A B C D E F G H I J K L M N O P Q R S T U V W X Z
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A

AbstractBaseCodeOntologyService - Class in ubic.basecode.ontology.providers

Base class for all ontologies built-in to the baseCode project.

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 Matrix2Dfrom a file.

AbstractMatrixReader() - Constructor for class ubic.basecode.io.reader.AbstractMatrixReader

AbstractOntologyService - Class in ubic.basecode.ontology.jena

Base class for Jena-based ontology services.

AbstractOntologyService - Class in ubic.basecode.ontology.providers

Base class for all ontology services.

AbstractOntologyService() - Constructor for class ubic.basecode.ontology.jena.AbstractOntologyService

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) - 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 class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

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(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

addNode(R) - Method in class ubic.basecode.dataStructure.graph.AbstractGraph

addNode(DirectedGraphNode<K, V>) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph

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, IntArrayList, DoubleArrayList) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix

addRow(R, DoubleMatrix1D) - 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

alternativeLabel - Static variable in class ubic.basecode.ontology.jena.IAO

AnnotationProperty - Interface in ubic.basecode.ontology.model

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)

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

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, double[]) - 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.JRIClient

assign(String, int[]) - Method in interface ubic.basecode.util.r.RClient

assign(String, int[]) - Method in class ubic.basecode.util.r.RServeClient

assign(String, String) - Method in class ubic.basecode.util.r.JRIClient

assign(String, String) - Method in interface ubic.basecode.util.r.RClient

assign(String, String) - Method in class ubic.basecode.util.r.RServeClient

assign(String, String[]) - Method in class ubic.basecode.util.r.JRIClient

assign(String, String[]) - Method in interface ubic.basecode.util.r.RClient

assign(String, String[]) - Method in class ubic.basecode.util.r.RServeClient

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.

assignFactor(String, List<String>) - Method in class ubic.basecode.util.r.AbstractRClient

assignFactor(String, List<String>) - Method in interface ubic.basecode.util.r.RClient

assignFactor(List<String>) - Method in class ubic.basecode.util.r.AbstractRClient

assignFactor(List<String>) - Method in interface ubic.basecode.util.r.RClient

assignMatrix(double[][]) - 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 class ubic.basecode.util.r.AbstractRClient

assignMatrix(DoubleMatrix<?, ?>) - Method in interface ubic.basecode.util.r.RClient

Assign a 2-d matrix.

assignMatrix(DoubleMatrix<?, ?>, Transformer) - Method in class ubic.basecode.util.r.AbstractRClient

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.

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".

B

batches(Collection<E>, int) - Static method in class ubic.basecode.util.BatchIterator

Returns a BatchIterator over the specified collection.

BatchIterator<E> - Class in ubic.basecode.util

Example usage:

BatchIterator(Collection<E>, int) - Constructor for class ubic.basecode.util.BatchIterator

Returns a BatchIterator over the specified collection.

benjaminiHochberg(DoubleArrayList) - Static method in class ubic.basecode.math.MultipleTestCorrection

benjaminiHochberg(DoubleMatrix1D) - Static method in class ubic.basecode.math.MultipleTestCorrection

benjaminiHochbergCut(DoubleArrayList, double) - Static method in class ubic.basecode.math.MultipleTestCorrection

Benjamini-Hochberg method.

BenjaminiYekuteliCut(DoubleArrayList, double) - Static method in class ubic.basecode.math.MultipleTestCorrection

Benjamini-Yekuteli method.

BinaryTree<T> - Class in ubic.basecode.dataStructure.tree

BinaryTree(T) - Constructor for class ubic.basecode.dataStructure.tree.BinaryTree

BinaryTreeNode<T> - Class in ubic.basecode.dataStructure.tree

BinaryTreeNode() - Constructor for class ubic.basecode.dataStructure.tree.BinaryTreeNode

BinaryTreeNode(T) - Constructor for class ubic.basecode.dataStructure.tree.BinaryTreeNode

BinaryTreeNode(BinaryTreeNode<T>) - Constructor for class ubic.basecode.dataStructure.tree.BinaryTreeNode

BIT1 - Static variable in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

bitCount(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

Count the number of one-bits at the specified cell position

BITS_PER_ELEMENT - Static variable in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

BitUtil - Class in ubic.basecode.dataStructure

Based on code from: Derby - Class org.apache.derbyTesting.unitTests.util.BitUtil

BitUtil() - Constructor for class ubic.basecode.dataStructure.BitUtil

BLACKBODY_COLORMAP - Static variable in class ubic.basecode.graphics.ColorMap

Blas - Class in ubic.basecode.math.linalg

This class contains Java versions of a number of the LINPACK basic linear algebra subroutines (blas): isamax_j daxpy_j ddot_j dscal_j dswap_j dnrm2_j dcopy_j drotg_j It also contains utility routines that the translator found useful while translating the FORTRAN code to Java code.

Blas() - Constructor for class ubic.basecode.math.linalg.Blas

blobToString(Blob) - Static method in class ubic.basecode.util.SQLUtils

Convert a java.sql.Blob array to a string

BonferroniCut(DoubleArrayList, double) - Static method in class ubic.basecode.math.MultipleTestCorrection

Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are independent).

booleanArrayToBytes(boolean[]) - Method in class ubic.basecode.io.ByteArrayConverter

booleanDoubleArrayEval(String, String, double[]) - Method in class ubic.basecode.util.r.AbstractRClient

booleanDoubleArrayEval(String, String, double[]) - Method in interface ubic.basecode.util.r.RClient

Run a command that takes a double array as an argument and returns a boolean.

BrowserLauncher - Class in ubic.basecode.util

BrowserLauncher() - Constructor for class ubic.basecode.util.BrowserLauncher

ByteArrayConverter - Class in ubic.basecode.io

Class to convert byte arrays (e.g., Blobs) to and from other types of arrays.

