AbstractFilter <M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Base implementation of the filter interface.
AbstractFilter() - Constructor for class ubic.basecode.datafilter.AbstractFilter
AbstractGraph <R extends GraphNode <K ,V >,K ,V > - Class in ubic.basecode.dataStructure.graph
AbstractGraph() - Constructor for class ubic.basecode.dataStructure.graph.AbstractGraph
AbstractGraph(Set<R>) - Constructor for class ubic.basecode.dataStructure.graph.AbstractGraph
Create a new graph from a set of nodes.
AbstractGraphNode <K ,V > - Class in ubic.basecode.dataStructure.graph
AbstractGraphNode(K) - Constructor for class ubic.basecode.dataStructure.graph.AbstractGraphNode
Create a new node when given only a key.
AbstractGraphNode(K, V) - Constructor for class ubic.basecode.dataStructure.graph.AbstractGraphNode
AbstractLevelFilter <R ,C > - Class in ubic.basecode.datafilter
Abstract class representing a filter that removes things from DoubleMatrixNamed matrices based on the values
themselves.
AbstractLevelFilter() - Constructor for class ubic.basecode.datafilter.AbstractLevelFilter
AbstractMatrix <R ,C ,V > - Class in ubic.basecode.dataStructure.matrix
AbstractMatrix() - Constructor for class ubic.basecode.dataStructure.matrix.AbstractMatrix
AbstractMatrix3D <R ,C ,S ,V > - Class in ubic.basecode.dataStructure.matrix
TODO Document Me
AbstractMatrix3D() - Constructor for class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
AbstractMatrixReader <M extends Matrix2D <String ,String ,V >,V > - Class in ubic.basecode.io.reader
Abstract class representing an object that can read in a
Matrix2D
from a file.
AbstractMatrixReader() - Constructor for class ubic.basecode.io.reader.AbstractMatrixReader
AbstractOntologyMemoryBackedService - Class in ubic.basecode.ontology.providers
This class has some stuff that's specific to in-memory ontologies.
AbstractOntologyMemoryBackedService() - Constructor for class ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService
AbstractOntologyResource - Class in ubic.basecode.ontology.model
AbstractOntologyResource() - Constructor for class ubic.basecode.ontology.model.AbstractOntologyResource
AbstractOntologyService - Class in ubic.basecode.ontology.providers
AbstractOntologyService() - Constructor for class ubic.basecode.ontology.providers.AbstractOntologyService
AbstractRClient - Class in ubic.basecode.util.r
Base class for RClients
AbstractRClient() - Constructor for class ubic.basecode.util.r.AbstractRClient
accept(HSSFSheet, int) - Method in interface ubic.basecode.io.excel.SpreadSheetFilter
add(ObjectMatrix<String, String, Object>) - Method in class ubic.basecode.math.linearmodels.DesignMatrix
Append additional factors/covariates to this
addChild(K) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
addChildTo(K, K) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
Add a child to a particular node identified by key; if the node is not in the graph, an exception is thrown.
addChildTo(K, K, V) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
Add a child to a particualar node identified by key.
addColumnName(C) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
Add a column name when we don't care what the index will be.
addColumnName(C, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
addColumnName(C) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Add a column name, to the end of the current column names.
addColumnName(C, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Add a column name associated with an index.
addDataExtension(String) - Static method in class ubic.basecode.util.FileTools
addImageExtension(String) - Static method in class ubic.basecode.util.FileTools
addInteraction() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
Add interaction term; only works if there exactly two factors so this can figure out which interaction to add.
addInteraction(String...) - Method in class ubic.basecode.math.linearmodels.DesignMatrix
This will not add the interaction unless all of the terms are already part of the design, and interactions that
obviously can't be estimated will be dropped if possible, but otherwise this is fairly brain dead.
addNode(K, V) - Method in class ubic.basecode.dataStructure.graph.AbstractGraph
addNode(R) - Method in class ubic.basecode.dataStructure.graph.AbstractGraph
addNode(DirectedGraphNode<K, V>) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
addNode(K, V) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
Will not be attached to any other node.
addNode(K, V) - Method in interface ubic.basecode.dataStructure.graph.Graph
addParamInstance(Map<String, String>) - Method in class ubic.basecode.dataStructure.params.ParamKeeper
addParent(K) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
addParentTo(K, K) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
addParentTo(K, K, V) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
addPut(K, Double) - Method in class ubic.basecode.dataStructure.DoubleAddingMap
adds the current value to the value of this key.
addPutAll(Map<? extends K, ? extends Double>) - Method in class ubic.basecode.dataStructure.DoubleAddingMap
addRow(R, DoubleMatrix1D) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
addRow(R, IntArrayList, DoubleArrayList) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
addRowName(R) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
Add a row name when we don't care what the index will be.
addRowName(R, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
addRowName(R, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Add a row name associated with a row index.
addSliceName(S, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
addSliceName(S, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Add a slice name
addStatement(CharacteristicStatement) - Method in interface ubic.basecode.ontology.model.ChainedStatementObject
AFFX - Static variable in class ubic.basecode.datafilter.AffymetrixProbeNameFilter
Filter probes that have the AFFX prefix.
AffymetrixProbeNameFilter <M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Remove probes that have names meeting certain rules indicating they may have low reliability.
AffymetrixProbeNameFilter() - Constructor for class ubic.basecode.datafilter.AffymetrixProbeNameFilter
Filter probes with all criteria switched on.
AffymetrixProbeNameFilter(int[]) - Constructor for class ubic.basecode.datafilter.AffymetrixProbeNameFilter
AnnotationProperty - Interface in ubic.basecode.ontology.model
AnnotationPropertyImpl - Class in ubic.basecode.ontology.model
Note that this is a concrete instance of the annotation.
AnnotationPropertyImpl(AnnotationProperty, RDFNode) - Constructor for class ubic.basecode.ontology.model.AnnotationPropertyImpl
AnnotatorClient - Class in ubic.basecode.ontology.ncbo
Use the NCBO annotator to find ontology terms matching strings.
AnnotatorClient() - Constructor for class ubic.basecode.ontology.ncbo.AnnotatorClient
AnnotatorResponse - Class in ubic.basecode.ontology.ncbo
This represents an Ontology terms returned by the AnnotatorClient
AnnotatorResponse(String, String, String, Integer, Integer, String, String) - Constructor for class ubic.basecode.ontology.ncbo.AnnotatorResponse
anova() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
Compute ANOVA based on the model fit (Type I SSQ, sequential)
The idea is to add up the sums of squares (and dof) for all parameters associated with a particular factor.
AnovaEffect - Class in ubic.basecode.util.r.type
Represents one row of an ANOVA table
AnovaEffect(String, Double, Double, Double, Double, boolean) - Constructor for class ubic.basecode.util.r.type.AnovaEffect
AnovaResult - Class in ubic.basecode.util.r.type
AnovaResult() - Constructor for class ubic.basecode.util.r.type.AnovaResult
append(String, String, String) - Static method in class ubic.basecode.util.StringUtil
applyToIndicesMatchingCriteria(DoubleMatrix1D, DoubleFunction<Boolean>, DoubleFunction<Double>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
aroc(int, List<Double>) - Static method in class ubic.basecode.math.ROC
Calculate area under ROC, up to a given number of False positives.
asArray() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
asArray() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
asArray() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
asArray() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
asArray() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
asArray() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
asBools(byte[]) - Static method in class ubic.basecode.dataStructure.BitUtil
asDoubles() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
asDoubles() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Attempt to coerce the entries into doubles.
asId(Object) - Static method in class ubic.basecode.util.SQLUtils
asProperty(OntProperty) - Static method in class ubic.basecode.ontology.model.PropertyFactory
Convert a Jena property.
asRestriction(Restriction) - Static method in class ubic.basecode.ontology.model.RestrictionFactory
assign(V) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
assign(V) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Set all values in the matrix to the given value.
assign(double[]) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
assign(DoubleFunction) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
WARNING this only assigns to the non-empty values, for performance reasons.
assign(String, double[]) - Method in class ubic.basecode.util.r.JRIClient
assign(String, int[]) - Method in class ubic.basecode.util.r.JRIClient
assign(String, String) - Method in class ubic.basecode.util.r.JRIClient
assign(String, String[]) - Method in class ubic.basecode.util.r.JRIClient
assign(String, double[]) - Method in interface ubic.basecode.util.r.RClient
assign(String, int[]) - Method in interface ubic.basecode.util.r.RClient
assign(String, String) - Method in interface ubic.basecode.util.r.RClient
assign(String, String[]) - Method in interface ubic.basecode.util.r.RClient
assign(String, double[]) - Method in class ubic.basecode.util.r.RServeClient
assign(String, int[]) - Method in class ubic.basecode.util.r.RServeClient
assign(String, String) - Method in class ubic.basecode.util.r.RServeClient
assign(String, String[]) - Method in class ubic.basecode.util.r.RServeClient
assignFactor(List<String>) - Method in class ubic.basecode.util.r.AbstractRClient
assignFactor(String, List<String>) - Method in class ubic.basecode.util.r.AbstractRClient
assignFactor(List<String>) - Method in interface ubic.basecode.util.r.RClient
assignFactor(String, List<String>) - Method in interface ubic.basecode.util.r.RClient
assignMatrix(double[][]) - Method in class ubic.basecode.util.r.AbstractRClient
assignMatrix(DoubleMatrix<?, ?>) - Method in class ubic.basecode.util.r.AbstractRClient
assignMatrix(DoubleMatrix<?, ?>, Transformer) - Method in class ubic.basecode.util.r.AbstractRClient
assignMatrix(double[][]) - Method in interface ubic.basecode.util.r.RClient
Assign a 2-d matrix.
assignMatrix(DoubleMatrix<?, ?>) - Method in interface ubic.basecode.util.r.RClient
Assign a 2-d matrix.
assignMatrix(DoubleMatrix<?, ?>, Transformer) - Method in interface ubic.basecode.util.r.RClient
Assign a 2-d matrix.
assignStringList(List<?>) - Method in class ubic.basecode.util.r.AbstractRClient
assignStringList(List<?>) - Method in interface ubic.basecode.util.r.RClient
Define a variable corresponding to a character array in the R context, given a List of Strings.
asString(RDFNode) - Static method in class ubic.basecode.ontology.OntologyUtil
Use to pretty-print a RDFNode
autoCorrelation(DoubleArrayList, int, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Not supported.
averagePrecision(List<Double>) - Static method in class ubic.basecode.math.PrecisionRecall
"Average Precision is the average of the precision value obtained for the set of top $k$ documents existing after
each relevant document is retrieved, and this value is then averaged over information needs".
cancelInitializationThread() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
Cancel the initialization thread.
cancelInitializationThread() - Method in interface ubic.basecode.ontology.providers.OntologyService
cardinality() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
cardinality() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
cdf(DoubleArrayList) - Static method in class ubic.basecode.math.Stats
Convert an array into a cumulative density function (CDF).
CellLineOntologyService - Class in ubic.basecode.ontology.providers
See http://www.obofoundry.org/cgi-bin/detail.cgi?
CellLineOntologyService() - Constructor for class ubic.basecode.ontology.providers.CellLineOntologyService
CellTypeOntologyService - Class in ubic.basecode.ontology.providers
See http://www.obofoundry.org/cgi-bin/detail.cgi?
CellTypeOntologyService() - Constructor for class ubic.basecode.ontology.providers.CellTypeOntologyService
ChainedStatement - Interface in ubic.basecode.ontology.model
ChainedStatementObject - Interface in ubic.basecode.ontology.model
Acts as an 'anonymous' node in a statement
changeExtension(String, String) - Static method in class ubic.basecode.util.FileTools
CharacteristicStatement - Interface in ubic.basecode.ontology.model
charArrayToBytes(char[]) - Method in class ubic.basecode.io.ByteArrayConverter
ChebiOntologyService - Class in ubic.basecode.ontology.providers
Loads the CHEBI Ontology at startup in its own thread.
ChebiOntologyService() - Constructor for class ubic.basecode.ontology.providers.ChebiOntologyService
checkColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
checkForFile(FTPClient, String) - Static method in class ubic.basecode.util.NetUtils
determine if a file exists on the remote server.
checkPathIsReadableFile(String) - Static method in class ubic.basecode.util.FileTools
checkRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
children - Variable in class ubic.basecode.dataStructure.graph.DirectedGraphNode
chol2inv() - Method in class ubic.basecode.math.linalg.QRDecomposition
Used for computing standard errors of parameter estimates for least squares; copies functionality of R chol2inv.
chompExtension(String) - Static method in class ubic.basecode.util.FileTools
chooserandom(double[], int) - Static method in class ubic.basecode.math.RandomChooser
Random numbers from sourcedata, without replacement.
chooserandom(int, int) - Static method in class ubic.basecode.math.RandomChooser
choose n random integers from 0 (inclusive) to max (exclusive) without repeating
chooserandom(int[], int) - Static method in class ubic.basecode.math.RandomChooser
choose k random integers from 0 to max (exclusive) without repeating
chooserandom(List<? extends Object>, int) - Static method in class ubic.basecode.math.RandomChooser
chooseRandomSubset(int, Collection<? extends T>) - Static method in class ubic.basecode.math.RandomChooser
Select a random subset of size n from collection superSet
chooseRandomSubset(int, List<? extends T>) - Static method in class ubic.basecode.math.RandomChooser
Select a random subset of size n from List superSet
chooserandomWrep(int, int) - Static method in class ubic.basecode.math.RandomChooser
Same as chooserandom, but with replacement -- that is, repeats are allowed.
ClassStatement - Interface in ubic.basecode.ontology.model
cleanForFileName(String) - Static method in class ubic.basecode.util.FileTools
Avoid getting file names with spaces, slashes, quotes, # etc; replace them with "_".
clear(byte[], int) - Static method in class ubic.basecode.dataStructure.BitUtil
Clear the bit at the specified position
clear() - Method in class ubic.basecode.dataStructure.CountingMap
clear() - Method in class ubic.basecode.util.StatusDebugLogger
clear() - Method in class ubic.basecode.util.StatusStderr
clear() - Method in interface ubic.basecode.util.StatusViewer
Clear the status display.
clone() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Makes a copy of this node.
clone() - Method in class ubic.basecode.graphics.ColorMatrix
closeEnough(double[], double[], double) - Static method in class ubic.basecode.util.RegressionTesting
closeEnough(DoubleArrayList, DoubleArrayList, double) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two DoubleArrayLists are 'close enough' to call equal.
closeEnough(DoubleMatrix<?, ?>, DoubleMatrix<?, ?>, double) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.
closeEnough(DoubleMatrix1D, DoubleMatrix1D, double) - Static method in class ubic.basecode.util.RegressionTesting
closeEnough(DoubleMatrix2D, DoubleMatrix2D, double) - Static method in class ubic.basecode.util.RegressionTesting
closeEnough(Object[], Object[]) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two object arrays are the same.
closeIndex() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
Do not do this except before re-indexing.
colaxpy_j(int, double, double[][], int, int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method multiplies a constant times a portion of a column
of a matrix and adds the product to the corresponding portion
of another column of the matrix --- a portion of col2 is
replaced by the corresponding portion of a*col1 + col2.
coldot_j(int, double[][], int, int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method calculates the dot product of portions of two
columns of a matrix.
colisamax_j(int, double[][], int, int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method finds the index of the element of a portion of a
column of a matrix that has the maximum absolute value.
colMap - Variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
colNameMap - Variable in class ubic.basecode.io.writer.MatrixWriter
colNames - Variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
colnrm2_j(int, double[][], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method calculates the Euclidean norm of a portion of a
column of a matrix.
