecode.ontology - package ubic.basecode.ontology
ubic.basecode.ontology.jena - package ubic.basecode.ontology.jena
ubic.basecode.ontology.ncbo - package ubic.basecode.ontology.ncbo
ubic.basecode.ontology.providers - package ubic.basecode.ontology.providers
ubic.basecode.util - package ubic.basecode.util
ubic.basecode.util.r - package ubic.basecode.util.r
UniformDensityComputerTest - Class in ubic.basecode.math.distribution
UniformDensityComputerTest() - Constructor for class ubic.basecode.math.distribution.UniformDensityComputerTest

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