ByteArrayConverter() - Constructor for class ubic.basecode.io.ByteArrayConverter

byteArrayToAsciiString(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

Convert a byte array with one-byte-per-character ASCII encoding (aka ISO-8859-1).

byteArrayToBooleans(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

byteArrayToChars(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

byteArrayToDoubleMatrix(byte[], int) - Method in class ubic.basecode.io.ByteArrayConverter

byteArrayToDoubles(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

byteArrayToInts(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

byteArrayToLongs(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

byteArrayToStrings(byte[]) - Method in class ubic.basecode.io.ByteArrayConverter

Convert a byte array into a array of Strings.

byteArrayToTabbedString(byte[], Class<?>) - Method in class ubic.basecode.io.ByteArrayConverter

Convert a byte array to a tab-delimited string.

byteToCorrel(int) - Static method in class ubic.basecode.math.CorrelationStats

byteToPvalue(int) - Static method in class ubic.basecode.math.CorrelationStats

C

cancelInitializationThread() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

Cancel the initialization thread.

cancelInitializationThread() - Method in interface ubic.basecode.ontology.providers.OntologyService

Cancel a running initialization thread.

cardinality() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

cardinality() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix

CARDINALITY - ubic.basecode.ontology.model.OntologyCardinalityRestriction.CardinalityType

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

Cell Line Ontology

CellLineOntologyService() - Constructor for class ubic.basecode.ontology.providers.CellLineOntologyService

CellTypeOntologyService - Class in ubic.basecode.ontology.providers

Cell Ontology

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

Chemical Entities of Biological Interest

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 k random integers from 0 to max (exclusive) without repeating

chooserandom(int, int) - Static method in class ubic.basecode.math.RandomChooser

choose n random integers from 0 (inclusive) 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() - 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.

clear(byte[], int) - Static method in class ubic.basecode.dataStructure.BitUtil

Clear the bit at the specified position

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(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.

closeEnough(DoubleMatrix<?, ?>, DoubleMatrix<?, ?>, double) - Static method in class ubic.basecode.util.RegressionTesting

Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.

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 - Variable in class ubic.basecode.graphics.ColorMatrix

ColorMap - Class in ubic.basecode.graphics

ColorMap() - 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(Color[]) - Constructor for class ubic.basecode.graphics.ColorMap

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." It is a modification of the LINPACK function DROT.

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.

compare(OntologySearchResult<?>, OntologySearchResult<?>) - Method in class ubic.basecode.ontology.search.OntologySearchResult

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(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

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() - Method in class ubic.basecode.util.r.RServeClient

connect(int, String, String, String) - Static method in class ubic.basecode.util.NetUtils

Convenient method to get a FTP connection.

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(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

containsColumnName(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

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(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

containsRowName(R) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix

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(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.

containsSame(Collection<? extends Object>, Collection<? extends Object>) - Static method in class ubic.basecode.util.RegressionTesting

Test whether two collections contain the same items.

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.

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(DoubleArrayList) - Static method in class ubic.basecode.math.Stats

Compute the coefficient of variation of an array (standard deviation / mean).

CV - Static variable in class ubic.basecode.datafilter.RowLevelFilter

Use the coefficient of variation as the criterion

cvs2tsv(String) - Static method in class ubic.basecode.util.StringUtil

Made by Nicolas

D

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

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

dense(double[][]) - Static method in class ubic.basecode.dataStructure.matrix.DoubleMatrixFactory

dense(int, int) - 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.

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(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

DenseObject3DMatrix(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, ?>, boolean) - 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, Object>, boolean, boolean) - Constructor for class ubic.basecode.math.linearmodels.DesignMatrix

DesignMatrix(StringMatrix<String, String>) - 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)

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

Deprecated.

use MONDO instead

DiseaseOntologyService() - Constructor for class ubic.basecode.ontology.providers.DiseaseOntologyService

Deprecated.

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

DL - ubic.basecode.ontology.providers.OntologyService.LanguageLevel

OWL-DL

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(DoubleArrayList) - Method in class ubic.basecode.io.ByteArrayConverter

doubleArrayToBytes(Double[]) - 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." For details, see the comments in the code.

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.

E

ebayes(LeastSquaresFit) - Static method in class ubic.basecode.math.linearmodels.ModeratedTstat

Does essentially the same thing as limma::ebayes

ebayesUpdate(double, double, DoubleMatrix1D) - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit

Provide results of limma eBayes algorithm.

editDistance(String, String) - Static method in class ubic.basecode.math.StringDistance

The edit distance counts the differences between two strings, where we would count a difference not only when strings have different characters but also when one has a character whereas the other does not.

effects(DoubleMatrix1D) - Method in class ubic.basecode.math.linalg.QRDecomposition

Compute effects matrix Q'y (as in Rb = Q'y).

effects(DoubleMatrix2D) - Method in class ubic.basecode.math.linalg.QRDecomposition

Compute effects matrix Q'y (as in Rb = Q'y)

EMPTY - Static variable in class ubic.basecode.graphics.JGradientBar

entries() - Method in class ubic.basecode.math.distribution.Histogram

The number of entries in the histogram (the number of times fill has been called).

entrySet() - Method in class ubic.basecode.dataStructure.CountingMap

equals(Object) - Method in class ubic.basecode.dataStructure.CountingMap

equals(Object) - Method in class ubic.basecode.dataStructure.Link

equals(Object) - Method in class ubic.basecode.dataStructure.Point

equals(Object) - Method in class ubic.basecode.ontology.model.OntologyTermSimple

equals(Object) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse

equals(Object) - Method in class ubic.basecode.ontology.search.OntologySearchResult

equals(Object) - Method in class ubic.basecode.util.r.type.AnovaResult

euclDistance(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.Distance

Calculate the Euclidean distance between two vectors.

eval(String) - Method in class ubic.basecode.util.r.JRIClient

eval(String) - Method in interface ubic.basecode.util.r.RClient

Evaluate the given command

eval(String) - Method in class ubic.basecode.util.r.RServeClient

exactWilcoxonP(double[], double[]) - Static method in class ubic.basecode.math.Wilcoxon

Convenience method that computes a p-value using input of two double arrays.

exactWilcoxonP(int, int, int) - Static method in class ubic.basecode.math.Wilcoxon

ExcelUtil - Class in ubic.basecode.io.excel

Utilities for dealign with Microsoft Excel spreadsheets as implemented in commons-poi.