ColorMap - Class in ubic.basecode.graphics
ColorMap() - Constructor for class ubic.basecode.graphics.ColorMap
ColorMap(Color[]) - Constructor for class ubic.basecode.graphics.ColorMap
ColorMap(int) - Constructor for class ubic.basecode.graphics.ColorMap
ColorMap(int, Color[]) - Constructor for class ubic.basecode.graphics.ColorMap
Pre-condition: suggestedNumberOfColors > colorMap.length
colorMap - Variable in class ubic.basecode.graphics.ColorMatrix
ColorMatrix <A ,B > - Class in ubic.basecode.graphics
Creates a color matrix from a matrix of doubles
ColorMatrix(DoubleMatrix<A, B>) - Constructor for class ubic.basecode.graphics.ColorMatrix
ColorMatrix(DoubleMatrix<A, B>, Color[], Color) - Constructor for class ubic.basecode.graphics.ColorMatrix
colors - Variable in class ubic.basecode.graphics.ColorMatrix
colrot_j(int, double[][], int, int, double, double) - Static method in class ubic.basecode.math.linalg.Blas
This method "applies a plane rotation."
colscal_j(int, double, double[][], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method scales a portion of a column of a matrix by a constant.
colSums(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
NaN values are omitted from calculations.
colswap_j(int, double[][], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method interchanges two columns of a matrix.
columns() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
columns() - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
columns() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Get the number of columns the matrix has.
columns() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get the number of columns the matrix has.
columns() - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
columns() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
columns() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
Returns the size of the widest row.
columns() - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
colvaxpy_j(int, double, double[][], double[], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method multiplies a constant times a portion of a column
of a matrix x[ ][ ] and adds the product to the corresponding portion
of a vector y[ ] --- a portion of y[ ] is replaced by the corresponding
portion of ax[ ][j] + y[ ].
colvdot_j(int, double[][], double[], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method calculates the dot product of a portion of a
column of a matrix and the corresponding portion of a
vector.
colvraxpy_j(int, double, double[], double[][], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method multiplies a constant times a portion of a vector y[ ]
and adds the product to the corresponding portion
of a column of a matrix x[ ][ ] --- a portion of column j of x[ ][ ]
is replaced by the corresponding
portion of ay[ ] + x[ ][j].
commonPrefix(Collection<String>) - Static method in class ubic.basecode.util.StringUtil
Given a set of strings, identify any prefix they have in common.
commonSuffix(Collection<String>) - Static method in class ubic.basecode.util.StringUtil
Given a set of strings, identify any suffix they have in common.
compare(double, int, double, int) - Static method in class ubic.basecode.math.CorrelationStats
Statistical comparison of two Pearson correlations.
compareTo(DirectedGraphNode<K, V>) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Uses the topological sort order.
compareTo(UndirectedGraphNode<K, V>) - Method in class ubic.basecode.dataStructure.graph.UndirectedGraphNode
compareTo(Link) - Method in class ubic.basecode.dataStructure.Link
compareTo(OntologyResource) - Method in class ubic.basecode.ontology.model.AbstractOntologyResource
compareTo(AnnotatorResponse) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
CompressedBitMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
Named compressed sparse bit matrix.
CompressedBitMatrix(int, int, int) - Constructor for class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
Constructs a matrix with specified rows, columns, and total bits per cell
Implementation note: this is created by maintaining one or more Double matrices; the Doubles are used as bit
fields.
compressedsparse(int, int) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
CompressedSparseDoubleMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
Supports sparse matrices (where sparse means most values are zero, not that they are missing).
CompressedSparseDoubleMatrix(double[][]) - Constructor for class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
CompressedSparseDoubleMatrix(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
computeSize(boolean, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
compute the size of the matrix in pixels.
cond() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition
Configuration - Class in ubic.basecode.util
Configuration of ontology services and other things.
Configuration() - Constructor for class ubic.basecode.util.Configuration
ConfigUtils - Class in ubic.basecode.util
Convenience methods for loading configurations
ConfigUtils() - Constructor for class ubic.basecode.util.ConfigUtils
conjunction(BooleanArrayList, BooleanArrayList) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
Compute the conjuction (logical 'and') of two boolean vectors
connect(int, String, String, String) - Static method in class ubic.basecode.util.NetUtils
Convenient method to get a FTP connection.
connect() - Method in class ubic.basecode.util.r.RServeClient
Constants - Class in ubic.basecode.math
Used in some ports of statistical code.
Constants() - Constructor for class ubic.basecode.math.Constants
containsColumnName(C) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
containsColumnName(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
containsColumnName(C) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
containsColumnName(C) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Check if the matrix contains a column name
containsKey(Object) - Method in class ubic.basecode.dataStructure.CountingMap
containsKey(K) - Method in class ubic.basecode.dataStructure.graph.AbstractGraph
containsKey(K) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
containsKey(K) - Method in interface ubic.basecode.dataStructure.graph.Graph
containsNearlyZeros(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
containsRowName(R) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
containsRowName(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
containsRowName(R) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
containsRowName(R) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Check if the matrix contains a row name
containsSame(Collection<? extends Object>, Collection<? extends Object>) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two collections contain the same items.
containsSame(double[], double[]) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two double arrays contain the same items in any order (tolerance is ZERO)
containsSame(Object[], Object[]) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two object arrays contain the same items in any order.
containsSliceName(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
containsSliceName(S) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Check if the matrix contains a slice name
containsValidCharacter(String) - Static method in class ubic.basecode.util.StringUtil
Checks a string to find "strange" character, used by phenocarta to check evidence description
containsValue(Object) - Method in class ubic.basecode.dataStructure.CountingMap
convertDateToString(Date) - Static method in class ubic.basecode.util.DateUtil
This method generates a string representation of a date based on the System Property 'dateFormat' in the format
you specify on input
convertStringToDate(String, String) - Static method in class ubic.basecode.util.DateUtil
This method generates a string representation of a date/time in the format you specify on input
convertToLog2(DoubleMatrix<R, C>, double) - Static method in class ubic.basecode.math.MatrixStats
Convert a log_b-transformed data set to log 2.
convertToLog2Cpm(DoubleMatrix<R, C>, DoubleMatrix1D) - Static method in class ubic.basecode.math.MatrixStats
Convert a count matrix to log2 counts per million.
convertType(DatatypeProperty) - Static method in class ubic.basecode.ontology.model.PropertyFactory
copy() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
copy() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
copy() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
Create a deep copy of this
copy() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
copy() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
copy() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
copy(InputStream, OutputStream) - Static method in class ubic.basecode.util.FileTools
On completion streams are closed.
copyPlainOrCompressedFile(String, String) - Static method in class ubic.basecode.util.FileTools
correl(double[], double[]) - Static method in class ubic.basecode.math.CorrelationStats
Compute the Pearson correlation, missing values are permitted.
correlAsByte(double) - Static method in class ubic.basecode.math.CorrelationStats
correlation(double[], double[], double[], double[], boolean[], boolean[]) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Highly optimized version of the correlation computation, where as much information is precomputed as possible.
correlation(DoubleArrayList, double, DoubleArrayList, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the correlation of two data sequences.
correlation(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Calculate the pearson correlation of two arrays.
CorrelationEffectMetaAnalysis - Class in ubic.basecode.math.metaanalysis
Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of
Research Synthesis".
CorrelationEffectMetaAnalysis() - Constructor for class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
CorrelationEffectMetaAnalysis(boolean, boolean) - Constructor for class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
correlationForPvalue(double, int) - Static method in class ubic.basecode.math.CorrelationStats
Find the approximate Pearson correlation required to meet a particular pvalue.
correlationMatrix(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
Compute the correlation matrix of the rows of a matrix.
correlationMatrix(DoubleMatrix<R, C>, double) - Static method in class ubic.basecode.math.MatrixStats
correlationOfStandardized(double[], double[]) - Static method in class ubic.basecode.math.Distance
Highly optimized implementation of the Pearson correlation.
correlationOfStandardized(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.Distance
Like correlationofNormedFast, but takes DoubleArrayLists as inputs, handles missing values correctly, and does
more error checking.
CorrelationStats - Class in ubic.basecode.math
Statistical evaluation and transformation tools for correlations.
CorrelationStats() - Constructor for class ubic.basecode.math.CorrelationStats
correlationTstat(double, int) - Static method in class ubic.basecode.math.CorrelationStats
Compute the t-statistic associated with a Pearson correlation.
correlFast(double[], double[], double, double, double, double) - Static method in class ubic.basecode.math.CorrelationStats
Compute Pearson correlation when there are no missing values.
count(byte[]) - Static method in class ubic.basecode.dataStructure.BitUtil
count(K) - Method in class ubic.basecode.dataStructure.CountingMap
Returns the count associated with the specified key, or zero if the key has never been incremented.
CountingMap <K > - Class in ubic.basecode.dataStructure
Convenience Map that has a count as the value for each key.
CountingMap() - Constructor for class ubic.basecode.dataStructure.CountingMap
Constructs a CountingMap backed by a simple HashMap.
CountingMap(Map<K, Integer>) - Constructor for class ubic.basecode.dataStructure.CountingMap
Constructs a CountingMap backed by the specified Map.
cov2cor(DoubleMatrix2D) - Static method in class ubic.basecode.math.MatrixStats
Scale a covariance matrix to the corresponding correlation matrix.
covariance(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the SAMPLE covariance of two data sequences.
createColorPalette(int, Color[]) - Method in class ubic.basecode.graphics.ColorMap
Allocates colors across a range.
createDir(String) - Static method in class ubic.basecode.util.FileTools
Creates the directory if it does not exist.
createEmptyRow(int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
createMatrix(List<DoubleArrayList>, List<String>, List<String>) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
createRowKeys() - Method in class ubic.basecode.graphics.ColorMatrix
To be able to sort the rows by an arbitrary key.
CreateSpreadSheet - Class in ubic.basecode.io.excel
TODO Document Me
CreateSpreadSheet(String, SpreadSheetSchema) - Constructor for class ubic.basecode.io.excel.CreateSpreadSheet
csvSplit(String) - Static method in class ubic.basecode.util.StringUtil
cumulate(DoubleArrayList) - Static method in class ubic.basecode.math.Stats
Convert an array into a cumulative array.
cumulateRight(DoubleArrayList) - Static method in class ubic.basecode.math.Stats
Convert an array into a cumulative array.
CV - Static variable in class ubic.basecode.datafilter.RowLevelFilter
Use the coefficient of variation as the criterion
cv(DoubleArrayList) - Static method in class ubic.basecode.math.Stats
Compute the coefficient of variation of an array (standard deviation / mean).
cvs2tsv(String) - Static method in class ubic.basecode.util.StringUtil
Made by Nicolas
DARK_RED - Static variable in class ubic.basecode.graphics.ColorMap
DATA_EXTENSIONS - Static variable in class ubic.basecode.util.FileTools
dataFrame(ObjectMatrix<String, String, Object>) - Method in class ubic.basecode.util.r.AbstractRClient
dataFrame(ObjectMatrix<String, String, Object>) - Method in interface ubic.basecode.util.r.RClient
Convert an object matrix into an R data frame.
dataFrameEval(String) - Method in class ubic.basecode.util.r.AbstractRClient
dataFrameEval(String) - Method in interface ubic.basecode.util.r.RClient
Evaluate a command that returns a dataFrame
DataStatement - Interface in ubic.basecode.ontology.model
DatatypeProperty - Interface in ubic.basecode.ontology.model
DatatypePropertyImpl - Class in ubic.basecode.ontology.model
DatatypePropertyImpl(DatatypeProperty) - Constructor for class ubic.basecode.ontology.model.DatatypePropertyImpl
DateUtil - Class in ubic.basecode.util
Date Utility Class
DateUtil() - Constructor for class ubic.basecode.util.DateUtil
daxpy_j(int, double, double[], int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method multiplies a constant times a vector and adds the product
to another vector --- dy[ ] = da*dx[ ] + dy[ ].
dbinom(double, double, double) - Static method in class ubic.basecode.math.SpecFunc
See dbinom_raw.
dcopy_j(int, double[], int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method copies the vector dx[ ] to the vector dy[ ].
dcopyp_j(int, double[], double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method copies a portion of vector x[ ] to the corresponding
portion of vector y[ ].
ddot_j(int, double[], int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method calculates the dot product of two vectors.
DEFAULT_DATA_EXTENSION - Static variable in class ubic.basecode.util.FileTools
DEFAULT_IMAGE_EXTENSION - Static variable in class ubic.basecode.util.FileTools
DEFAULT_SEP - Static variable in class ubic.basecode.io.writer.MatrixWriter
DEFAULT_TOP_LEFT - Static variable in class ubic.basecode.io.writer.MatrixWriter
DEFAULT_XML_EXTENSION - Static variable in class ubic.basecode.util.FileTools
deleteDir(File) - Static method in class ubic.basecode.util.FileTools
Deletes the directory and subdirectories if empty.
deleteFiles(Collection<File>) - Static method in class ubic.basecode.util.FileTools
Deletes the specified Collection of files.
deleteLeaf(K) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
deleteOldCache(String) - Static method in class ubic.basecode.ontology.OntologyLoader
dense(double[][]) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
dense(DoubleMatrix<String, String>) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
Creates a matrix in which the underlying data is a copy; the row and column labels are not copied.
dense(int, int) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
DenseDouble3dMatrix <R ,C ,S > - Class in ubic.basecode.dataStructure.matrix
DenseDouble3dMatrix(double[][][]) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
DenseDouble3dMatrix(double[][][], List<S>, List<R>, List<C>) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
DenseDouble3dMatrix(int, int, int) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
DenseDouble3dMatrix(List<S>, List<R>, List<C>) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
DenseDoubleMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
A dense matrix of doubles that knows about row and column names.
DenseDoubleMatrix(double[][]) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
DenseDoubleMatrix(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
DenseDoubleMatrix1D - Class in ubic.basecode.dataStructure.matrix
Use this class when fast iteration over the matrix is of primary interest.
DenseDoubleMatrix1D(double[]) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix1D(int) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix1D(int, double[], int, int) - Constructor for class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D
DenseObject3DMatrix <R ,C ,S > - Class in ubic.basecode.dataStructure.matrix
DenseObject3DMatrix(int, int, int) - Constructor for class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
DenseObject3DMatrix(List<S>, List<R>, List<C>) - Constructor for class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
DenseObject3DMatrix(Object[][][]) - Constructor for class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
DenseObject3DMatrix(Object[][][], List<S>, List<R>, List<C>) - Constructor for class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
density(double) - Method in interface ubic.basecode.math.distribution.DensityGenerator
density(double) - Method in class ubic.basecode.math.distribution.UniformDensityComputer
DensityGenerator - Interface in ubic.basecode.math.distribution
An interface that describes a class that can produce values from a particular probability density.
DescriptiveWithMissing - Class in ubic.basecode.math
Mathematical functions for statistics that allow missing values without scotching the calculations.
DesignMatrix - Class in ubic.basecode.math.linearmodels
Represents the A matrix in regression problems posed as Ax=b.
DesignMatrix(Object[], int, String) - Constructor for class ubic.basecode.math.linearmodels.DesignMatrix
DesignMatrix(ObjectMatrix<String, String, ? extends Object>) - Constructor for class ubic.basecode.math.linearmodels.DesignMatrix
DesignMatrix(ObjectMatrix<String, String, ?>, boolean) - Constructor for class ubic.basecode.math.linearmodels.DesignMatrix
DesignMatrix(StringMatrix<String, String>) - Constructor for class ubic.basecode.math.linearmodels.DesignMatrix
DesignMatrix(ObjectMatrix<String, String, Object>, boolean, boolean) - Constructor for class ubic.basecode.math.linearmodels.DesignMatrix
dhyper(int, int, int, int) - Static method in class ubic.basecode.math.SpecFunc
Ported from R (Catherine Loader)
DESCRIPTION
Given a sequence of r successes and b failures, we sample n (\le b+r) items without replacement.
diagnose() - Method in class ubic.basecode.math.linalg.QRDecomposition
diagonal(DoubleMatrix2D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
Extract the diagonal from a matrix.
DirectedGraph <K ,V > - Class in ubic.basecode.dataStructure.graph
A graph that contains DirectedGraphNodes.
DirectedGraph() - Constructor for class ubic.basecode.dataStructure.graph.DirectedGraph
DirectedGraphNode <K ,V > - Class in ubic.basecode.dataStructure.graph
A graph node that has the concept of parents and children.
DirectedGraphNode(K, V, DirectedGraph<K, V>) - Constructor for class ubic.basecode.dataStructure.graph.DirectedGraphNode
Dirichlet - Class in ubic.basecode.math.distribution
Dirichlet(DoubleArrayList, RandomEngine) - Constructor for class ubic.basecode.math.distribution.Dirichlet
disconnect() - Method in class ubic.basecode.util.r.AbstractRClient
disconnect() - Method in class ubic.basecode.util.r.JRIClient
disconnect() - Method in class ubic.basecode.util.r.RServeClient
DiseaseOntologyService - Class in ubic.basecode.ontology.providers
Holds a copy of the Disease Ontology.
