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
All Classes All Packages
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
- testInsertRight() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
- 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
All Classes All Packages