ExcelUtil() - Constructor for class ubic.basecode.io.excel.ExcelUtil

ExperimentalFactorOntologyService - Class in ubic.basecode.ontology.providers

Experimental Factor Ontology

ExperimentalFactorOntologyService() - Constructor for class ubic.basecode.ontology.providers.ExperimentalFactorOntologyService

F

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(int, int) - Method in class ubic.basecode.math.distribution.Histogram

Add the given number of counts to the given bin.

fill(DoubleMatrix1D) - Method in class ubic.basecode.math.distribution.Histogram

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) - Method in interface ubic.basecode.datafilter.Filter

Filter the data

filter(M) - Method in class ubic.basecode.datafilter.RowAbsentFilter

The data is going to be filtered in accordance to strings in 'flags'.

filter(M) - Method in class ubic.basecode.datafilter.RowMissingFilter

filter(M) - Method in class ubic.basecode.datafilter.RowNameFilter

Filter according to row names.

filter(DoubleMatrix<R, C>) - Method in class ubic.basecode.datafilter.ItemLevelFilter

filter(DoubleMatrix<R, C>) - Method in class ubic.basecode.datafilter.RowLevelFilter

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.

finalize() - Method in class ubic.basecode.util.r.RServeClient

findCondition(boolean) - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse

findIndividuals(String, int) - Method in interface ubic.basecode.ontology.providers.OntologyService

Looks for any individuals that match the given search string.

findIndividuals(String, int, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

findIndividuals(String, int, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Looks for any individuals 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, int) - Method in interface ubic.basecode.ontology.providers.OntologyService

Looks for any resources (terms or individuals) that match the given search string

findResources(String, int, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

findResources(String, int, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Looks for any resources (terms or individuals) 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, int) - Method in interface ubic.basecode.ontology.providers.OntologyService

Looks for any terms that match the given search string.

findTerm(String, int, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

findTerm(String, int, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Looks for any terms that match the given search string.

findUsingAlternativeId(String) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

findUsingAlternativeId(String) - Method in interface ubic.basecode.ontology.providers.OntologyService

Find a term using an alternative ID.

fisherCombineLogPvalues(DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis

Fisher's method for combining p values (Cooper and Hedges 15-8)

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

Deprecated.

this ontology is inactive, use UBERON instead

FMAOntologyService() - Constructor for class ubic.basecode.ontology.providers.FMAOntologyService

Deprecated.

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.

FULL - ubic.basecode.ontology.providers.OntologyService.InferenceMode

Complete inference.

FULL - ubic.basecode.ontology.providers.OntologyService.LanguageLevel

The full OWL language.

G

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 in-memory ontology services.

GenericOntologyService(String, String) - Constructor for class ubic.basecode.ontology.providers.GenericOntologyService

GenericOntologyService(String, String, boolean) - Constructor for class ubic.basecode.ontology.providers.GenericOntologyService

Deprecated.

use GenericOntologyService(String, String, String) with an explicit cache name instead

GenericOntologyService(String, String, boolean, boolean) - Constructor for class ubic.basecode.ontology.providers.GenericOntologyService

Deprecated.

use GenericOntologyService(String, String, String) with an explicit cache name instead and AbstractOntologyService.setProcessImports(boolean)

GenericOntologyService(String, String, String) - 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() - Method in class ubic.basecode.dataStructure.DoublePoint

get() - Method in class ubic.basecode.dataStructure.Point

get(byte[], int) - Static method in class ubic.basecode.dataStructure.BitUtil

Check to see if the specified bit is set

get(int) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

get(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

get(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

get(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

get(int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix

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(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(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, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

get(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix

get(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

get(Object) - Method in class ubic.basecode.dataStructure.CountingMap

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(R, C) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

get(R, C) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix

getAdditionalPropertyUris() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getAdditionalPropertyUris() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain the URIs used as additional properties when inferring parents and children.

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.jena.AbstractOntologyService

getAllURIs() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain all the resource URIs in this ontology.

getAlternative() - Method in class ubic.basecode.util.r.type.HTest

getAlternativeIds() - Method in interface ubic.basecode.ontology.model.OntologyTerm

Obtain alternative IDs for this term.

getAlternativeIds() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getAnnotation(String) - Method in interface ubic.basecode.ontology.model.OntologyTerm

Obtain an annotation by property URI.

getAnnotation(String) - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getAnnotations() - Method in interface ubic.basecode.ontology.model.OntologyTerm

Obtain all annotations for this term.

getAnnotations() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getAnnotations(String) - Method in interface ubic.basecode.ontology.model.OntologyTerm

Obtain all the annotations for a given property URI.

getAnnotations(String) - 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

Obtain a boolean configuration value by key.

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

getCacheName() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

A name for caching this ontology, or null to disable caching.

getCacheName() - Method in class ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

getCacheName() - Method in class ubic.basecode.ontology.providers.GenericOntologyService

getCardinality() - Method in interface ubic.basecode.ontology.model.OntologyCardinalityRestriction

getCardinalityType() - Method in interface ubic.basecode.ontology.model.OntologyCardinalityRestriction

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

Obtain the children of this term via subclasses and additional properties.

getChildren(boolean, boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm

getChildren(boolean, boolean, boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm

Obtain the children of this term via subclass relationships and possibly some additional properties.

getChildren(boolean, boolean, boolean) - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getChildren(Collection<OntologyTerm>, boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain all the children of a given set of terms, excluding obsolete terms.

getChildren(Collection<OntologyTerm>, boolean, boolean, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getChildren(Collection<OntologyTerm>, boolean, boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain all the children of a given set of terms.

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(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.

getColIndexByName(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

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.OntologyResource

A comment for the resource, if available, otherwise null.

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

The value associated to this annotation as a string.

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

getDescription() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getDescription() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain a description of this ontology if available.

getDf() - Method in class ubic.basecode.util.r.type.OneWayAnovaResult

getDfPrior() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFit

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

getExcludedWordsFromStemming() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getExcludedWordsFromStemming() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain the words that should be excluded from stemming.

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.

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(boolean) - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getInferenceMode() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getInferenceMode() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain the inference mode used for this ontology.

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.

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 interface ubic.basecode.ontology.model.OntologyResource

A label, if known, otherwise null.

getLabel() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getLanguageLevel() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getLanguageLevel() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain the OWL language level supported by this ontology.

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.OntologyResource

A local name for this resource.

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

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.

getName() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getName() - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain the name of this ontology if available.

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() - 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(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

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) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix

getObject(int, int) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix

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(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

getObject(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix

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

getOntologyName() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

The simple getOntologyName() of the ontology.

getOntologyName() - Method in class ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

getOntologyName() - Method in class ubic.basecode.ontology.providers.GenericOntologyService

getOntologyUrl() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

Defines the location of the ontology eg: MGED

getOntologyUrl() - Method in class ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

getOntologyUrl() - Method in class ubic.basecode.ontology.providers.ExperimentalFactorOntologyService

getOntologyUrl() - Method in class ubic.basecode.ontology.providers.GenericOntologyService

getOntologyUrl() - Method in class ubic.basecode.ontology.providers.MedicOntologyService

Deprecated.

getOntologyUrl() - Method in class ubic.basecode.ontology.providers.NIFSTDOntologyService

Deprecated.