DiseaseOntologyService() - Constructor for class ubic.basecode.ontology.providers.DiseaseOntologyService
displayMax - Variable in class ubic.basecode.graphics.ColorMatrix
displayMin - Variable in class ubic.basecode.graphics.ColorMatrix
Min and max values to display, which might not be the actual min and max values in the matrix.
Distance - Class in ubic.basecode.math
Alternative distance and similarity metrics for vectors.
Distance() - Constructor for class ubic.basecode.math.Distance
dnrm2_j(int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method calculates the Euclidean norm of the vector
stored in dx[ ] with storage increment incx.
dnrm2p_j(int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method calculates the Euclidean norm of a portion
of a vector x[ ].
dof(DoubleArrayList, IntArrayList) - Static method in class ubic.basecode.math.KruskalWallis
DOID_ONTOLOGY - Static variable in class ubic.basecode.ontology.ncbo.AnnotatorClient
DoubleAddingMap <K > - Class in ubic.basecode.dataStructure
Similar to ubic.gemma.util.CountingMap.
DoubleAddingMap() - Constructor for class ubic.basecode.dataStructure.DoubleAddingMap
doubleArrayDoubleArrayEval(String, String, double[]) - Method in class ubic.basecode.util.r.AbstractRClient
doubleArrayDoubleArrayEval(String, String, double[]) - Method in interface ubic.basecode.util.r.RClient
Run a command that has a single double array parameter, and returns a double array.
doubleArrayEval(String) - Method in class ubic.basecode.util.r.AbstractRClient
doubleArrayEval(String) - Method in interface ubic.basecode.util.r.RClient
Run a command that returns a double array with no arguments.
doubleArrayToBytes(double[]) - Method in class ubic.basecode.io.ByteArrayConverter
doubleArrayToBytes(Double[]) - Method in class ubic.basecode.io.ByteArrayConverter
doubleArrayToBytes(DoubleArrayList) - Method in class ubic.basecode.io.ByteArrayConverter
doubleArrayToString(double[]) - Method in class ubic.basecode.io.StringConverter
Convert a double array to a delimited string.
doubleArrayTwoDoubleArrayEval(String, String, double[], String, double[]) - Method in class ubic.basecode.util.r.AbstractRClient
doubleArrayTwoDoubleArrayEval(String, String, double[], String, double[]) - Method in interface ubic.basecode.util.r.RClient
Run a command that takes two double array arguments and returns a double array.
DoubleMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
Abstract base class for 2D matrices of double values with named columns and rows.
DoubleMatrix() - Constructor for class ubic.basecode.dataStructure.matrix.DoubleMatrix
DoubleMatrix3D <R ,C ,S > - Class in ubic.basecode.dataStructure.matrix
TODO Document Me
DoubleMatrix3D() - Constructor for class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
DoubleMatrixFactory - Class in ubic.basecode.dataStructure.matrix
Use this factory to create matrices of type selected at runtime (String parameterization only)
DoubleMatrixFactory() - Constructor for class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
DoubleMatrixReader - Class in ubic.basecode.io.reader
Reader for basecode.dataStructure.matrix.DoubleMatrix
.
DoubleMatrixReader() - Constructor for class ubic.basecode.io.reader.DoubleMatrixReader
doubleMatrixToBytes(double[][]) - Method in class ubic.basecode.io.ByteArrayConverter
DoublePoint - Class in ubic.basecode.dataStructure
DoublePoint(double, double) - Constructor for class ubic.basecode.dataStructure.DoublePoint
doubleStandardize(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
Iteratively standardize the columns and rows of the matrix.
doubleTwoDoubleArrayEval(String, String, double[], String, double[]) - Method in class ubic.basecode.util.r.AbstractRClient
doubleTwoDoubleArrayEval(String, String, double[], String, double[]) - Method in interface ubic.basecode.util.r.RClient
Run a command that takes two double arrays as arguments and returns a double value.
dqrdc_j(double[][], int, int, double[], int[], int) - Static method in class ubic.basecode.math.linalg.Dqrsl
This method decomposes an n by p matrix X into a product, QR, of
an orthogonal n by n matrix Q and an upper triangular n by p matrix R.
Dqrsl - Class in ubic.basecode.math.linalg
This class contains the LINPACK DQRDC (QR decomposition)
and DQRSL (QR solve) routines.
Dqrsl() - Constructor for class ubic.basecode.math.linalg.Dqrsl
dqrsl_j(double[][], int, int, double[], double[], double[], double[], double[], double[], double[], int) - Static method in class ubic.basecode.math.linalg.Dqrsl
This method "applies the output of DQRDC to compute coordinate
transformations, projections, and least squares solutions."
drawColumnNames(Graphics, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
Draws column names vertically (turned 90 degrees counter-clockwise)
drawMatrix(ColorMatrix<R, C>, Graphics, boolean, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
Gets called from #paintComponent and #saveImage.
drawRowNames(Graphics, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
Draws row names (horizontally)
draws(int) - Method in class ubic.basecode.math.distribution.Dirichlet
drawScaleBar(Graphics, Dimension, double, double) - Method in class ubic.basecode.graphics.MatrixDisplay
drawVerticalString(Graphics, String, Font, int, int) - Static method in class ubic.basecode.graphics.text.Util
Draws a string vertically, turned 90 degrees counter-clockwise.
dropColumn(DoubleMatrix2D, int) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
dropColumns(DoubleMatrix2D, Collection<Integer>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
drotg_j(double[]) - Static method in class ubic.basecode.math.linalg.Blas
This method constructs a Givens plane rotation.
dscal_j(int, double, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method scales a vector by a constant.
dscalp_j(int, double, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method scales a portion of a vector by a constant.
dswap_j(int, double[], int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method interchanges two vectors.
dtm - Variable in class ubic.basecode.dataStructure.graph.DirectedGraph
durbinWatson(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Durbin-Watson computation.
F - Static variable in class ubic.basecode.datafilter.AffymetrixProbeNameFilter
Filter probes that have the "_f_at" (family) tag.
fastrow(double[][]) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
fastrow(int, int) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
FastRowAccessDoubleMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
Dense 2D matrix implementation designed for very fast access of entire rows.
FastRowAccessDoubleMatrix(double[][]) - Constructor for class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
Implementation note: The input matrix is NOT COPIED (due to the way colt DoubleArrayList(double[]) is
implemented).F
FastRowAccessDoubleMatrix(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
filename - Variable in class ubic.basecode.io.excel.CreateSpreadSheet
FileTools - Class in ubic.basecode.util
FileTools() - Constructor for class ubic.basecode.util.FileTools
fill(double) - Method in class ubic.basecode.math.distribution.Histogram
Fill the histogram with x.
fill(DoubleMatrix1D) - Method in class ubic.basecode.math.distribution.Histogram
fill(int, int) - Method in class ubic.basecode.math.distribution.Histogram
Add the given number of counts to the given bin.
fillRange(int, int) - Static method in class ubic.basecode.math.MathUtil
Create an array filled with the integer values from a to b, inclusive.
filter(M) - Method in class ubic.basecode.datafilter.AffymetrixProbeNameFilter
Filter <M extends Matrix2D <R ,C ,V >,R ,C ,V > - Interface in ubic.basecode.datafilter
An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented
criteria.
filter(M) - Method in interface ubic.basecode.datafilter.Filter
Filter the data
filter(DoubleMatrix<R, C>) - Method in class ubic.basecode.datafilter.ItemLevelFilter
filter(M) - Method in class ubic.basecode.datafilter.RowAbsentFilter
The data is going to be filtered in accordance to strings in 'flags'.
filter(DoubleMatrix<R, C>) - Method in class ubic.basecode.datafilter.RowLevelFilter
filter(M) - Method in class ubic.basecode.datafilter.RowMissingFilter
filter(M) - Method in class ubic.basecode.datafilter.RowNameFilter
Filter according to row names.
finalize() - Method in class ubic.basecode.util.r.RServeClient
findCondition(boolean) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
findIndividuals(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
findIndividuals(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
Looks for any OntologyIndividuals that match the given search string.
findLabelForIdentifier(String, String) - Static method in class ubic.basecode.ontology.ncbo.AnnotatorClient
return the label associated with an conceptid.
findLinkedPublications(Collection<Long>, Map<Long, Collection<Long>>) - Static method in class ubic.basecode.ontology.ncbo.OmimAnnotatorClient
Giving a set of OMIM id return for each id its list of related publication
findResources(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
findResources(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
Looks for any OntologyIndividuals or ontologyTerms that match the given search string
findRserveCommand() - Static method in class ubic.basecode.util.r.RServeClient
findTerm(String) - Static method in class ubic.basecode.ontology.ncbo.AnnotatorClient
findTerm(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
findTerm(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
Looks for any ontologyTerms that match the given search string.
findUsingAlternativeId(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
findUsingAlternativeId(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
fisherCombineLogPvalues(DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
Fisher's method for combining p values (Cooper and Hedges 15-8)
Use for p values that have already been log transformed.
fisherCombinePvalues(DoubleArrayList) - Static method in class ubic.basecode.math.metaanalysis.MetaAnalysis
Fisher's method for combining p values.
fisherTransform(double) - Static method in class ubic.basecode.math.CorrelationStats
Compute the Fisher z transform of the Pearson correlation.
fisherTransform(DoubleArrayList) - Static method in class ubic.basecode.math.CorrelationStats
Fisher-transform a list of Pearson correlations.
fisherTransformedSamplingVariance(double) - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
Equation 18-8 from CH.
fisherTransformedSamplingVariances(DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
Run equation CH 18-8 on a list of sample sizes.
fitFDist(DoubleMatrix1D, DoubleMatrix1D) - Static method in class ubic.basecode.math.linearmodels.ModeratedTstat
FMAOntologyService - Class in ubic.basecode.ontology.providers
Holds a copy of the FMA Ontology on disk.
FMAOntologyService() - Constructor for class ubic.basecode.ontology.providers.FMAOntologyService
formatter - Variable in class ubic.basecode.io.writer.MatrixWriter
fractionDistinctValuesNonNA(DoubleArrayList, double) - Static method in class ubic.basecode.math.Stats
Compute the fraction of values which are distinct.
fromList(DoubleArrayList) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
Makes a copy
ftpDownloadFile(FTPClient, String, File, boolean) - Static method in class ubic.basecode.util.NetUtils
ftpDownloadFile(FTPClient, String, String, boolean) - Static method in class ubic.basecode.util.NetUtils
ftpFileSize(FTPClient, String) - Static method in class ubic.basecode.util.NetUtils
Get the size of a remote file.
G - Static variable in class ubic.basecode.datafilter.AffymetrixProbeNameFilter
Filter probes that have the "_g_at" (group) tag.
GenericAnovaResult - Class in ubic.basecode.math.linearmodels
A generic representation of an R-style ANOVA table, including interactions.
GenericAnovaResult(Collection<AnovaEffect>) - Constructor for class ubic.basecode.math.linearmodels.GenericAnovaResult
GenericAnovaResult(REXP) - Constructor for class ubic.basecode.math.linearmodels.GenericAnovaResult
GenericOntologyService - Class in ubic.basecode.ontology.providers
A way to create ad hoc ontology services (in memory) for testing
GenericOntologyService(String, String) - Constructor for class ubic.basecode.ontology.providers.GenericOntologyService
GenericOntologyService(String, String, boolean) - Constructor for class ubic.basecode.ontology.providers.GenericOntologyService
GenericStreamConsumer - Class in ubic.basecode.util
See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
GenericStreamConsumer(InputStream) - Constructor for class ubic.basecode.util.GenericStreamConsumer
geometricMean(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the geometric mean of a data sequence.
get(byte[], int) - Static method in class ubic.basecode.dataStructure.BitUtil
Check to see if the specified bit is set
get(Object) - Method in class ubic.basecode.dataStructure.CountingMap
get() - Method in class ubic.basecode.dataStructure.DoublePoint
get(K) - Method in class ubic.basecode.dataStructure.graph.AbstractGraph
Retrieve a node by key.
get(K) - Method in interface ubic.basecode.dataStructure.graph.Graph
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
get(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
Checks the bit of the specified cell at the specified index.
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
get(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
get(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
get(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
get(int, int) - Method in interface ubic.basecode.dataStructure.matrix.ObjectMatrix
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
get(R, C) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
get(int) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
get(int, int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
get(R, C) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
get() - Method in class ubic.basecode.dataStructure.Point
getAdjRSquared() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getAllBits(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
Returns all of the bits for a cell
getAllChildNodes() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Get all the children of this node, recursively.
getAllParentNodes() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Get all the parents of this node, recursively.
getAllURIs() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
getAllURIs() - Method in interface ubic.basecode.ontology.providers.OntologyService
getAlternative() - Method in class ubic.basecode.util.r.type.HTest
getAlternativeIds() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getAlternativeIds() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getAlternativeIds() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getAnnotations() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getAnnotations() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getAnnotations() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getAnova() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getApproximateQuantile(int) - Method in class ubic.basecode.math.distribution.Histogram
Find the bin below which i% of the values are contained.
getArray() - Method in class ubic.basecode.math.distribution.Histogram
Returns the bin heights.
getAssign() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getBaseline(String) - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getBiggestBinSize() - Method in class ubic.basecode.math.distribution.Histogram
getBinEdges() - Method in class ubic.basecode.math.distribution.Histogram
getBinEdgesStrings() - Method in class ubic.basecode.math.distribution.Histogram
getBinOf(double) - Method in class ubic.basecode.math.distribution.Histogram
getBitNum() - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
Returns the total number of bits in a matrix cell
getBoolean(String) - Static method in class ubic.basecode.util.Configuration
getBsv() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getBsv() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
getByKeys(R, C) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
getByKeys(R, C) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getByKeys(R, C) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getByKeys(R, C) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
getByKeys(R, C) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
getByKeys(R, C) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
getCardinality() - Method in interface ubic.basecode.ontology.model.OntologyCardinalityRestriction
getCardinality() - Method in class ubic.basecode.ontology.model.OntologyCardinalityRestrictionImpl
getCardinalityType() - Method in interface ubic.basecode.ontology.model.OntologyCardinalityRestriction
getCardinalityType() - Method in class ubic.basecode.ontology.model.OntologyCardinalityRestrictionImpl
getCause() - Method in exception ubic.basecode.ontology.search.OntologySearchJenaException
getChildCount() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
getChildGraph() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Get the subgraph starting from this node, including this node.
getChildKeys() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
getChildNodes() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Get the immediate children of this node.
getChildren(boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm
getChildren(boolean, boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm
getChildren(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getChildren(boolean, boolean) - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getChildren(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getCoefficients() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
The matrix of coefficients x for Ax = b (parameter estimates).
getCoefficients() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getCol(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
getColByName(C) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
Return a copy of a given column.
getColIndexByName(C) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getColIndexByName(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getColIndexByName(C) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Get the index of a column by name.
getColIndexByName(C) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get the index of a column by name.
getColName(int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getColName(int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getColName(int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Gte the column name for an index.
getColName(int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get the column name for an index.
getColNameIterator() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getColNameIterator() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getColNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getColNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getColNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
getColNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getColObj(int) - Method in interface ubic.basecode.dataStructure.matrix.PrimitiveMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getColObj(int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
getColor(int) - Method in class ubic.basecode.graphics.ColorMap
getColor(int, int) - Method in class ubic.basecode.graphics.ColorMatrix
getColor(int, int) - Method in class ubic.basecode.graphics.MatrixDisplay
getColorMap() - Method in class ubic.basecode.graphics.ColorMatrix
getColorMap() - Method in class ubic.basecode.graphics.MatrixDisplay
getColorMatrix() - Method in class ubic.basecode.graphics.MatrixDisplay
getColors() - Method in class ubic.basecode.graphics.ColorMatrix
getColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
getColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getColRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getColumn(int) - Method in interface ubic.basecode.dataStructure.matrix.ObjectMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getColumn(int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
getColumnByName(C) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getColumnByName(C) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getColumnCount() - Method in class ubic.basecode.graphics.ColorMatrix
getColumnCount() - Method in class ubic.basecode.graphics.MatrixDisplay
getColumnName(int) - Method in class ubic.basecode.graphics.ColorMatrix
getColumnName(int) - Method in class ubic.basecode.graphics.MatrixDisplay
getColumnNames() - Method in class ubic.basecode.graphics.ColorMatrix
getColumnNames() - Method in class ubic.basecode.graphics.MatrixDisplay
getComment() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getComment() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getComment() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getConfigBuilder(File) - Static method in class ubic.basecode.util.ConfigUtils
getConfigBuilder(String) - Static method in class ubic.basecode.util.ConfigUtils
getConfigBuilder(URL) - Static method in class ubic.basecode.util.ConfigUtils
getContents() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
getContents() - Method in interface ubic.basecode.ontology.model.AnnotationProperty
getContents() - Method in class ubic.basecode.ontology.model.AnnotationPropertyImpl
getContrastCoefficients() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getContrastCoefficients(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getContrastCoefficientStderr(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
For the requested factor, return the standard errors associated with the contrast coefficient estimates.