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, boolean, boolean) - Method in interface ubic.basecode.ontology.model.OntologyTerm

getParents(boolean, boolean, boolean) - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getParents(Collection<OntologyTerm>, boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain all the parents of a given set of terms, excluding obsolete terms.

getParents(Collection<OntologyTerm>, boolean, boolean, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getParents(Collection<OntologyTerm>, boolean, boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain all the parents of a given set of terms.

getPivotOrder() - Method in class ubic.basecode.math.linalg.QRDecomposition

getPosition(String) - Method in class ubic.basecode.io.excel.SpreadSheetSchema

getPriorDof() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary

getProcessImports() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

getProcessImports() - Method in interface ubic.basecode.ontology.providers.OntologyService

Check if this ontology will process imports.

getProperty() - Method in interface ubic.basecode.ontology.model.AnnotationProperty

A label for the property of this annotation.

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.HTest

getPValue() - Method in class ubic.basecode.util.r.type.AnovaEffect

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

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.jena.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 interface ubic.basecode.ontology.model.OntologyDatatypeRestriction

getRestrictionOn() - Method in interface ubic.basecode.ontology.model.OntologyRestriction

getRestrictions() - Method in interface ubic.basecode.ontology.model.OntologyTerm

getRestrictions() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getResult() - Method in class ubic.basecode.ontology.search.OntologySearchResult

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) - 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(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

getRow(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix

getRow(Matrix2D<R, C, V>, int) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil

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(A) - Method in class ubic.basecode.graphics.ColorMatrix

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(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(A) - Method in class ubic.basecode.graphics.ColorMatrix

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(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

getScore() - Method in class ubic.basecode.ontology.search.OntologySearchResult

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

Obtain a configuration value by key.

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

getTerm() - Method in interface ubic.basecode.ontology.model.OntologyTerm

Deprecated.

use OntologyResource.getLabel() instead.

getTerm() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

getTerm(String) - Method in class ubic.basecode.ontology.jena.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.jena.AbstractOntologyService

getTermIndividuals(String) - Method in interface ubic.basecode.ontology.providers.OntologyService

Obtain all the individuals for a given term URI.

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

getU() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition

getUri() - Method in interface ubic.basecode.ontology.model.OntologyResource

A URI if known, otherwise null.

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

H

hammingDistance(String, String) - Static method in class ubic.basecode.math.StringDistance

The Hamming distance H is defined only for strings of the same length.

hasChild(Object) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode

Check to see if this node has a particular immediate child.

hasColNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix

hasColNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

hasColNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D

Check if this matrix has a valid set of column names.

hasColNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D

Check if this matrix has a valid set of column names.

hasFullRank() - Method in class ubic.basecode.math.linalg.QRDecomposition

Returns whether the matrix A has full rank.

hashCode() - Method in class ubic.basecode.dataStructure.CountingMap

hashCode() - Method in class ubic.basecode.dataStructure.Link

hashCode() - Method in class ubic.basecode.dataStructure.Point

hashCode() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

hashCode() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse

hashCode() - Method in class ubic.basecode.ontology.search.OntologySearchResult

hashCode() - Method in class ubic.basecode.util.r.type.AnovaResult

hasImageExtension(String) - Static method in class ubic.basecode.util.FileTools

hasInteractions() - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult

hasInteractions() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary

hasIntercept() - Method in class ubic.basecode.math.linearmodels.DesignMatrix

hasMissingValues() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix

Test for the presence of missing values (null, or in the case of numbers, NaN)

hasNext() - Method in class ubic.basecode.util.BatchIterator

hasParent(Object) - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode

Check to see if this node has a particular immediate parent.

hasRow(Object) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

hasRow(R) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix

hasRow(R) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D

hasRow(R) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D

hasRowNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix

hasRowNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

hasRowNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D

hasRowNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D

hasSliceNames() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

hasSliceNames() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D

hasXMLExtension(String) - Static method in class ubic.basecode.util.FileTools

highCut - Variable in class ubic.basecode.datafilter.AbstractLevelFilter

Histogram - Class in ubic.basecode.math.distribution

A simple histogram.

Histogram(String, int, double, double) - Constructor for class ubic.basecode.math.distribution.Histogram

Histogram(String, int, DoubleMatrix1D) - Constructor for class ubic.basecode.math.distribution.Histogram

HistogramReader - Class in ubic.basecode.io.reader

Reads histograms stored in flat files

HistogramReader(Reader, String) - Constructor for class ubic.basecode.io.reader.HistogramReader

HistogramReader(String) - Constructor for class ubic.basecode.io.reader.HistogramReader

HistogramSampler - Class in ubic.basecode.math.distribution

Implements a simple (not very efficient) sampling algorithm for empirical distributions.

HistogramSampler(int[], double, double) - Constructor for class ubic.basecode.math.distribution.HistogramSampler

HistogramSampler(Histogram1D) - Constructor for class ubic.basecode.math.distribution.HistogramSampler

HistogramWriter - Class in ubic.basecode.io.writer

Print an hep.aidia.IHistogram1Dobject to a text file.

HistogramWriter() - Constructor for class ubic.basecode.io.writer.HistogramWriter

HP_ONTOLOGY - Static variable in class ubic.basecode.ontology.ncbo.AnnotatorClient

HTest - Class in ubic.basecode.util.r.type

Representation of the R htest class.

HTest() - Constructor for class ubic.basecode.util.r.type.HTest

HTest(RList) - Constructor for class ubic.basecode.util.r.type.HTest

HumanDevelopmentOntologyService - Class in ubic.basecode.ontology.providers

Deprecated.

this ontology was last updated in unmaintained since 2013

HumanDevelopmentOntologyService() - Constructor for class ubic.basecode.ontology.providers.HumanDevelopmentOntologyService

Deprecated.