getContrastPValues(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getContrastTStats(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getDataname() - Method in class ubic.basecode.util.r.type.HTest
getDateTime(String, Date) - Static method in class ubic.basecode.util.DateUtil
This method generates a string representation of a date's date/time in the format you specify on input
getDegreesOfFreedom() - Method in class ubic.basecode.util.r.type.AnovaEffect
getDf() - Method in class ubic.basecode.util.r.type.OneWayAnovaResult
getDfPrior() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getDiskCachePath(String) - Static method in class ubic.basecode.ontology.OntologyLoader
getDisplayMax() - Method in class ubic.basecode.graphics.ColorMatrix
getDisplayMax() - Method in class ubic.basecode.graphics.MatrixDisplay
getDisplayMin() - Method in class ubic.basecode.graphics.ColorMatrix
getDisplayMin() - Method in class ubic.basecode.graphics.MatrixDisplay
getDisplayRange() - Method in class ubic.basecode.graphics.MatrixDisplay
getDoubleMatrix() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getE() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getE() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
getEffectName() - Method in class ubic.basecode.util.r.type.AnovaEffect
getEffects() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getEntry(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
getEntry(int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getEntry(int, int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getEntry(int, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
getEntry(int, int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
getEntry(int, int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
getEstimate() - Method in class ubic.basecode.util.r.type.HTest
getExpandedSize() - Method in class ubic.basecode.dataStructure.StringToStringSetMap
getExpandedValues() - Method in class ubic.basecode.dataStructure.StringToStringSetMap
getExtension(String) - Static method in class ubic.basecode.util.FileTools
Returns the extension of a file.
getF() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getFactorAName() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getFactorBName() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getFactorName() - Method in class ubic.basecode.util.r.type.OneWayAnovaResult
getFactorNames() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getFactorValueNames(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
Return the factor names in the order they are stored here.
getFirstAttemptCause() - Method in exception ubic.basecode.ontology.search.RetryWithoutWildcardFailedException
Obtain the cause or error for the first attempt.
getFitted() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getFormula() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getFStatistic() - Method in class ubic.basecode.util.r.type.AnovaEffect
getFVal() - Method in class ubic.basecode.util.r.type.OneWayAnovaResult
getGraph() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
getGraph() - Method in interface ubic.basecode.dataStructure.graph.GraphNode
getGraph() - Method in class ubic.basecode.dataStructure.graph.UndirectedGraphNode
getHeaderRow() - Method in class ubic.basecode.io.excel.SpreadSheetSchema
getIndexFrom() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getIndexTo() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getIndividuals() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getIndividuals(boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm
getIndividuals() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getIndividuals(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getIndividuals() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getIndividuals(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getInputStreamFromPlainOrCompressedFile(String) - Static method in class ubic.basecode.util.FileTools
Open a non-compresed, zipped, or gzipped file.
getInstanceOf() - Method in interface ubic.basecode.ontology.model.OntologyIndividual
Return the term that this is an instance of.
getInstanceOf() - Method in class ubic.basecode.ontology.model.OntologyIndividualImpl
getInteractionDf() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getInteractionEffectF() - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getInteractionEffectP() - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getInteractionEffectP(String...) - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getInteractionEffectP(String...) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getInteractionfVal() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getInteractionPval() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getInteractionTerms() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getInterceptCoeff() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getInterceptP() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getInterceptT() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getItem() - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode
Get the actual contents of the node.
getItem() - Method in interface ubic.basecode.dataStructure.graph.GraphNode
getItems() - Method in class ubic.basecode.dataStructure.graph.AbstractGraph
getItems() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
getKey() - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode
Get the key for the node.
getKey() - Method in interface ubic.basecode.dataStructure.graph.GraphNode
getKey() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getKey() - Method in class ubic.basecode.util.r.type.AnovaResult
getLabel() - Method in class ubic.basecode.ontology.model.DatatypePropertyImpl
getLabel() - Method in class ubic.basecode.ontology.model.ObjectPropertyImpl
getLabel() - Method in class ubic.basecode.ontology.model.OntologyIndividualImpl
getLabel() - Method in interface ubic.basecode.ontology.model.OntologyResource
getLabel() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getLabel() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getLastError() - Method in class ubic.basecode.util.r.JRIClient
getLastError() - Method in interface ubic.basecode.util.r.RClient
getLastError() - Method in class ubic.basecode.util.r.RServeClient
getLeft() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
getLevelsForFactors() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getLibrarySize() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimator
getLines(File) - Static method in class ubic.basecode.util.FileTools
opens a file and returns its contents as a list of lines.
getLines(String) - Static method in class ubic.basecode.util.FileTools
opens a file and returns its contents as a list of lines.
getLocalName() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getLocalName() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getLocalName() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getLoess() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimator
getMainEffectADf() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getMainEffectAfVal() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getMainEffectAPval() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getMainEffectBDf() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getMainEffectBfVal() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getMainEffectBPval() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
getMainEffectDof(String) - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getMainEffectF(String) - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getMainEffectFactorNames() - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getMainEffectFactorNames() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getMainEffectP(String) - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult
getMainEffectP(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getMatchType() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getMatrix() - Method in class ubic.basecode.graphics.ColorMatrix
getMatrix() - Method in class ubic.basecode.graphics.MatrixDisplay
getMatrix() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getMax() - Method in class ubic.basecode.graphics.ColorMatrix
getMax() - Method in class ubic.basecode.graphics.MatrixDisplay
getMaxColumnLength() - Method in class ubic.basecode.graphics.MatrixDisplay
getMaxtrix() - Method in class ubic.basecode.graphics.ColorMatrix
getMeanSq() - Method in class ubic.basecode.util.r.type.AnovaEffect
getMeanVariance() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimator
getMethod() - Method in class ubic.basecode.util.r.type.HTest
getMin() - Method in class ubic.basecode.graphics.ColorMatrix
getMin() - Method in class ubic.basecode.graphics.MatrixDisplay
getMissingColor() - Method in class ubic.basecode.graphics.ColorMatrix
getMissingColor() - Method in class ubic.basecode.graphics.MatrixDisplay
getModel() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getModel() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getModel() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getN() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getN() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
getName() - Method in class ubic.basecode.math.distribution.Histogram
The name of the histogram.
getNodeContents(K) - Method in class ubic.basecode.dataStructure.graph.AbstractGraph
Retrieve the contents of a node by key.
getNodeContents(K) - Method in interface ubic.basecode.dataStructure.graph.Graph
getNormalizedValue() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimator
getNullvalue() - Method in class ubic.basecode.util.r.type.HTest
getNumeratorDof() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getObject(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
Converts to a String that can be read by read.table in R, using default parameters
getObject(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getObject(int, int, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getObject(Matrix2D<R, C, V>, int, int) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
getObject(int, int) - Method in interface ubic.basecode.dataStructure.matrix.PrimitiveMatrix
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
getObject() - Method in interface ubic.basecode.ontology.model.CharacteristicStatement
getObject() - Method in interface ubic.basecode.ontology.model.ClassStatement
getObject() - Method in interface ubic.basecode.ontology.model.DataStatement
getObject() - Method in interface ubic.basecode.ontology.model.InstanceStatement
getObject() - Method in class ubic.basecode.ontology.search.IndexerSelector
getOntologyName() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
The simple getOntologyName() of the ontology.
getOntologyName() - Method in class ubic.basecode.ontology.providers.CellLineOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.CellTypeOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.ChebiOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.DiseaseOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.ExperimentalFactorOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.FMAOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.GenericOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.HumanDevelopmentOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.HumanPhenotypeOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.MammalianPhenotypeOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.MedicOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.MouseDevelopmentOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.NIFSTDOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.ObiService
getOntologyName() - Method in class ubic.basecode.ontology.providers.SequenceOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.UberonOntologyService
getOntologyName() - Method in class ubic.basecode.ontology.providers.UnitsOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
Defines the location of the ontology eg:
MGED
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.CellLineOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.CellTypeOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.ChebiOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.DiseaseOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.ExperimentalFactorOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.FMAOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.GenericOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.HumanDevelopmentOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.HumanPhenotypeOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.MammalianPhenotypeOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.MedicOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.MouseDevelopmentOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.NIFSTDOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.ObiService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.SequenceOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.UberonOntologyService
getOntologyUrl() - Method in class ubic.basecode.ontology.providers.UnitsOntologyService
getOntologyUsed() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getOutputMatrix(M, int, int) - Method in class ubic.basecode.datafilter.AbstractFilter
getP() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
Overall p value for F stat of model fit (upper tail probability)
getP() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getP() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
getPalette() - Method in class ubic.basecode.graphics.ColorMap
getPaletteSize() - Method in class ubic.basecode.graphics.ColorMap
getParameter() - Method in class ubic.basecode.util.r.type.HTest
getParams(Class<?>, Object) - Static method in class ubic.basecode.dataStructure.params.ParameterGrabber
Given an instance of a class this method will extract its primitive variable names and their values using
reflection.
getParentKeys() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
getParentNodes() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Get the immediate parents of this node.
getParents(boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm
Note that any restriction superclasses are not returned, unless they are has_proper_part
getParents(boolean, boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm
getParents(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getParents(boolean, boolean) - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getParents(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getPivotOrder() - Method in class ubic.basecode.math.linalg.QRDecomposition
getPosition(String) - Method in class ubic.basecode.io.excel.SpreadSheetSchema
getPredicate() - Method in class ubic.basecode.ontology.search.IndexerSelector
getPriorDof() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getProperty() - Method in interface ubic.basecode.ontology.model.AnnotationProperty
getProperty() - Method in class ubic.basecode.ontology.model.AnnotationPropertyImpl
getProperty() - Method in interface ubic.basecode.ontology.model.CharacteristicStatement
getPval() - Method in class ubic.basecode.util.r.type.OneWayAnovaResult
getPValue() - Method in class ubic.basecode.util.r.type.AnovaEffect
getPvalue() - Method in class ubic.basecode.util.r.type.HTest
getQ() - Method in class ubic.basecode.math.linalg.QRDecomposition
Generates and returns the (economy-sized - first p columns only) orthogonal factor Q .
getQ() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getQ() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
getQR() - Method in class ubic.basecode.math.linalg.QRDecomposition
For testing.
getQraux() - Method in class ubic.basecode.math.linalg.QRDecomposition
getQuery() - Method in exception ubic.basecode.ontology.search.OntologySearchException
getQuick(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D
This is an optimized version of getQuick.
getQuick(int) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
getR() - Method in class ubic.basecode.math.linalg.QRDecomposition
Returns the upper triangular factor, R .
getRange() - Method in interface ubic.basecode.ontology.model.ObjectProperty
getRange() - Method in class ubic.basecode.ontology.model.ObjectPropertyImpl
getRank() - Method in class ubic.basecode.math.linalg.QRDecomposition
getRawMatrix() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getRawValue(int, int) - Method in class ubic.basecode.graphics.MatrixDisplay
getRConnection() - Static method in class ubic.basecode.util.r.RConnectionFactory
Get connection; if Rserve is used, connect to localhost.
getRConnection(String) - Static method in class ubic.basecode.util.r.RConnectionFactory
getRelativeDate(Date, String) - Static method in class ubic.basecode.util.DateUtil
Turn a string like '-7d' into the date equivalent to "seven days ago".
getResidualDf() - Method in class ubic.basecode.util.r.type.AnovaResult
getResidualDof() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getResidualDof() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getResidualDofs() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getResiduals() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getResiduals() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getResource(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
getResource(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given.
getRestrictedTo() - Method in interface ubic.basecode.ontology.model.OntologyClassRestriction
getRestrictedTo() - Method in class ubic.basecode.ontology.model.OntologyClassRestrictionImpl
getRestrictedTo() - Method in interface ubic.basecode.ontology.model.OntologyDatatypeRestriction
getRestrictedTo() - Method in class ubic.basecode.ontology.model.OntologyDatatypeRestrictionImpl
getRestrictionOn() - Method in interface ubic.basecode.ontology.model.OntologyRestriction
getRestrictionOn() - Method in class ubic.basecode.ontology.model.OntologyRestrictionImpl
getRestrictions() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getRestrictions() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getRestrictions() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getRight() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
getRoot() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
getRoot() - Method in class ubic.basecode.dataStructure.tree.BinaryTree
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
Return a reference to a specific row.
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
Return a reference to a specific row.
getRow(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getRow(Matrix2D<R, C, V>, int) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
getRow(int) - Method in interface ubic.basecode.dataStructure.matrix.ObjectMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
Return a reference to a specific row.
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getRow(int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
getRow(int) - Method in class ubic.basecode.graphics.ColorMatrix
getRow(int) - Method in class ubic.basecode.graphics.MatrixDisplay
getRowArrayList(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getRowArrayList(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
getRowArrayList(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getRowArrayList(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getRowArrayList(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getRowArrayList(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
This gives just the list of values in the row - make sure this is what you want.
getRowBitCount(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
getRowByName(R) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getRowByName(R) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
Return a reference to a specific row.
getRowByName(R) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getRowByName(R) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getRowByName(R) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getRowByName(A) - Method in class ubic.basecode.graphics.ColorMatrix
getRowByName(R) - Method in class ubic.basecode.graphics.MatrixDisplay
getRowCount() - Method in class ubic.basecode.graphics.ColorMatrix
getRowCount() - Method in class ubic.basecode.graphics.MatrixDisplay
getRowHeight() - Method in class ubic.basecode.graphics.MatrixDisplay
getRowIndexByName(R) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getRowIndexByName(R) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getRowIndexByName(R) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Get the index of a row by name..
getRowIndexByName(R) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get the index of a row by name.
getRowIndexByName(A) - Method in class ubic.basecode.graphics.ColorMatrix
getRowIndexByName(R) - Method in class ubic.basecode.graphics.MatrixDisplay
getRowName(int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getRowName(int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getRowName(int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Get the row name for an index
getRowName(int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get the row name for an index
getRowName(int) - Method in class ubic.basecode.graphics.ColorMatrix
getRowName(int) - Method in class ubic.basecode.graphics.MatrixDisplay
getRowNameIterator() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getRowNameIterator() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getRowNameMapIterator() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getRowNameMapIterator() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
getRowNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
getRowNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getRowNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
getRowNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getRowNames() - Method in class ubic.basecode.graphics.ColorMatrix
getRowNames() - Method in class ubic.basecode.graphics.MatrixDisplay
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
getRowObj(int) - Method in interface ubic.basecode.dataStructure.matrix.PrimitiveMatrix
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getRowObj(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
getRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
getRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
getRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
getRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
getRowRange(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
getRSquared() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
getS() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition
getSearchQueryUsed() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getSeenValues() - Method in class ubic.basecode.dataStructure.StringToStringSetMap
getSheetFromFile(String, String) - Static method in class ubic.basecode.io.excel.ExcelUtil
getSigma() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
Residual standard deviation
getSingularValues() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition
getSize(String) - Method in class ubic.basecode.dataStructure.StringToStringSetMap
getSlice(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getSlice(int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
getSlice(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getSliceByName(S) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getSliceIndexByName(S) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getSliceIndexByName(S) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get a slice index
getSliceName(int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getSliceName(int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get a slice name
getSliceNameIterator() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getSliceNameIterator() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getSliceNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
getSliceNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
getSliceObj(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
getSliceObj(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
getSsQ() - Method in class ubic.basecode.util.r.type.AnovaEffect
getStandardizedEnabled() - Method in class ubic.basecode.graphics.MatrixDisplay
getStatistic() - Method in class ubic.basecode.util.r.type.HTest
getStdevUnscaled() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
Unscaled standard deviations for the coefficient estimators in same order as coefficients.