HumanPhenotypeOntologyService - Class in ubic.basecode.ontology.providers

Human Phenotype Ontology

HumanPhenotypeOntologyService() - Constructor for class ubic.basecode.ontology.providers.HumanPhenotypeOntologyService

I

IAO - Class in ubic.basecode.ontology.jena

IAO() - Constructor for class ubic.basecode.ontology.jena.IAO

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.jena.AbstractOntologyService

index(boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Index the ontology for performing full-text searches.

indexes - Variable in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

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.

init(ColorMatrix<R, C>) - Method in class ubic.basecode.graphics.MatrixDisplay

initialize(boolean, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

initialize(boolean, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Initialize this ontology service.

initialize(InputStream, boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

initialize(InputStream, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Initialize this ontology service from a stream.

initSize() - Method in class ubic.basecode.graphics.MatrixDisplay

Sets the display size

insertLeft(T) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode

insertLeft(BinaryTreeNode<T>, T) - Method in class ubic.basecode.dataStructure.tree.BinaryTree

insertRight(T) - Method in class ubic.basecode.dataStructure.tree.BinaryTreeNode

insertRight(BinaryTreeNode<T>, T) - Method in class ubic.basecode.dataStructure.tree.BinaryTree

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.jena.AbstractOntologyService

isEnabled() - Method in interface ubic.basecode.ontology.providers.OntologyService

Check if this ontology is enabled.

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

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.jena.AbstractOntologyService

isInitializationThreadAlive() - Method in interface ubic.basecode.ontology.providers.OntologyService

Check if the initialization thread is alive.

isInitializationThreadCancelled() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

isInitializationThreadCancelled() - Method in interface ubic.basecode.ontology.providers.OntologyService

Check if the initialization thread is cancelled.

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) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

isMissing(int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

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) - 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.

isMissing(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

isMissing(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

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, int) - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D

Check if the value at a given index is missing.

isObsolete() - Method in interface ubic.basecode.ontology.model.OntologyResource

Whether the resource is marked as obsolete.

isObsolete() - Method in class ubic.basecode.ontology.model.OntologyTermSimple

isOntologyEnabled() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

Indicate if this ontology is enabled.

isOntologyEnabled() - Method in class ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

isOntologyEnabled() - Method in class ubic.basecode.ontology.providers.GenericOntologyService

isOntologyLoaded() - Method in class ubic.basecode.ontology.jena.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.OntologyTermSimple

isSearchEnabled() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

isSearchEnabled() - Method in interface ubic.basecode.ontology.providers.OntologyService

Check if this ontology has full-text search enabled.

isShrunken() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary

Whether this is the result of emprical bayes shrinkage of variance estimates

isTermObsolete() - Method in interface ubic.basecode.ontology.model.OntologyTerm

Deprecated.

use OntologyResource.isObsolete() instead

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

J

JGradientBar - Class in ubic.basecode.graphics

A GUI legend component that displays a color map as a color gradient from min to max, traversing all the colors in the color map.

JGradientBar() - Constructor for class ubic.basecode.graphics.JGradientBar

JGradientBar(Color[]) - Constructor for class ubic.basecode.graphics.JGradientBar

JRIClient - Class in ubic.basecode.util.r

R connection implementation that uses the dynamic library interface JRI.

JRIClient() - Constructor for class ubic.basecode.util.r.JRIClient

K

key - Variable in class ubic.basecode.dataStructure.graph.AbstractGraphNode

keySet() - Method in class ubic.basecode.dataStructure.CountingMap

KruskalWallis - Class in ubic.basecode.math

Perform a Kruskal-Wallis test.

KruskalWallis() - Constructor for class ubic.basecode.math.KruskalWallis

KSTest - Class in ubic.basecode.math

Class to perform the Kolmogorov-Smirnov test.

KSTest() - Constructor for class ubic.basecode.math.KSTest

kurtosis(double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the kurtosis (aka excess) of a data sequence.

kurtosis(DoubleArrayList, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the kurtosis (aka excess) of a data sequence, which is -3 + moment(data,4,mean) / standardDeviation⁴.

kwStatistic(DoubleArrayList, IntArrayList) - Static method in class ubic.basecode.math.KruskalWallis

L

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(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.

LeastSquaresFit(DesignMatrix, DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.LeastSquaresFit

Preferred interface for weighted least squares fit between two matrices

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

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[], 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 class ubic.basecode.util.r.AbstractRClient

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() - Constructor for class ubic.basecode.math.linearmodels.LinearModelSummary

Construct an empty summary.

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(REXP, REXP, String[]) - Constructor for class ubic.basecode.math.linearmodels.LinearModelSummary

Construct from the result of evaluation of an R call.

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.

LITE - ubic.basecode.ontology.providers.OntologyService.LanguageLevel

OWL/Lite

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

loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

Delegates the call as to load the model into memory or leave it on disk.

loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.basecode.ontology.providers.MedicOntologyService

Deprecated.

loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.basecode.ontology.providers.NIFSTDOntologyService

Deprecated.

loadModelFromStream(InputStream, boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

Load a model from a given input stream.

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.jena.AbstractOntologyService

loadTermsInNameSpace(InputStream, boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Deprecated.

use OntologyService.initialize(InputStream, boolean) instead and possibly OntologyService.cancelInitializationThread() prior to get any running initialization thread out of the way

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.jena.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

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

Mammalian Phenotype Ontology

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

matchingCriteria(DoubleMatrix1D, DoubleFunction<Boolean>) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil

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(DoubleMatrix<R, C>) - Constructor for class ubic.basecode.graphics.MatrixDisplay

MatrixDisplay(ColorMatrix<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(Writer) - Constructor for class ubic.basecode.io.writer.MatrixWriter

MatrixWriter(Writer, String) - 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(String, Format) - Constructor for class ubic.basecode.io.writer.MatrixWriter

MatrixWriter(String, Format, 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 - Variable in class ubic.basecode.graphics.ColorMatrix

max() - Method in class ubic.basecode.dataStructure.CountingMap

max() - Method in class ubic.basecode.math.distribution.Histogram

max(double[]) - Static method in class ubic.basecode.math.MathUtil

max(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

max(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats

Compute the maximum value in the matrix.

MAX - Static variable in class ubic.basecode.datafilter.RowLevelFilter

Use the maximum of the row as the criterion.

MAX_CARDINALITY - ubic.basecode.ontology.model.OntologyCardinalityRestriction.CardinalityType

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(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.

MEAN - Static variable in class ubic.basecode.datafilter.RowLevelFilter

Use the mean as the criterion.

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

MeanDifferenceMetaAnalysis(boolean) - Constructor for class ubic.basecode.math.metaanalysis.MeanDifferenceMetaAnalysis

means(DoubleMatrix2D) - Static method in class ubic.basecode.math.MatrixRowStats

Calculate the means of a matrix's rows

means(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixRowStats

Calculates 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(DoubleMatrix2D) - Constructor for class ubic.basecode.math.linearmodels.MeanVarianceEstimator

Generic method for calculating mean and variance, as a data diagnostic.

MeanVarianceEstimator(DesignMatrix, DoubleMatrix2D, DoubleMatrix1D) - Constructor for class ubic.basecode.math.linearmodels.MeanVarianceEstimator

Executes voom() to calculate weights.

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.

median(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the median.

MEDIAN - Static variable in class ubic.basecode.datafilter.RowLevelFilter

Use the median as the criterion.

MedicOntologyService - Class in ubic.basecode.ontology.providers

Deprecated.

MedicOntologyService() - Constructor for class ubic.basecode.ontology.providers.MedicOntologyService

Deprecated.

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.

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.

metaZscore(double, double) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis

Test statistic for H0: effectSize == 0.

MICRO - ubic.basecode.ontology.providers.OntologyService.InferenceMode

Very limited inference.

min - Variable in class ubic.basecode.graphics.ColorMatrix

min() - Method in class ubic.basecode.math.distribution.Histogram

min(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

min(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats

Find the minimum of the entire matrix.

MIN - Static variable in class ubic.basecode.datafilter.RowLevelFilter

Use the minimum of the row as the criterion.

MIN_CARDINALITY - ubic.basecode.ontology.model.OntologyCardinalityRestriction.CardinalityType

MINI - ubic.basecode.ontology.providers.OntologyService.InferenceMode

Limited inference.

missingColor - Variable in class ubic.basecode.graphics.ColorMatrix

ModeratedTstat - Class in ubic.basecode.math.linearmodels

Implements methods described in

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

Mouse Developmental Anatomy Ontology

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.

N

nanStatusMatrix(double[][]) - Static method in class ubic.basecode.math.MatrixStats

NetUtils - Class in ubic.basecode.util

NetUtils() - Constructor for class ubic.basecode.util.NetUtils

newInstance(DoubleMatrix<R, C>) - Static method in class ubic.basecode.graphics.ColorMatrix

newInstance(ColorMatrix<R, C>) - Static method in class ubic.basecode.graphics.MatrixDisplay

next() - Method in class ubic.basecode.util.BatchIterator

nextDouble() - Method in class ubic.basecode.math.distribution.Dirichlet

nextDoubleMatrix() - Method in class ubic.basecode.math.distribution.Wishart

Based on R code from Francesca Dominici, http ://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html

nextSample() - Method in class ubic.basecode.math.distribution.HistogramSampler

NIFSTDOntologyService - Class in ubic.basecode.ontology.providers

Deprecated.

NIFSTDOntologyService() - Constructor for class ubic.basecode.ontology.providers.NIFSTDOntologyService

Deprecated.

NONE - ubic.basecode.ontology.providers.OntologyService.InferenceMode

No inference is supported, only the axioms defined in the ontology are considered.

norm2() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition

normalize(DoubleArrayList) - Static method in class ubic.basecode.math.Stats

Adjust the elements of an array so they total to 1.0.

normalize(DoubleArrayList, double) - Static method in class ubic.basecode.math.Stats

Divide the elements of an array by a given factor.

NormalProbabilityComputer - Class in ubic.basecode.math.distribution

NormalProbabilityComputer(double, double) - Constructor for class ubic.basecode.math.distribution.NormalProbabilityComputer

notNearlyZeroIndices(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil

numberOfBins() - Method in class ubic.basecode.math.distribution.Histogram

Get the number of bins in the histogram.

numberofDistinctValues(DoubleArrayList, double) - Static method in class ubic.basecode.math.Stats

numberofDistinctValuesNonNA(DoubleArrayList, double) - Static method in class ubic.basecode.math.Stats

numberOfSecondsBetweenDates(Collection<Date>) - Static method in class ubic.basecode.util.DateUtil

Compute the number of seconds spanned by the given dates.

numMissing() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix

numMissing() - Method in class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

numMissing() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

numMissing() - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix

numMissing() - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D

Return the number of missing values in the matrix.

numMissing() - Method in interface ubic.basecode.dataStructure.matrix.Matrix3D

Return the number of missing values in the matrix.

numNeighbors() - Method in class ubic.basecode.dataStructure.graph.UndirectedGraphNode

numParents() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode

O

ObiService - Class in ubic.basecode.ontology.providers

Ontology for Biomedical Investigations

ObiService() - Constructor for class ubic.basecode.ontology.providers.ObiService

ObjectMatrix<R,C,V> - Interface in ubic.basecode.dataStructure.matrix

ObjectMatrixImpl<R,C,V> - Class in ubic.basecode.dataStructure.matrix

Matrix that can hold any type of object

ObjectMatrixImpl(int, int) - Constructor for class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

ObjectProperty - Interface in ubic.basecode.ontology.model

OmimAnnotatorClient - Class in ubic.basecode.ontology.ncbo

to use the OMIM api TODO Document Me

OmimAnnotatorClient() - Constructor for class ubic.basecode.ontology.ncbo.OmimAnnotatorClient

oneSample(DoubleArrayList, ProbabilityComputer) - Static method in class ubic.basecode.math.KSTest

oneSampleProbability(double, int) - Static method in class ubic.basecode.math.KSTest

oneSampleStatistic(DoubleArrayList, ProbabilityComputer) - Static method in class ubic.basecode.math.KSTest

oneWayAnova(double[], List<String>) - Method in class ubic.basecode.util.r.AbstractRClient

oneWayAnova(double[], List<String>) - Method in interface ubic.basecode.util.r.RClient

Lower-level access to a simple one-way ANOVA

oneWayAnovaEval(String) - Method in class ubic.basecode.util.r.AbstractRClient

oneWayAnovaEval(String) - Method in interface ubic.basecode.util.r.RClient

OneWayAnovaResult - Class in ubic.basecode.util.r.type

OneWayAnovaResult() - Constructor for class ubic.basecode.util.r.type.OneWayAnovaResult

A null result.