getStepSize(int, int, int) - Method in class ubic.basecode.graphics.ColorMap
Calculate how fast we have to change color components.
getString(String) - Static method in class ubic.basecode.util.Configuration
getStringListFromFile(File) - Static method in class ubic.basecode.util.FileTools
Used for reading output generated by Collection.toString().
getStudentizedResiduals() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getSubject() - Method in interface ubic.basecode.ontology.model.CharacteristicStatement
getSubject() - Method in class ubic.basecode.ontology.search.IndexerSelector
getSubjectIndex(String) - Static method in class ubic.basecode.ontology.search.OntologyIndexer
getTerm() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getTerm() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getTerm() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getTerm(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
getTerm(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
Looks for a OntologyTerm that has the match in URI given
getTermIndividuals(String) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
getTermIndividuals(String) - Method in interface ubic.basecode.ontology.providers.OntologyService
getTerms() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getTodayDate(boolean) - Static method in class ubic.basecode.util.DateUtil
return today date as a String
getTolerance() - Method in class ubic.basecode.math.linalg.QRDecomposition
getTopoSortOrder() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
getTreeModel() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
getTrueRowIndex(int) - Method in class ubic.basecode.graphics.ColorMatrix
getTxtMatched() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getType() - Method in interface ubic.basecode.ontology.model.DatatypeProperty
getType() - Method in class ubic.basecode.ontology.model.DatatypePropertyImpl
getU() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition
getUri() - Method in class ubic.basecode.ontology.model.AbstractOntologyResource
getUri() - Method in class ubic.basecode.ontology.model.DatatypePropertyImpl
getUri() - Method in class ubic.basecode.ontology.model.ObjectPropertyImpl
getUri() - Method in class ubic.basecode.ontology.model.OntologyIndividualImpl
getUri() - Method in interface ubic.basecode.ontology.model.OntologyResource
getUri() - Method in interface ubic.basecode.ontology.model.OntologyTerm
getUri() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
getUri() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
getV() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition
getV() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getV() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
getValue(int, int) - Method in class ubic.basecode.graphics.ColorMatrix
getValue(int, int) - Method in class ubic.basecode.graphics.MatrixDisplay
getValue(HSSFSheet, int, int) - Static method in class ubic.basecode.io.excel.ExcelUtil
getValues() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
Get all the values in thee graph.
getValuesForFactors() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
getValueUri() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
getVarPost() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getVarPrior() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getWeight() - Method in class ubic.basecode.dataStructure.Link
getWeights() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
getWeights() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimator
getx() - Method in class ubic.basecode.dataStructure.DoublePoint
getx() - Method in class ubic.basecode.dataStructure.Point
gety() - Method in class ubic.basecode.dataStructure.DoublePoint
gety() - Method in class ubic.basecode.dataStructure.Point
getZ() - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
getZ() - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
GIF_EXTENSION - Static variable in class ubic.basecode.util.FileTools
grabColumnValues(HSSFSheet, int, boolean, boolean) - Static method in class ubic.basecode.io.excel.ExcelUtil
grabColumnValues(HSSFSheet, int, boolean, boolean, SpreadSheetFilter) - Static method in class ubic.basecode.io.excel.ExcelUtil
Gets all the strings from a column, possibly excluding header and possibly trimming and lowercasing
grabColumnValuesList(HSSFSheet, int, boolean, boolean) - Static method in class ubic.basecode.io.excel.ExcelUtil
grabColumnValuesList(HSSFSheet, int, boolean, boolean, SpreadSheetFilter) - Static method in class ubic.basecode.io.excel.ExcelUtil
gradient - Variable in class ubic.basecode.graphics.JGradientBar
Graph <R extends GraphNode <K ,V >,K ,V > - Interface in ubic.basecode.dataStructure.graph
GraphNode <K ,V > - Interface in ubic.basecode.dataStructure.graph
GREENRED_COLORMAP - Static variable in class ubic.basecode.graphics.ColorMap
IMAGE_EXTENSIONS - Static variable in class ubic.basecode.util.FileTools
in - Variable in class ubic.basecode.io.reader.HistogramReader
increment(K) - Method in class ubic.basecode.dataStructure.CountingMap
Increments the count associated with the specified key and returns the incremented count.
incrementAll(Collection<K>) - Method in class ubic.basecode.dataStructure.CountingMap
Increments the count associated with the specified keys.
incrementalUpdate(DoubleArrayList, int, int, double[]) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Incrementally maintains and updates minimum, maximum, sum and sum of squares of a data sequence.
incrementalUpdateSumsOfPowers(DoubleArrayList, int, int, int, int, double[]) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Not supported.
incrementalWeightedUpdate(DoubleArrayList, DoubleArrayList, int, int, double[]) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Not supported.
inDegree() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
index(boolean) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
index(boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService
Index the ontology for performing full-text searches.
IndexerSelector - Class in ubic.basecode.ontology.search
Used to limit which parts of ontologies get indexed for searching.
IndexerSelector() - Constructor for class ubic.basecode.ontology.search.IndexerSelector
indexes - Variable in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
indexOntology(String, OntModel) - Static method in class ubic.basecode.ontology.search.OntologyIndexer
indexOntology(String, OntModel, boolean) - Static method in class ubic.basecode.ontology.search.OntologyIndexer
Loads or creates an index from an existing OntModel.
init(ColorMatrix<R, C>) - Method in class ubic.basecode.graphics.MatrixDisplay
init() - Method in class ubic.basecode.io.excel.CreateSpreadSheet
init(long) - Static method in class ubic.basecode.math.RandomChooser
Initialized the random number generator with a given seed.
initialize(boolean, boolean) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
initialize(boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService
Initialize this ontology service.
initSize() - Method in class ubic.basecode.graphics.MatrixDisplay
Sets the display size
insertLeft(BinaryTreeNode<T>, T) - Method in class ubic.basecode.dataStructure.tree.BinaryTree
insertLeft(T) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
insertRight(BinaryTreeNode<T>, T) - Method in class ubic.basecode.dataStructure.tree.BinaryTree
insertRight(T) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
InstanceStatement - Interface in ubic.basecode.ontology.model
intArrayEval(String) - Method in class ubic.basecode.util.r.AbstractRClient
intArrayEval(String) - Method in interface ubic.basecode.util.r.RClient
intArrayToBytes(int[]) - Method in class ubic.basecode.io.ByteArrayConverter
IntegerMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
IntegerMatrix(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.IntegerMatrix
INTERCEPT_COEFFICIENT_NAME - Static variable in class ubic.basecode.math.linearmodels.LinearModelSummary
interpolate(double[], double[], double[]) - Static method in class ubic.basecode.math.Smooth
Linearlly interpolate values from a given data set
Similar implementation of R's stats.approxfun(..., rule = 2) where values outside the interval ['min(x)',
'max(x)'] get the value at the closest data extreme.
isamax_j(int, double[], int) - Static method in class ubic.basecode.math.linalg.Blas
This method finds the index of the element of a vector
that has the maximum absolute value.
isBaseline(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
isConnected() - Method in class ubic.basecode.util.r.JRIClient
isConnected() - Method in interface ubic.basecode.util.r.RClient
isConnected() - Method in class ubic.basecode.util.r.RServeClient
isDiseaseUsed() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
isEmpty() - Method in class ubic.basecode.dataStructure.CountingMap
isEmpty() - Method in class ubic.basecode.dataStructure.tree.BinaryTree
isEnabled() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
isEnabled() - Method in interface ubic.basecode.ontology.providers.OntologyService
isExactMatch() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
isExactSynonym() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
isFunctional() - Method in interface ubic.basecode.ontology.model.OntologyProperty
isFunctional - Variable in class ubic.basecode.ontology.model.OntologyPropertyImpl
isFunctional() - Method in class ubic.basecode.ontology.model.OntologyPropertyImpl
isGZipped(String) - Static method in class ubic.basecode.util.FileTools
isHasBeenShrunken() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
isHasInteractionEstimate() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult
isHasIntercept() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
isHasMissing() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
isHpUsed() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
isInitializationThreadAlive() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
isInitializationThreadAlive() - Method in interface ubic.basecode.ontology.providers.OntologyService
isInitializationThreadCancelled() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
isInitializationThreadCancelled() - Method in interface ubic.basecode.ontology.providers.OntologyService
isInteraction() - Method in class ubic.basecode.util.r.type.AnovaEffect
isLatinLetter(char) - Static method in class ubic.basecode.util.StringUtil
isLeaf() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
isLeaf() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
isMissing(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
isMissing(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
isMissing(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
isMissing(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
isMissing(int, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Check if the value at a given index is missing.
isMissing(int, int, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Check if the value at a given index is missing.
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
(non-Javadoc) Note that in a sparse matrix, zero values are considered "missing"!
isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
Strings are considered missing if they are whitespace, null or empty.
isOntologyLoaded() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
isOntologyLoaded() - Method in interface ubic.basecode.ontology.providers.OntologyService
Used for determining if the Ontology has finished loading into memory.
isPivoting() - Method in class ubic.basecode.math.linalg.QRDecomposition
isRoot() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
isRoot() - Method in interface ubic.basecode.ontology.model.OntologyTerm
isRoot() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
isRoot() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
isShrunken() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
Whether this is the result of emprical bayes shrinkage of variance estimates
isSimple() - Method in class ubic.basecode.ontology.search.IndexerSelector
isTermObsolete() - Method in interface ubic.basecode.ontology.model.OntologyTerm
check to see if the term is obsolete, if it is it should not be used
isTermObsolete() - Method in class ubic.basecode.ontology.model.OntologyTermImpl
isTermObsolete() - Method in class ubic.basecode.ontology.model.OntologyTermSimple
isValidFraction(double) - Static method in class ubic.basecode.math.Stats
Test whether a value is a valid fractional or probability value.
isValidPearsonCorrelation(double) - Static method in class ubic.basecode.math.CorrelationStats
Test if a value is a reasonable Pearson correlation (in the range -1 to 1; values outside of this range are
acceptable within a small roundoff.
isVisited() - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode
isVisited() - Method in class ubic.basecode.dataStructure.Visitable
isZipped(String) - Static method in class ubic.basecode.util.FileTools
item - Variable in class ubic.basecode.dataStructure.graph.AbstractGraphNode
ItemLevelFilter <R ,C > - Class in ubic.basecode.datafilter
Filter that removes individual values that are outside of a range.
ItemLevelFilter() - Constructor for class ubic.basecode.datafilter.ItemLevelFilter
items - Variable in class ubic.basecode.dataStructure.graph.DirectedGraph
iterator() - Method in class ubic.basecode.util.BatchIterator
lag1(DoubleArrayList, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Not supported.
LeastSquaresFit - Class in ubic.basecode.math.linearmodels
For performing "bulk" linear model fits, but also offers simple methods for simple univariate and multivariate
regression for a single vector of dependent variables (data).
LeastSquaresFit(DesignMatrix, DoubleMatrix<String, String>) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
Preferred interface if you want control over how the design is set up.
LeastSquaresFit(DesignMatrix, DoubleMatrix<String, String>, DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
Weighted least squares fit between two matrices
LeastSquaresFit(DesignMatrix, DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
Preferred interface for weighted least squares fit between two matrices
LeastSquaresFit(DoubleMatrix1D, DoubleMatrix1D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
Least squares fit between two vectors.
LeastSquaresFit(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
Stripped-down interface for simple use.
LeastSquaresFit(DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
ANOVA not possible (use the other constructors)
LeastSquaresFit(DoubleMatrix2D, DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
Weighted least squares fit between two matrices
LeastSquaresFit(ObjectMatrix<String, String, Object>, DenseDoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
LeastSquaresFit(ObjectMatrix<String, String, Object>, DenseDoubleMatrix2D, boolean) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
LeastSquaresFit(ObjectMatrix<String, String, Object>, DoubleMatrix<String, String>) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
NamedMatrix allows easier handling of the results.
LeastSquaresFit(ObjectMatrix<String, String, Object>, DoubleMatrix<String, String>, boolean) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit
NamedMatrix allows easier handling of the results.
like(int) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
like2D(int, int) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
linearModel(double[], Map<String, List<?>>) - Method in class ubic.basecode.util.r.AbstractRClient
linearModel(double[], ObjectMatrix<String, String, Object>) - Method in class ubic.basecode.util.r.AbstractRClient
linearModel(double[], Map<String, List<?>>) - Method in interface ubic.basecode.util.r.RClient
Lower level access to linear model.
linearModel(double[], ObjectMatrix<String, String, Object>) - Method in interface ubic.basecode.util.r.RClient
LinearModelSummary - Class in ubic.basecode.math.linearmodels
Represents the results of a linear model analysis from R.
LinearModelSummary(REXP, REXP, String[]) - Constructor for class ubic.basecode.math.linearmodels.LinearModelSummary
Construct from the result of evaluation of an R call. should be deprecated because we're not using R integration
LinearModelSummary(String) - Constructor for class ubic.basecode.math.linearmodels.LinearModelSummary
Construct an empty summary.
LinearModelSummary(String, Double[], Double[], List<String>, DoubleMatrix<String, String>, Double[], Double[], double, double, double, Integer, Integer, GenericAnovaResult, double, boolean) - Constructor for class ubic.basecode.math.linearmodels.LinearModelSummary
LinearModelSummary() - Constructor for class ubic.basecode.math.linearmodels.LinearModelSummary
Construct an empty summary.
Link - Class in ubic.basecode.dataStructure
Implements comparable, which sorts by the 'x' coordinate and then secondarily by the 'y' coordinate.
Link(int, int, double) - Constructor for class ubic.basecode.dataStructure.Link
listDirectoryFiles(File) - Static method in class ubic.basecode.util.FileTools
Given a File object representing a directory, return a collection of File objects representing the files
contained in that directory.
listEval(Class<?>, String) - Method in class ubic.basecode.util.r.AbstractRClient
FIXME only partly implemented, possibly not going to stay.
listEval(Class<?>, String) - Method in interface ubic.basecode.util.r.RClient
listSubDirectories(File) - Static method in class ubic.basecode.util.FileTools
Given a File object representing a directory, return a collection of File objects representing the directories
contained in that directory.
loadClasspathConfig(String) - Static method in class ubic.basecode.util.ConfigUtils
loadConfig(File) - Static method in class ubic.basecode.util.ConfigUtils
loadConfig(String) - Static method in class ubic.basecode.util.ConfigUtils
loadConfig(URL) - Static method in class ubic.basecode.util.ConfigUtils
loadLibrary(String) - Method in class ubic.basecode.util.r.AbstractRClient
loadLibrary(String) - Method in interface ubic.basecode.util.r.RClient
loadMedicOntologyFromFile() - Method in class ubic.basecode.ontology.providers.MedicOntologyService
Warning, this uses a method intended only for tests.
loadMemoryModel(InputStream, String) - Static method in class ubic.basecode.ontology.OntologyLoader
Load an ontology into memory.
loadMemoryModel(String) - Static method in class ubic.basecode.ontology.OntologyLoader
Load an ontology into memory.
loadMemoryModel(String, String) - Static method in class ubic.basecode.ontology.OntologyLoader
Load an ontology into memory.
loadModel() - Method in class ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService
loadModel() - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
Delegates the call as to load the model into memory or leave it on disk.
loadModel() - Method in class ubic.basecode.ontology.providers.GenericOntologyService
loadScript(InputStream) - Method in class ubic.basecode.util.r.AbstractRClient
There is a pretty annoying limitation of this.
loadTermsInNameSpace(InputStream, boolean) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
loadTermsInNameSpace(InputStream, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService
For testing!
locate(String) - Static method in class ubic.basecode.util.ConfigUtils
loessFit(DoubleMatrix2D) - Static method in class ubic.basecode.math.Smooth
loessFit(DoubleMatrix2D, double) - Static method in class ubic.basecode.math.Smooth
Computes a loess regression line to fit the data
log - Static variable in class ubic.basecode.datafilter.AbstractFilter
log - Static variable in class ubic.basecode.io.reader.AbstractMatrixReader
log - Static variable in class ubic.basecode.ontology.model.AbstractOntologyResource
log - Static variable in class ubic.basecode.ontology.providers.AbstractOntologyService
log - Static variable in class ubic.basecode.util.r.AbstractRClient
logTransform(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
Log-transform the values in a matrix (log base 2).
longArrayToBytes(long[]) - Method in class ubic.basecode.io.ByteArrayConverter
lowCut - Variable in class ubic.basecode.datafilter.AbstractLevelFilter
M_1_PI - Static variable in class ubic.basecode.math.Constants
M_1_SQRT_2 - Static variable in class ubic.basecode.math.Constants
M_1_SQRT_2PI - Static variable in class ubic.basecode.math.Constants
m_cellSize - Variable in class ubic.basecode.graphics.MatrixDisplay
m_colorPalette - Variable in class ubic.basecode.graphics.ColorMap
m_columnLabelHeight - Variable in class ubic.basecode.graphics.MatrixDisplay
m_currentColorMap - Variable in class ubic.basecode.graphics.ColorMap
m_customColorMap - Variable in class ubic.basecode.graphics.ColorMap
m_defaultResolution - Variable in class ubic.basecode.graphics.MatrixDisplay
m_defaultSuggestedNumberOfColors - Static variable in class ubic.basecode.graphics.ColorMap
m_fontGutter - Variable in class ubic.basecode.graphics.MatrixDisplay
m_fontSize - Variable in class ubic.basecode.graphics.MatrixDisplay
m_isShowLabels - Variable in class ubic.basecode.graphics.MatrixDisplay
m_isShowScale - Variable in class ubic.basecode.graphics.MatrixDisplay
m_labelFont - Variable in class ubic.basecode.graphics.MatrixDisplay
m_labelGutter - Variable in class ubic.basecode.graphics.MatrixDisplay
M_LN_2 - Static variable in class ubic.basecode.math.Constants
M_LN_SQRT_2PI - Static variable in class ubic.basecode.math.Constants
M_LN_SQRT_PI - Static variable in class ubic.basecode.math.Constants
M_LN_SQRT_PId2 - Static variable in class ubic.basecode.math.Constants
M_LOG10_2 - Static variable in class ubic.basecode.math.Constants
m_matrixReader - Variable in class ubic.basecode.graphics.ColorMatrix
m_max - Variable in class ubic.basecode.graphics.JGradientBar
m_maxColor - Variable in class ubic.basecode.graphics.ColorMap
last color in the current color map
m_maxColumnLength - Variable in class ubic.basecode.graphics.MatrixDisplay
m_maxFontSize - Variable in class ubic.basecode.graphics.MatrixDisplay
m_min - Variable in class ubic.basecode.graphics.JGradientBar
m_minColor - Variable in class ubic.basecode.graphics.ColorMap
first color in the current color map
M_PI_2 - Static variable in class ubic.basecode.math.Constants
M_PI_4 - Static variable in class ubic.basecode.math.Constants
M_PI_half - Static variable in class ubic.basecode.math.Constants
m_ratioWidth - Variable in class ubic.basecode.graphics.MatrixDisplay
m_resolution - Variable in class ubic.basecode.graphics.MatrixDisplay
m_rowKeys - Variable in class ubic.basecode.graphics.ColorMatrix
to be able to sort the rows by an arbitrary key
m_rowLabelWidth - Variable in class ubic.basecode.graphics.MatrixDisplay
M_SQRT_2 - Static variable in class ubic.basecode.math.Constants
M_SQRT_2dPI - Static variable in class ubic.basecode.math.Constants
M_SQRT_PI - Static variable in class ubic.basecode.math.Constants
m_textSize - Variable in class ubic.basecode.graphics.MatrixDisplay
m_totalColumns - Variable in class ubic.basecode.graphics.ColorMatrix
m_totalRows - Variable in class ubic.basecode.graphics.ColorMatrix
mad(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
main(String[]) - Static method in class ubic.basecode.io.excel.ExcelUtil
makeContrasts() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
In limma, the contrasts are built by referring to the coefficients by name, which isn't what we want.
makeValidForR(String) - Static method in class ubic.basecode.util.StringUtil
Mimics the make.names method in R (character.c) to make valid variables names; we use this for column headers in
some output files.
MammalianPhenotypeOntologyService - Class in ubic.basecode.ontology.providers
MammalianPhenotypeOntologyService() - Constructor for class ubic.basecode.ontology.providers.MammalianPhenotypeOntologyService
manhattanDistance(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.Distance
Calculate the Manhattan distance between two vectors.
MapReader - Class in ubic.basecode.io.reader
Reads a tab-delimited file with keys in first column, values in second.
MapReader() - Constructor for class ubic.basecode.io.reader.MapReader
mapValuesToColors() - Method in class ubic.basecode.graphics.ColorMatrix
mark() - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode
mark() - Method in class ubic.basecode.dataStructure.Visitable
maskMissing(DoubleMatrix2D, DoubleMatrix2D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
matchClasses(OntModel, SearchIndex, String) - Static method in class ubic.basecode.ontology.search.OntologySearch
Find classes that match the query string.
matchIndividuals(OntModel, SearchIndex, String) - Static method in class ubic.basecode.ontology.search.OntologySearch
Find individuals that match the query string
matchingCriteria(DoubleMatrix1D, DoubleFunction<Boolean>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
matchResources(OntModel, SearchIndex, String) - Static method in class ubic.basecode.ontology.search.OntologySearch
Find OntologyIndividuals and OntologyTerms that match the query string.
MathUtil - Class in ubic.basecode.math
MathUtil() - Constructor for class ubic.basecode.math.MathUtil
matmat_j(double[][], double[][], double[][], int, int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method multiplies an n x p matrix by a p x r matrix.
Matrix2D <R ,C ,V > - Interface in ubic.basecode.dataStructure.matrix
Represents a matrix with index columns and rows.
Matrix3D <R ,C ,S ,V > - Interface in ubic.basecode.dataStructure.matrix
MatrixDisplay <R ,C > - Class in ubic.basecode.graphics
A visual component for displaying a color matrix
MatrixDisplay(ColorMatrix<R, C>) - Constructor for class ubic.basecode.graphics.MatrixDisplay
MatrixDisplay(DoubleMatrix<R, C>) - Constructor for class ubic.basecode.graphics.MatrixDisplay
MatrixNormalizer <R ,C > - Class in ubic.basecode.math
MatrixNormalizer() - Constructor for class ubic.basecode.math.MatrixNormalizer
MatrixRowStats - Class in ubic.basecode.math
Convenience functions for getting row statistics from matrices.
MatrixStats - Class in ubic.basecode.math
MatrixStats() - Constructor for class ubic.basecode.math.MatrixStats
MatrixUtil - Class in ubic.basecode.dataStructure.matrix
MatrixUtil() - Constructor for class ubic.basecode.dataStructure.matrix.MatrixUtil
MatrixWriter <R ,C > - Class in ubic.basecode.io.writer
Class for writing matrices to disk
MatrixWriter(OutputStream) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(OutputStream, Format) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(OutputStream, Format, String) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(String, Format) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(String, Format, String) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(Writer) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(Writer, Format) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(Writer, Format, String) - Constructor for class ubic.basecode.io.writer.MatrixWriter
MatrixWriter(Writer, String) - Constructor for class ubic.basecode.io.writer.MatrixWriter
mattran_j(double[][], double[][], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method obtains the transpose of an n x p matrix.
matvec_j(double[][], double[], double[], int, int) - Static method in class ubic.basecode.math.linalg.Blas
This method multiplies an n x p matrix by a p x 1 vector.
MAX - Static variable in class ubic.basecode.datafilter.RowLevelFilter
Use the maximum of the row as the criterion.
max() - Method in class ubic.basecode.dataStructure.CountingMap
max - Variable in class ubic.basecode.graphics.ColorMatrix
max(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
max() - Method in class ubic.basecode.math.distribution.Histogram
max(double[]) - Static method in class ubic.basecode.math.MathUtil
max(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
Compute the maximum value in the matrix.
MAX_ROWS_TO_PRINT - Static variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix
MAX_ROWS_TO_PRINT - Static variable in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
MAX_SLICES_TO_PRINT - Static variable in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
maxStringPixelWidth(String[], FontMetrics) - Static method in class ubic.basecode.graphics.text.Util
maxtrix - Variable in class ubic.basecode.graphics.ColorMatrix
MEAN - Static variable in class ubic.basecode.datafilter.RowLevelFilter
Use the mean as the criterion.
mean(double[], int) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Special mean calculation where we use the effective size as an input.
mean(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
mean(DoubleArrayList, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Special mean calculation where we use the effective size as an input.
meanAboveQuantile(double, DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Calculate the mean of the values above to a particular quantile of an array.
meanAboveQuantile(int, double[], int) - Static method in class ubic.basecode.math.Stats
calculate the mean of the values above (NOT greater or equal to) a particular index rank of an array.
MeanDifferenceMetaAnalysis - Class in ubic.basecode.math.metaanalysis
Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
These methods use the standardized mean difference statistic d:
d_i = ( X_i ˆ t - X_i ˆ c ) / s_i
where X i t is the mean of the treatment group in the ith study, X i ct
is the mean of the control group in the treatment group in the ith study, and s i is the pooled
standard deviation of the two groups.
MeanDifferenceMetaAnalysis(boolean) - Constructor for class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
means(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixRowStats
Calculates the means of a matrix's rows.
means(DoubleMatrix2D) - Static method in class ubic.basecode.math.MatrixRowStats
Calculate the means of a matrix's rows
MeanVarianceEstimator - Class in ubic.basecode.math.linearmodels
Estimate mean-variance relationship and use this to compute weights for least squares fitting.
MeanVarianceEstimator(DesignMatrix, DoubleMatrix<String, String>, DoubleMatrix1D) - Constructor for class ubic.basecode.math.linearmodels.MeanVarianceEstimator
Preferred interface if you want control over how the design is set up.
MeanVarianceEstimator(DesignMatrix, DoubleMatrix2D, DoubleMatrix1D) - Constructor for class ubic.basecode.math.linearmodels.MeanVarianceEstimator
Executes voom() to calculate weights.
MeanVarianceEstimator(DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.MeanVarianceEstimator
Generic method for calculating mean and variance, as a data diagnostic.
MEDIAN - Static variable in class ubic.basecode.datafilter.RowLevelFilter
Use the median as the criterion.
median(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the median.
MedicOntologyService - Class in ubic.basecode.ontology.providers
MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a
normal mesh term doesnt have
MEDIC comes from the CTD folks.
MedicOntologyService() - Constructor for class ubic.basecode.ontology.providers.MedicOntologyService
Warning, this constructor initializes the ontology no matter what
MetaAnalysis - Class in ubic.basecode.math.metaanalysis
Statistics for meta-analysis.
MetaAnalysis() - Constructor for class ubic.basecode.math.metaanalysis.MetaAnalysis
metaFEWeights(DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
Weights under a fixed effects model.
metaRESampleVariance(DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
CH sample variance under random effects model, equation 18-20
metaREVariance(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
CH equation 18-23.
metaREWeights(DoubleArrayList, double) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
Under a random effects model, CH eqn. 18-24, we replace the conditional variance with the sum of the
between-sample variance and the conditional variance.
metaVariance(DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
CH 18-3.
metaVariance(DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
CH 18-3 version 2 for quality weighted. ( page 266 ) in Fixed effects model.
metaZscore(double, double) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis
Test statistic for H0: effectSize == 0.
MIN - Static variable in class ubic.basecode.datafilter.RowLevelFilter
Use the minimum of the row as the criterion.
min - Variable in class ubic.basecode.graphics.ColorMatrix
min(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
min() - Method in class ubic.basecode.math.distribution.Histogram
min(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
Find the minimum of the entire matrix.
missingColor - Variable in class ubic.basecode.graphics.ColorMatrix
ModeratedTstat - Class in ubic.basecode.math.linearmodels
Implements methods described in
Smyth, G.
ModeratedTstat() - Constructor for class ubic.basecode.math.linearmodels.ModeratedTstat
moment(DoubleArrayList, int, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the moment of k -th order with constant c of a data sequence, which is
Sum( (data[i]-c)k ) /
data.size() .
MouseDevelopmentOntologyService - Class in ubic.basecode.ontology.providers
MouseDevelopmentOntologyService() - Constructor for class ubic.basecode.ontology.providers.MouseDevelopmentOntologyService
movingAverage(DoubleMatrix1D, int) - Static method in class ubic.basecode.math.Smooth
Simple moving average that sums the points "backwards".
MultipleTestCorrection - Class in ubic.basecode.math
Methods for p-value correction of sets of hypothesis tests.
MultipleTestCorrection() - Constructor for class ubic.basecode.math.MultipleTestCorrection
multWithMissing(DoubleMatrix1D, DoubleMatrix2D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
multWithMissing(DoubleMatrix2D, DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
multWithMissing(DoubleMatrix2D, DoubleMatrix2D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
Multiple two matrices, tolerate missing values.
paintComponent(Graphics) - Method in class ubic.basecode.graphics.MatrixDisplay
ParameterGrabber - Class in ubic.basecode.dataStructure.params
Generates a parameter map from a class using reflection, usefull for storing experimental parameters
ParameterGrabber() - Constructor for class ubic.basecode.dataStructure.params.ParameterGrabber
ParamKeeper - Class in ubic.basecode.dataStructure.params
Keeps track of results in the form of several key/value maps (each one can represent an experiment run), can output
to spreadsheet or csv file
ParamKeeper() - Constructor for class ubic.basecode.dataStructure.params.ParamKeeper
ParamSpreadSheet - Class in ubic.basecode.dataStructure.params
A class to convert parametergrabber information/instances into excel speadsheet lines
ParamSpreadSheet(String, SpreadSheetSchema) - Constructor for class ubic.basecode.dataStructure.params.ParamSpreadSheet
paramsToLine(Map<String, String>) - Static method in class ubic.basecode.dataStructure.params.ParameterGrabber
paramsToLine(Map<String, String>, boolean) - Static method in class ubic.basecode.dataStructure.params.ParameterGrabber
parents - Variable in class ubic.basecode.dataStructure.graph.DirectedGraphNode
phyper(int, int, int, int, boolean) - Static method in class ubic.basecode.math.SpecFunc
Ported from R phyper.c
Sample of n balls from NR red and NB black ones; x are red
plot() - Method in class ubic.basecode.math.distribution.Histogram
Provide graph for JFreePlot; counts expressed as a fraction.
Point - Class in ubic.basecode.dataStructure
Point(int, int) - Constructor for class ubic.basecode.dataStructure.Point
populate(List<Map<String, String>>) - Method in class ubic.basecode.dataStructure.params.ParamSpreadSheet
positions - Variable in class ubic.basecode.io.excel.SpreadSheetSchema
PrecisionRecall - Class in ubic.basecode.math
Compute area under precision recall
PrecisionRecall() - Constructor for class ubic.basecode.math.PrecisionRecall
prefixWeightedHammingDistance(String, String, double) - Static method in class ubic.basecode.math.StringDistance
Compute the Hamming distance between two strings of equal length (if they are of unequal length the longer one is
trimmed), giving higher weight to characters at the start of the strings, so strings that are similar at the
starts are given higher scores (shorter distances) than strings that are similar at the ends.
prettyPrint(byte[]) - Static method in class ubic.basecode.dataStructure.BitUtil
PrettyPrinter - Class in ubic.basecode.util
Very simple class to produce String versions of beans and other objects.