OneWayAnovaResult(REXP) - Constructor for class ubic.basecode.util.r.type.OneWayAnovaResult

OntologyCardinalityRestriction - Interface in ubic.basecode.ontology.model

OntologyCardinalityRestriction.CardinalityType - Enum in ubic.basecode.ontology.model

OntologyClassRestriction - Interface in ubic.basecode.ontology.model

OntologyDatatypeRestriction - Interface in ubic.basecode.ontology.model

OntologyIndividual - Interface in ubic.basecode.ontology.model

OntologyModel - Interface in ubic.basecode.ontology.model

OntologyProperty - Interface in ubic.basecode.ontology.model

OntologyResource - Interface in ubic.basecode.ontology.model

OntologyRestriction - Interface in ubic.basecode.ontology.model

Note: this only handle 'someof' and 'allof' restrictions, not cardinality.

OntologySearchException - Exception in ubic.basecode.ontology.search

Base class for exceptions raised by OntologyService#findTerm(String) and others.

OntologySearchException(String, String, Throwable) - Constructor for exception ubic.basecode.ontology.search.OntologySearchException

OntologySearchResult<T extends OntologyResource> - Class in ubic.basecode.ontology.search

Represents a search result from an ontology.

OntologySearchResult(T, double) - Constructor for class ubic.basecode.ontology.search.OntologySearchResult

OntologyService - Interface in ubic.basecode.ontology.providers

OntologyService.InferenceMode - Enum in ubic.basecode.ontology.providers

OntologyService.LanguageLevel - Enum in ubic.basecode.ontology.providers

OntologyTerm - Interface in ubic.basecode.ontology.model

OntologyTermSimple - Class in ubic.basecode.ontology.model

A light-weight version of OntologyTerms.

OntologyTermSimple(String, String) - Constructor for class ubic.basecode.ontology.model.OntologyTermSimple

OntologyTermSimple(String, String, String, boolean) - Constructor for class ubic.basecode.ontology.model.OntologyTermSimple

openURL(String) - Static method in class ubic.basecode.util.BrowserLauncher

Attempts to open the default web browser to the given URL.

order(DoubleArrayList) - Static method in class ubic.basecode.math.Rank

Return a permutation which puts the array in sorted order.

out - Variable in class ubic.basecode.io.writer.MatrixWriter

outDegree() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode

overflow() - Method in class ubic.basecode.math.distribution.Histogram

The height of the overflow bin.

overlap(int, int, int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

Counts the number of one-bits that are in common between the two specified cells; i.e.

P

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

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>, 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.

print(Collection<String>, Collection<Object>) - Static method in class ubic.basecode.util.PrettyPrinter

Print out a collection of beans in a relatively pleasing format.

probability(double) - 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) - Method in class ubic.basecode.math.distribution.UniformProbabilityComputer

probability(double, boolean) - Method in class ubic.basecode.math.distribution.NormalProbabilityComputer

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, 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] ).

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(String, String) - Method in class ubic.basecode.dataStructure.StringToStringSetMap

put(K, Integer) - Method in class ubic.basecode.dataStructure.CountingMap

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.

Q

QRDecomposition - Class in ubic.basecode.math.linalg

QR with pivoting.

QRDecomposition(DoubleMatrix2D) - Constructor for class ubic.basecode.math.linalg.QRDecomposition

QRDecomposition(DoubleMatrix2D, boolean) - Constructor for class ubic.basecode.math.linalg.QRDecomposition

Construct the QR decomposition of A.

qStatistic(DoubleArrayList, DoubleArrayList, double) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis

The "Q" statistic used to test homogeneity of effect sizes.

qTest(double, double) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis

Test for statistical significance of Q.

quantile(int, double[], int) - Static method in class ubic.basecode.math.Stats

Given a double array, calculate the quantile requested.

quantile(DoubleArrayList, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the phi- quantile; that is, an element elem for which holds that phi percent of data elements are less than elem.

quantileInverse(DoubleArrayList, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns how many percent of the elements contained in the receiver are <= element.

quantileNormalize(DoubleMatrix<R, C>) - Method in class ubic.basecode.math.MatrixNormalizer

Rows with all missing will not be returned.

quantiles(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the quantiles of the specified percentages.

quarterRootVariance(LeastSquaresFit) - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimator

R

RandomChooser - Class in ubic.basecode.math

Fill arrays with random values

range(DoubleArrayList) - Static method in class ubic.basecode.math.Stats

Compute the range of an array.

RANGE - Static variable in class ubic.basecode.datafilter.RowLevelFilter

Use the range as the criterion

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(InputStream) - Method in class ubic.basecode.io.reader.DoubleMatrixReader

read(InputStream) - 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:

read(InputStream) - Method in class ubic.basecode.io.reader.StringMatrixReader

read(InputStream, boolean) - Method in class ubic.basecode.io.reader.MapReader

read(InputStream, int) - Method in class ubic.basecode.io.reader.SparseRaggedMatrixReader

Read an entire sparse matrix from a stream (JW format).

read(InputStream, int, int) - Method in class ubic.basecode.io.reader.StringMatrixReader

read(InputStream, Collection<String>) - Method in class ubic.basecode.io.reader.DoubleMatrixReader

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.DoubleMatrixReader

read(InputStream, Collection<String>, boolean, int, int) - Method in class ubic.basecode.io.reader.SparseDoubleMatrixReader

read(InputStream, Collection<String>, int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader

read(String) - Method in class ubic.basecode.io.reader.AbstractMatrixReader

read(String) - Method in class ubic.basecode.io.reader.DoubleMatrixReader

read(String) - Method in class ubic.basecode.io.reader.MapReader

read(String) - Method in class ubic.basecode.io.reader.StringMatrixReader

read(String, boolean) - Method in class ubic.basecode.io.reader.MapReader

read(String, int) - Method in class ubic.basecode.io.reader.AbstractMatrixReader

read(String, int) - Method in class ubic.basecode.io.reader.DoubleMatrixReader

read(String, int) - Method in class ubic.basecode.io.reader.StringMatrixReader

read(String, int, int) - Method in class ubic.basecode.io.reader.StringMatrixReader

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

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:

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() - Method in class ubic.basecode.util.BatchIterator

remove(Object) - Method in class ubic.basecode.dataStructure.CountingMap

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(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Makes a copy of the list that doesn't have the missing values.

removeMissing(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil

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() - Static method in class ubic.basecode.util.Configuration

Reset all configurations set at runtime.

reset(int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

reset(String) - Static method in class ubic.basecode.util.Configuration

Reset a specific configuration by key.