PrimitiveMatrix <R ,C ,V > - Interface in ubic.basecode.dataStructure.matrix
Matrix that holds primitives, with an available object representation of the values.
print(Collection<String>, Collection<Object>) - Static method in class ubic.basecode.util.PrettyPrinter
Print out a collection of beans in a relatively pleasing format.
print(Collection<String>, Object) - Static method in class ubic.basecode.util.PrettyPrinter
Pretty-print a single bean.
print(Collection<String>, Object[]) - Static method in class ubic.basecode.util.PrettyPrinter
Print out a collection of objects in a relatively pleasing format.
probability(double) - Method in class ubic.basecode.math.distribution.NormalProbabilityComputer
probability(double, boolean) - Method in class ubic.basecode.math.distribution.NormalProbabilityComputer
probability(double) - Method in interface ubic.basecode.math.distribution.ProbabilityComputer
Return the probability associated with a certain value.The upper tail of the associated distribution is returned.
probability(double, boolean) - Method in interface ubic.basecode.math.distribution.ProbabilityComputer
Return the probability associated with a certain value, with choice of tail.
probability(double) - Method in class ubic.basecode.math.distribution.UniformProbabilityComputer
probability(double, boolean) - Method in class ubic.basecode.math.distribution.UniformProbabilityComputer
ProbabilityComputer - Interface in ubic.basecode.math.distribution
An interface that describes objects that can produce probabilities according to some distribution.
product(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the product of a data sequence, which is Prod( data[i] ) .
PropertyFactory - Class in ubic.basecode.ontology.model
PropertyFactory() - Constructor for class ubic.basecode.ontology.model.PropertyFactory
prune() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph
Remove edges to nodes that aren't in the graph.
prune() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
Remove connections that are to nodes not contained in this graph
put(K, Integer) - Method in class ubic.basecode.dataStructure.CountingMap
put(String, String) - Method in class ubic.basecode.dataStructure.StringToStringSetMap
putAll(Map<? extends K, ? extends Integer>) - Method in class ubic.basecode.dataStructure.CountingMap
pvalue(double, int) - Static method in class ubic.basecode.math.CorrelationStats
Compute pvalue for the pearson correlation, using the t distribution method.
pvalueAsByte(double, int) - Static method in class ubic.basecode.math.CorrelationStats
Convert a p value into a value between 0 and 255 inclusive.
RandomChooser - Class in ubic.basecode.math
Fill arrays with random values
RANGE - Static variable in class ubic.basecode.datafilter.RowLevelFilter
Use the range as the criterion
range(DoubleArrayList) - Static method in class ubic.basecode.math.Stats
Compute the range of an array.
rank() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition
Rank - Class in ubic.basecode.math
Calculate rank statistics for arrays.
Rank() - Constructor for class ubic.basecode.math.Rank
rankInterpolated(DoubleArrayList, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the linearly interpolated number of elements in a list less or equal to a given element.
rankSum(List<Double>) - Static method in class ubic.basecode.math.Rank
rankTransform(DoubleArrayList) - Static method in class ubic.basecode.math.Rank
Rank transform an array.
rankTransform(DoubleArrayList, boolean) - Static method in class ubic.basecode.math.Rank
Rank transform an array.
rankTransform(Map<K, ? extends Comparable<?>>) - Static method in class ubic.basecode.math.Rank
Rank transform a map, where the values are Comparable values we wish to rank.
rankTransform(Map<K, ? extends Comparable<?>>, boolean) - Static method in class ubic.basecode.math.Rank
Ties are broken as for the other methods.
rbfNormalize(DoubleMatrix<R, C>, double) - Static method in class ubic.basecode.math.MatrixStats
Normalize a matrix in place to be a transition matrix.
RCDoubleMatrix1D - Class in ubic.basecode.dataStructure.matrix
A row-compressed 1D matrix.
RCDoubleMatrix1D(double[]) - Constructor for class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
RCDoubleMatrix1D(int) - Constructor for class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
RCDoubleMatrix1D(IntArrayList, DoubleArrayList) - Constructor for class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
RClient - Interface in ubic.basecode.util.r
Abstraction of a connection to R
RConnectionFactory - Class in ubic.basecode.util.r
Get a connection to R, somehow (if possible).
RConnectionFactory() - Constructor for class ubic.basecode.util.r.RConnectionFactory
read(InputStream) - Method in class ubic.basecode.io.reader.AbstractMatrixReader
read(String) - Method in class ubic.basecode.io.reader.AbstractMatrixReader
read(String, int) - Method in class ubic.basecode.io.reader.AbstractMatrixReader
read(InputStream) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(InputStream, Collection<String>) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(InputStream, Collection<String>, boolean, int, int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(InputStream, Collection<String>, int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(String) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(String, Collection<String>) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
Read a matrix from a file, subject to filtering criteria.
read(String, Collection<String>, int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(String, int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader
read(InputStream) - Method in class ubic.basecode.io.reader.MapReader
read(InputStream, boolean) - Method in class ubic.basecode.io.reader.MapReader
read(String) - Method in class ubic.basecode.io.reader.MapReader
read(String, boolean) - Method in class ubic.basecode.io.reader.MapReader
read(InputStream) - Method in class ubic.basecode.io.reader.SparseDoubleMatrixReader
Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
item1 item2 weight
item1 item5 weight
By definition the resulting matrix is square and symmetric.
read(InputStream, Collection<String>) - Method in class ubic.basecode.io.reader.SparseDoubleMatrixReader
read(InputStream, Collection<String>, boolean, int, int) - Method in class ubic.basecode.io.reader.SparseDoubleMatrixReader
read(InputStream, int) - Method in class ubic.basecode.io.reader.SparseRaggedMatrixReader
Read an entire sparse matrix from a stream (JW format).
read(InputStream) - Method in class ubic.basecode.io.reader.StringMatrixReader
read(InputStream, int, int) - Method in class ubic.basecode.io.reader.StringMatrixReader
read(String) - Method in class ubic.basecode.io.reader.StringMatrixReader
read(String, int) - Method in class ubic.basecode.io.reader.StringMatrixReader
read(String, int, int) - Method in class ubic.basecode.io.reader.StringMatrixReader
read1D() - Method in class ubic.basecode.io.reader.HistogramReader
readFromAdjList(InputStream) - Method in class ubic.basecode.io.reader.SparseRaggedMatrixReader
readFromAdjList(String) - Method in class ubic.basecode.io.reader.SparseRaggedMatrixReader
Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
item1 item2 weight
item1 item5 weight
IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not
explicitly listed.
readHeader(BufferedReader, int) - Method in class ubic.basecode.io.reader.AbstractMatrixReader
readJW(InputStream) - Method in class ubic.basecode.io.reader.SparseDoubleMatrixReader
Read a sparse matrix in "JW" (Jason Weston) format.
readOneRow(BufferedReader, int) - Method in class ubic.basecode.io.reader.SparseRaggedMatrixReader
Use this to read one row from a matrix (JW format).
readTestResult(File) - Static method in class ubic.basecode.util.RegressionTesting
readTestResult(InputStream) - Static method in class ubic.basecode.util.RegressionTesting
readTestResult(String) - Static method in class ubic.basecode.util.RegressionTesting
readTestResultFromFile(String) - Static method in class ubic.basecode.util.RegressionTesting
ready() - Static method in class ubic.basecode.util.r.JRIClient
rebuild() - Method in class ubic.basecode.math.linearmodels.DesignMatrix
Refresh the design matrix, for example after releveling.
REDGREEN_COLORMAP - Static variable in class ubic.basecode.graphics.ColorMap
RegressionTesting - Class in ubic.basecode.util
Tools to help make regression testing easier, but also useful for other purposes.
remove(Object) - Method in class ubic.basecode.dataStructure.CountingMap
remove() - Method in class ubic.basecode.util.BatchIterator
remove(String) - Method in class ubic.basecode.util.r.AbstractRClient
remove(String) - Method in interface ubic.basecode.util.r.RClient
Remove a variable from the R namespace
removeMissing(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
removeMissing(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Makes a copy of the list that doesn't have the missing values.
removeMissingOrInfinite(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
removeMissingOrInfinite(DoubleMatrix1D, DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
Remove values from data corresponding to missing values in reference.
removeSpecialCharacters(String) - Static method in class ubic.basecode.ontology.ncbo.AnnotatorClient
replaceValues(DoubleMatrix1D, BooleanArrayList, DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
Perform the awkward operation of substituting certain values in a vector from values in another vector.
reset(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
resetRowKeys() - Method in class ubic.basecode.graphics.ColorMatrix
resetRowKeys() - Method in class ubic.basecode.graphics.MatrixDisplay
residualDf - Variable in class ubic.basecode.util.r.type.AnovaResult
resourceToPath(String) - Static method in class ubic.basecode.util.FileTools
RestrictionFactory - Class in ubic.basecode.ontology.model
RestrictionFactory() - Constructor for class ubic.basecode.ontology.model.RestrictionFactory
restrictionOn - Variable in class ubic.basecode.ontology.model.OntologyRestrictionImpl
retrieveMatrix(String) - Method in class ubic.basecode.util.r.JRIClient
retrieveMatrix(String) - Method in interface ubic.basecode.util.r.RClient
Get a matrix back out of the R context.
retrieveMatrix(String) - Method in class ubic.basecode.util.r.RServeClient
RetryWithoutWildcardFailedException - Exception in ubic.basecode.ontology.search
Exception raised when retrying a search without a wildcard still fails.
RetryWithoutWildcardFailedException(String, String, JenaException, JenaException) - Constructor for exception ubic.basecode.ontology.search.RetryWithoutWildcardFailedException
ROC - Class in ubic.basecode.math
Functions for calculating Receiver operator characteristics.
ROC() - Constructor for class ubic.basecode.math.ROC
rocpval(int, List<Double>) - Static method in class ubic.basecode.math.ROC
For an AROC value, calculates a p value.
RowAbsentFilter <M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Filter a data matrix according to flags given in a separate matrix.
RowAbsentFilter() - Constructor for class ubic.basecode.datafilter.RowAbsentFilter
rowApplyLinearModel(String, String, String[]) - Method in class ubic.basecode.util.r.AbstractRClient
rowApplyLinearModel(String, String, String[]) - Method in interface ubic.basecode.util.r.RClient
Run lm with anova on all the rows of a matrix
RowLevelFilter <R ,C > - Class in ubic.basecode.datafilter
Remove rows from a matrix based on some row-based statistic.
RowLevelFilter() - Constructor for class ubic.basecode.datafilter.RowLevelFilter
rowMap - Variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
RowMissingFilter <M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Remove rows from a matrix that are missing too many points.
RowMissingFilter() - Constructor for class ubic.basecode.datafilter.RowMissingFilter
RowNameFilter <M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Remove or retain rows that are on a list.
RowNameFilter() - Constructor for class ubic.basecode.datafilter.RowNameFilter
RowNameFilter(Set<R>) - Constructor for class ubic.basecode.datafilter.RowNameFilter
RowNameFilter(Set<R>, boolean) - Constructor for class ubic.basecode.datafilter.RowNameFilter
rowNameMap - Variable in class ubic.basecode.io.writer.MatrixWriter
rowNames - Variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
rows() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
rows() - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
rows() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
rows() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Get the number of rows the matrix has
rows() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
Get the number of rows the matrix has
rows() - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
rows() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
rows() - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
RServeClient - Class in ubic.basecode.util.r
RServeClient() - Constructor for class ubic.basecode.util.r.RServeClient
Gets connection on default host (localhost) and port (6311)
RServeClient(String) - Constructor for class ubic.basecode.util.r.RServeClient
run(DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
Following CH section 2.2.
run(DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
run(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
run() - Method in class ubic.basecode.util.GenericStreamConsumer
sameArray(int[], int[]) - Static method in class ubic.basecode.util.RegressionTesting
Test whether two double arrays contain the same items in the same order
sampleKurtosis(DoubleArrayList, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sample kurtosis (aka excess) of a data sequence.
sampleSkew(DoubleArrayList, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sample skew of a data sequence.
sampleStandardDeviation(int, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sample standard deviation.
sampleStandardDeviations(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixRowStats
Calculates the sample standard deviation of each row of a matrix
sampleVariance(DoubleArrayList, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sample variance of a data sequence.
samplingVariance(double, double) - Static method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
Equation 18-10 from CH.
samplingVariance(double, double, double) - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
CH eqn 18-7
samplingVariances(DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
Run equation CH 18-10 on a list of sample sizes and effects.
samplingVariances(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis
Run eqn 18-7 on a set of effect sizes.
save() - Method in class ubic.basecode.io.excel.CreateSpreadSheet
saveImage(ColorMatrix<R, C>, String, boolean, boolean, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
saveImage(String) - Method in class ubic.basecode.graphics.MatrixDisplay
Saves the image to a png file.
saveImage(String, boolean, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
saveImageToPng(ColorMatrix<R, C>, OutputStream, boolean, boolean, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
schema - Variable in class ubic.basecode.io.excel.CreateSpreadSheet
search(String) - Method in class ubic.basecode.ontology.search.SearchIndex
SearchIndex - Class in ubic.basecode.ontology.search
Customization to deal with MultiReader and 'open' while indexing is going on ...?
SearchIndex(IndexReader) - Constructor for class ubic.basecode.ontology.search.SearchIndex
SearchIndex(MultiReader, Analyzer) - Constructor for class ubic.basecode.ontology.search.SearchIndex
seen(K) - Method in class ubic.basecode.dataStructure.CountingMap
Returns true if the specified key has ever been incremented, false otherwise.
select(DoubleMatrix1D, Collection<Integer>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
selectColumns(DoubleMatrix2D, Collection<Integer>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
selectColumnsAndRows(DoubleMatrix2D, Collection<Integer>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
selectRows(DoubleMatrix2D, Collection<Integer>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
selfSquaredMatrix(double[][]) - Static method in class ubic.basecode.math.MatrixStats
sep - Variable in class ubic.basecode.io.writer.MatrixWriter
SequenceOntologyService - Class in ubic.basecode.ontology.providers
Support for the Sequence Ontology
SequenceOntologyService() - Constructor for class ubic.basecode.ontology.providers.SequenceOntologyService
set(byte[], int) - Static method in class ubic.basecode.dataStructure.BitUtil
Set the bit at the specified position
set(double, double) - Method in class ubic.basecode.dataStructure.DoublePoint
set(int, int, double[]) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
Set the matrix cell to the specified bit vector
set(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
Sets the bit of the specified cell at the specified index to 1.
set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
set(int, int, int, double) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
set(int, int, int, Object) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
set(int, int, int, double) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
set(int, int, Integer) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
set(int, int, V) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
set(int, int, V) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
set(int, int, String) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
set(int, int) - Method in class ubic.basecode.dataStructure.Point
setAnova(GenericAnovaResult) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
setBaseline(String, String) - Method in class ubic.basecode.math.linearmodels.DesignMatrix
setByKeys(R, C, double[]) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
setByKeys(R, C, Double) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
setByKeys(R, C, Integer) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
setByKeys(R, C, V) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
setByKeys(R, C, V) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
setByKeys(R, C, String) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
setCellSize(Dimension) - Method in class ubic.basecode.graphics.MatrixDisplay
setColNameMap(Map<C, String>) - Method in class ubic.basecode.io.writer.MatrixWriter
Use to customize the labels instead of relying on the toString method of the column object
setColor(int, int, Color) - Method in class ubic.basecode.graphics.ColorMatrix
setColorMap(Color[]) - Method in class ubic.basecode.graphics.ColorMatrix
setColorMap(Color[]) - Method in class ubic.basecode.graphics.JGradientBar
setColorMap(Color[]) - Method in class ubic.basecode.graphics.MatrixDisplay
setColumnName(C, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
setColumnName(C, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Add a column name associated with an index.
setColumnNames(List<C>) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
setColumnNames(List<C>) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
setColumnNames(List<C>) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
setColumnNames(List<C>) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
setContents(T) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
setDelimiter(String) - Method in class ubic.basecode.io.StringConverter
setDisplayRange(double, double) - Method in class ubic.basecode.graphics.ColorMatrix
Standardized display range
setDisplayRange(double, double) - Method in class ubic.basecode.graphics.MatrixDisplay
setExactMatch(boolean) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setExactSynonym(boolean) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setFilterNames(Set<R>, boolean) - Method in class ubic.basecode.datafilter.RowNameFilter
setFixed(boolean) - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
setFlagMatrix(StringMatrix<R, C>) - Method in class ubic.basecode.datafilter.RowAbsentFilter
setFormula(HSSFSheet, int, int, String) - Static method in class ubic.basecode.io.excel.ExcelUtil
setGraph(DirectedGraph<K, V>) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
setHighCut(double) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
Set the high threshold for removal.
setHighCut(double, boolean) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
setIndexFrom(Integer) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setIndexTo(Integer) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setItem(V) - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode
setItem(V) - Method in interface ubic.basecode.dataStructure.graph.GraphNode
Set the contents of the node.
setKeepMarginal(boolean) - Method in class ubic.basecode.datafilter.RowAbsentFilter
setKey(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
setKey(Object) - Method in class ubic.basecode.util.r.type.AnovaResult
setLabels(double, double) - Method in class ubic.basecode.graphics.JGradientBar
setLabelsVisible(boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
setLeft(BinaryTreeNode<T>) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
setLowCut(double) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
Set the low threshold for removal.
setLowCut(double, boolean) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
setMapToMatrix(StringToStringSetMap) - Static method in class ubic.basecode.dataStructure.StringToStringSetMap
setMatchType(String) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setMatrix(ColorMatrix<R, C>) - Method in class ubic.basecode.graphics.MatrixDisplay
setMaxColumnLength(int) - Method in class ubic.basecode.graphics.MatrixDisplay
setMaxFractionRemoved(double) - Method in class ubic.basecode.datafilter.RowMissingFilter
Set the maximum fraction of rows which will be removed from the data set.
setMethod(int) - Method in class ubic.basecode.datafilter.RowLevelFilter
Choose the method that will be used for filtering.
setMinPresentCount(int) - Method in class ubic.basecode.datafilter.RowAbsentFilter
setMinPresentCount(int) - Method in class ubic.basecode.datafilter.RowMissingFilter
Set the minimum number of values that must be present in each row.
setMinPresentFraction(double) - Method in class ubic.basecode.datafilter.RowAbsentFilter
setMinPresentFraction(double) - Method in class ubic.basecode.datafilter.RowMissingFilter
setObj(int, int, Integer) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
setObject(ChainedStatementObject) - Method in interface ubic.basecode.ontology.model.ChainedStatement
setOntologyUsed(String) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setPriorDof(Double) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary
setQuick(int, int, int, double) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
setQuick(int, int, int, double) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
setQuick(int, double) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D
setRemoveAllNegative(boolean) - Method in class ubic.basecode.datafilter.RowLevelFilter
Set the filter to remove all rows that have only negative values.
setRight(BinaryTreeNode<T>) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode
setRow(int, double[]) - Method in class ubic.basecode.graphics.ColorMatrix
Changes values in a row, clipping if there are more values than columns.
setRowHeight(int) - Method in class ubic.basecode.graphics.MatrixDisplay
setRowKeys(int[]) - Method in class ubic.basecode.graphics.ColorMatrix
setRowKeys(int[]) - Method in class ubic.basecode.graphics.MatrixDisplay
setRowName(R, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
setRowName(R, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
Add a row name associated with a row index.
setRowNameMap(Map<R, String>) - Method in class ubic.basecode.io.writer.MatrixWriter
Use to customize the labels instead of relying on the toString method of the row object
setRowNames(List<R>) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
setRowNames(List<R>) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
setRowNames(List<R>) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D
setRowNames(List<R>) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
setScaleBarVisible(boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
setSearchQueryUsed(String) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setSep(String) - Method in class ubic.basecode.io.writer.MatrixWriter
setSliceNameMap(Map<?, String>) - Method in class ubic.basecode.io.writer.MatrixWriter
setSliceNames(List<S>) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
setSliceNames(List<S>) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
setStandardizedEnabled(boolean) - Method in class ubic.basecode.graphics.MatrixDisplay
setString(String, Object) - Static method in class ubic.basecode.util.Configuration
setTopLeft(String) - Method in class ubic.basecode.io.writer.MatrixWriter
setTopoSortOrder(int) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode
setTransform(boolean) - Method in class ubic.basecode.math.metaanalysis.CorrelationEffectMetaAnalysis
setTxtMatched(String) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
setUseAsFraction(boolean) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of
the rows with the lowest values.
setUseHighCutAsFraction(boolean) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
setUseLowCutAsFraction(boolean) - Method in class ubic.basecode.datafilter.AbstractLevelFilter
setValue(K, V) - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode
setValue(K, V) - Method in interface ubic.basecode.dataStructure.graph.GraphNode
Set the key and value associated with this node.
setValue(HSSFSheet, int, int, double) - Static method in class ubic.basecode.io.excel.ExcelUtil
setValue(HSSFSheet, int, int, int) - Static method in class ubic.basecode.io.excel.ExcelUtil
setValue(HSSFSheet, int, int, String) - Static method in class ubic.basecode.io.excel.ExcelUtil
setValueUri(String) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse
showError(String) - Method in class ubic.basecode.util.StatusDebugLogger
showError(String, Throwable) - Method in class ubic.basecode.util.StatusDebugLogger
showError(Throwable) - Method in class ubic.basecode.util.StatusDebugLogger
showError(String) - Method in class ubic.basecode.util.StatusStderr
showError(String, Throwable) - Method in class ubic.basecode.util.StatusStderr
showError(Throwable) - Method in class ubic.basecode.util.StatusStderr
showError(String) - Method in interface ubic.basecode.util.StatusViewer
Print an error status messge.
showError(String, Throwable) - Method in interface ubic.basecode.util.StatusViewer
showError(Throwable) - Method in interface ubic.basecode.util.StatusViewer
showProgress(String) - Method in class ubic.basecode.util.StatusDebugLogger
showProgress(String) - Method in class ubic.basecode.util.StatusStderr
showProgress(String) - Method in interface ubic.basecode.util.StatusViewer
showStatus(String) - Method in class ubic.basecode.util.StatusDebugLogger
showStatus(String, boolean) - Method in class ubic.basecode.util.StatusDebugLogger
showStatus(String) - Method in class ubic.basecode.util.StatusStderr
showStatus(String, boolean) - Method in class ubic.basecode.util.StatusStderr
showStatus(String) - Method in interface ubic.basecode.util.StatusViewer
Print the status to the location appropriate for this application.
showStatus(String, boolean) - Method in interface ubic.basecode.util.StatusViewer
showWarning(String) - Method in class ubic.basecode.util.StatusDebugLogger
showWarning(String) - Method in class ubic.basecode.util.StatusStderr
showWarning(String) - Method in interface ubic.basecode.util.StatusViewer
sign_j(double, double) - Static method in class ubic.basecode.math.linalg.Blas
This method implements the FORTRAN sign (not sin) function.
SingularValueDecomposition <R ,C > - Class in ubic.basecode.math.linalg
SVD for DoubleMatrix.
SingularValueDecomposition(DoubleMatrix<R, C>) - Constructor for class ubic.basecode.math.linalg.SingularValueDecomposition
size() - Method in class ubic.basecode.dataStructure.CountingMap
size() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
size() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
size() - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
sizeWithoutMissingValues(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
sizeWithoutMissingValues(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Return the size of the list, ignoring missing values.
skew(DoubleArrayList, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the skew of a data sequence, which is moment(data,3,mean) /
standardDeviation3 .
sliceMap - Variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
sliceNameMap - Variable in class ubic.basecode.io.writer.MatrixWriter
sliceNames - Variable in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
slices() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D
slices() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix
slices() - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix
slices() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D
slices() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D
SMALL - Static variable in class ubic.basecode.math.Constants
SMALLISH - Static variable in class ubic.basecode.math.Constants
Smooth - Class in ubic.basecode.math
Methods for moving averages, loess
Smooth() - Constructor for class ubic.basecode.math.Smooth
solve(DoubleMatrix2D) - Method in class ubic.basecode.math.linalg.QRDecomposition
Least squares solution of A*X = y ; returns X using the stored QR decomposition of A.
sortByColumnAbsoluteValues(int, boolean) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
sortedKeyList() - Method in class ubic.basecode.dataStructure.CountingMap
Returns a list of the keys in this map, sorted by ascending count.
sortedKeyList(boolean) - Method in class ubic.basecode.dataStructure.CountingMap
Returns a list of the keys in this map, sorted as specified.
sparse(double[][]) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
sparse(int, int) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory
SparseDoubleMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
A sparse matrix that knows about row and column names.
SparseDoubleMatrix(double[][]) - Constructor for class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
SparseDoubleMatrix(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
SparseDoubleMatrix(int, int, int, double, double) - Constructor for class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
SparseDoubleMatrixReader - Class in ubic.basecode.io.reader
SparseDoubleMatrixReader() - Constructor for class ubic.basecode.io.reader.SparseDoubleMatrixReader
SparseRaggedDoubleMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
A sparse matrix class where the rows are ragged and compressed.
SparseRaggedDoubleMatrix() - Constructor for class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
SparseRaggedMatrixReader - Class in ubic.basecode.io.reader
Best data structure for reading really big, really sparse matrices when a matrix represetation is needed.
SparseRaggedMatrixReader() - Constructor for class ubic.basecode.io.reader.SparseRaggedMatrixReader
spearmanPvalue(double, int) - Static method in class ubic.basecode.math.CorrelationStats
spearmanRankCorrelation(DoubleArrayList) - Static method in class ubic.basecode.math.Distance
Convenience function to compute the rank correlation when we just want to know if the values are "in order".
spearmanRankCorrelation(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.Distance
Spearman Rank Correlation.
SpecFunc - Class in ubic.basecode.math
Assorted special functions, primarily concerning probability distributions.
SpecFunc() - Constructor for class ubic.basecode.math.SpecFunc
spreadsheet - Variable in class ubic.basecode.io.excel.CreateSpreadSheet
SpreadSheetFilter - Interface in ubic.basecode.io.excel
Processing spreadsheet values.
SpreadSheetSchema - Class in ubic.basecode.io.excel
This class is to determine what information is put in the spreadsheet and its column position
SpreadSheetSchema() - Constructor for class ubic.basecode.io.excel.SpreadSheetSchema
SpreadSheetSchema(Map<String, Integer>) - Constructor for class ubic.basecode.io.excel.SpreadSheetSchema
SQLUtils - Class in ubic.basecode.util
SQLUtils() - Constructor for class ubic.basecode.util.SQLUtils
squeezeVar(DoubleMatrix1D, DoubleMatrix1D, LeastSquaresFit) - Static method in class ubic.basecode.math.linearmodels.ModeratedTstat
Ignoring robust and covariate for now
squeezeVariances(DoubleMatrix1D, DoubleMatrix1D, double[]) - Static method in class ubic.basecode.math.linearmodels.ModeratedTstat
ST - Static variable in class ubic.basecode.datafilter.AffymetrixProbeNameFilter
Filter probes that contain the '_st' (sense strand) tag
standardize() - Method in class ubic.basecode.graphics.ColorMatrix
Normalizes the elements of a matrix to variance one and mean zero, ignoring missing values todo move this to
matrixstats or something.
standardize(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Standardize.
standardize(DoubleArrayList, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Modifies a data sequence to be standardized.
standardize(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats
Scale the rows of the matrix; returns a new matrix.
startInitializationThread(boolean, boolean) - Method in class ubic.basecode.ontology.providers.AbstractOntologyService
startInitializationThread(boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService
Start the initialization thread.
Stats - Class in ubic.basecode.math
Miscellaneous functions used for statistical analysis.
StatusDebugLogger - Class in ubic.basecode.util
StatusDebugLogger() - Constructor for class ubic.basecode.util.StatusDebugLogger
StatusStderr - Class in ubic.basecode.util
Prints status info to stderr
StatusStderr() - Constructor for class ubic.basecode.util.StatusStderr
StatusViewer - Interface in ubic.basecode.util
Intended use is to display 'status' information or other messages to users in a non-disruptive fashion (though the
actual use is up to the implementer).
stepSize() - Method in class ubic.basecode.math.distribution.Histogram
stringArrayToBytes(Object[]) - Method in class ubic.basecode.io.ByteArrayConverter
Note that this method cannot differentiate between empty strings and null strings.
stringArrayToDoubles(String[]) - Method in class ubic.basecode.io.StringConverter
StringConverter - Class in ubic.basecode.io
StringConverter() - Constructor for class ubic.basecode.io.StringConverter
StringDistance - Class in ubic.basecode.math
StringDistance() - Constructor for class ubic.basecode.math.StringDistance
stringEval(String) - Method in class ubic.basecode.util.r.AbstractRClient
stringEval(String) - Method in interface ubic.basecode.util.r.RClient
Evaluate any command and return a string
stringListEval(String) - Method in class ubic.basecode.util.r.AbstractRClient
stringListEval(String) - Method in interface ubic.basecode.util.r.RClient
StringMatrix <R ,C > - Class in ubic.basecode.dataStructure.matrix
A NamedMatrix containing String objects.
StringMatrix(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.StringMatrix
StringMatrixReader - Class in ubic.basecode.io.reader
Reader for basecode.dataStructure.matrix.StringMatrix
StringMatrixReader() - Constructor for class ubic.basecode.io.reader.StringMatrixReader
stringPixelWidth(String, FontMetrics) - Static method in class ubic.basecode.graphics.text.Util
stringsToFile(Collection<String>, File) - Static method in class ubic.basecode.util.FileTools
Outputs a many strings to a file, one line at a time.
stringsToFile(Collection<String>, File, boolean) - Static method in class ubic.basecode.util.FileTools
Outputs many strings to a file, one line at a time.
stringsToFile(Collection<String>, String) - Static method in class ubic.basecode.util.FileTools
Outputs a many strings to a file, one line at a time.
stringToDoubles(String) - Method in class ubic.basecode.io.StringConverter
stringToFile(String, File) - Static method in class ubic.basecode.util.FileTools
Outputs a string to a file.
stringToFile(String, File, boolean) - Static method in class ubic.basecode.util.FileTools
Outputs a string to a file, one line at a time.
StringToStringSetMap - Class in ubic.basecode.dataStructure
Implemented to store string based many to many relationships.
StringToStringSetMap() - Constructor for class ubic.basecode.dataStructure.StringToStringSetMap
StringToStringSetMap(Map<String, Set<String>>) - Constructor for class ubic.basecode.dataStructure.StringToStringSetMap
StringUtil - Class in ubic.basecode.util
StringUtil() - Constructor for class ubic.basecode.util.StringUtil
stripByCriterion(DoubleMatrix1D, DoubleFunction<Boolean>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
stripInvalidCharacters(String) - Static method in class ubic.basecode.ontology.search.OntologySearch
Will remove characters that jena is unable to parse.
stripNegative(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
stripNonOK(DoubleMatrix1D, BooleanArrayList) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil
subset(int, int, int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
subset(int, int, int, int) - Method in interface ubic.basecode.dataStructure.matrix.ObjectMatrix
subset(int, int, int, int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
subset(int, int, int, int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
Create a copy of this matrix with only the selected columns, in the selected order.
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
subsetColumns(List<C>) - Method in interface ubic.basecode.dataStructure.matrix.ObjectMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
subsetColumns(List<C>) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix
subsetRows(List<R>) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix
subsetRows(List<R>) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix
subsetRows(List<R>) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix
Create a copy of this matrix with only the selected rows, in the selected order.
subsetRows(List<R>) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix
subsetRows(List<R>) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix
subsetRows(List<R>) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix
suffixWeightedHammingDistance(String, String, double) - Static method in class ubic.basecode.math.StringDistance
sum(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sum of a data sequence.
sumArray(int[]) - Static method in class ubic.basecode.math.MathUtil
summarize() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
summarize(boolean) - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
summarize(int) - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
Compute and organize the various summary statistics for a fit.
summarizeByKeys(boolean) - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit
sumOfInversions(DoubleArrayList, int, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sum of inversions of a data sequence, which is Sum( 1.0 /
data[i]) .
sumOfLogarithms(DoubleArrayList, int, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sum of logarithms of a data sequence, which is Sum(
Log(data[i]) .
sumOfPowerDeviations(DoubleArrayList, int, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns Sum( (data[i]-c)k ) ; optimized for common parameters like c == 0.0 and/or
k == -2 .. 4 .
sumOfPowerDeviations(DoubleArrayList, int, double, int, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns Sum( (data[i]-c)k ) for all i = from ..
sumOfPowers(DoubleArrayList, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sum of powers of a data sequence, which is Sum (
data[i]k ) .
sumOfSquaredDeviations(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Compute the sum of the squared deviations from the mean of a data sequence.
sumOfSquares(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing
Returns the sum of squares of a data sequence.
sumOfSquares(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixRowStats
Calculates the sum of squares for each row of a matrix
sums(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixRowStats
Calculate the sums of a matrix's rows.