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

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

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() - Method in class ubic.basecode.util.GenericStreamConsumer

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

S

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(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

saveImage(ColorMatrix<R, C>, String, boolean, 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

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

Sequence types and features 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) - Method in class ubic.basecode.dataStructure.Point

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, int, double) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

set(int, int, int, double) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

set(int, int, int, Object) - Method in class ubic.basecode.dataStructure.matrix.DenseObject3DMatrix

set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

set(int, int, Double) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix

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, Integer) - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix

set(int, int, String) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix

set(int, int, V) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D

set(int, int, V) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

setAdditionalPropertyUris(Set<String>) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

setAdditionalPropertyUris(Set<String>) - Method in interface ubic.basecode.ontology.providers.OntologyService

Set the URIs to be used as additional properties when inferring parents and children.

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, String) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix

setByKeys(R, C, V) - Method in interface ubic.basecode.dataStructure.matrix.Matrix2D

setByKeys(R, C, V) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

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

setExcludedWordsFromStemming(Set<String>) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

setExcludedWordsFromStemming(Set<String>) - Method in interface ubic.basecode.ontology.providers.OntologyService

Set words that should be excluded from stemming when searching.

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

setInferenceMode(OntologyService.InferenceMode) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

setInferenceMode(OntologyService.InferenceMode) - Method in interface ubic.basecode.ontology.providers.OntologyService

Set the inference mode used for this ontology.

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(Object) - Method in class ubic.basecode.util.r.type.AnovaResult

setKey(String) - Method in class ubic.basecode.math.linearmodels.LinearModelSummary

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

setLanguageLevel(OntologyService.LanguageLevel) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

setLanguageLevel(OntologyService.LanguageLevel) - Method in interface ubic.basecode.ontology.providers.OntologyService

Set the OWL language level supported by this ontology.

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

setProcessImports(boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

setProcessImports(boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Allow of forbid this ontology to process imports.

setQuick(int, double) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

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

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

setSearchEnabled(boolean) - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

setSearchEnabled(boolean) - Method in interface ubic.basecode.ontology.providers.OntologyService

Enable or disable search for this ontology.

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, String) - Static method in class ubic.basecode.util.Configuration

Set a configuration by key.

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) - 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 class ubic.basecode.util.StatusDebugLogger

showError(String, Throwable) - Method in class ubic.basecode.util.StatusStderr

showError(String, Throwable) - Method in interface ubic.basecode.util.StatusViewer

showError(Throwable) - Method in class ubic.basecode.util.StatusDebugLogger

showError(Throwable) - Method in class ubic.basecode.util.StatusStderr

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) - 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 class ubic.basecode.util.StatusDebugLogger

showStatus(String, boolean) - Method in class ubic.basecode.util.StatusStderr

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(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Return the size of the list, ignoring missing values.

sizeWithoutMissingValues(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil

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.jena.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

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 ..

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.

T

test(DoubleArrayList, IntArrayList) - Static method in class ubic.basecode.math.KruskalWallis

Perform a Kruskal-Wallis one-way ANOVA.

testDir(String) - Static method in class ubic.basecode.util.FileTools

testFile(File) - Static method in class ubic.basecode.util.FileTools

Test whether a File is writeable.

testFile(String) - Static method in class ubic.basecode.util.FileTools

TINY - Static variable in class ubic.basecode.math.Constants

toArray() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D

WARNING unlike the superclass, this returns the actual underlying array, not a copy.

toBytes(Object) - Method in class ubic.basecode.io.ByteArrayConverter

toBytes(Object[]) - Method in class ubic.basecode.io.ByteArrayConverter

Convert an array of Objects into an array of bytes.

toCSVString() - Method in class ubic.basecode.dataStructure.params.ParamKeeper

toFile(String) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

Save the matrix to the specified file

toList(DoubleMatrix1D) - Static method in class ubic.basecode.dataStructure.matrix.MatrixUtil

Makes a copy

TOOSMALL - Static variable in class ubic.basecode.math.linearmodels.ModeratedTstat

topLeft - Variable in class ubic.basecode.io.writer.MatrixWriter

topoSort() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph

Fills in the topoSortOrder for each node.

topoSortOrder - Variable in class ubic.basecode.dataStructure.graph.DirectedGraphNode

toPrettyString() - Method in class ubic.basecode.dataStructure.StringToStringSetMap

toString() - Method in class ubic.basecode.dataStructure.CountingMap

toString() - Method in class ubic.basecode.dataStructure.DoublePoint

toString() - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode

toString() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph

Shows the tree as a tabbed list.

toString() - Method in class ubic.basecode.dataStructure.graph.DirectedGraphNode

toString() - Method in class ubic.basecode.dataStructure.Link

toString() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix

toString() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

toString() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrix

toString() - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

toString() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

toString() - Method in class ubic.basecode.dataStructure.matrix.StringMatrix

toString() - Method in class ubic.basecode.dataStructure.Point

toString() - Method in class ubic.basecode.math.linalg.QRDecomposition

Returns a String with (propertyName, propertyValue) pairs.

toString() - Method in class ubic.basecode.math.linalg.SingularValueDecomposition

toString() - Method in class ubic.basecode.math.linearmodels.DesignMatrix

toString() - Method in class ubic.basecode.math.linearmodels.GenericAnovaResult

toString() - Method in class ubic.basecode.math.linearmodels.LinearModelSummary

toString() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

toString() - Method in class ubic.basecode.ontology.ncbo.AnnotatorResponse

toString() - Method in class ubic.basecode.util.r.type.AnovaEffect

toString() - Method in class ubic.basecode.util.r.type.OneWayAnovaResult

toString() - Method in class ubic.basecode.util.r.type.TwoWayAnovaResult

total() - Method in class ubic.basecode.dataStructure.CountingMap

Returns the sum of all counts in the map.

totalBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

Number of ones in the entire matrix.

touch(File) - Static method in class ubic.basecode.util.FileTools

Create or update the modification date of the given file.

TRANSITIVE - ubic.basecode.ontology.providers.OntologyService.InferenceMode

Only basic inference is supported for rdfs:subClassOf and rdfs:subPropertyOf.

transpose() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

transpose() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

transpose() - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix

transpose() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix

transpose() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix

transpose() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix

treeView() - Method in class ubic.basecode.dataStructure.graph.DirectedGraph

Generate a JTree corresponding to this graph.

treeView(Class<? extends DefaultMutableTreeNode>) - Method in class ubic.basecode.dataStructure.graph.DirectedGraph

Generate a JTree corresponding to this graph.

trigammaInverse(double) - Static method in class ubic.basecode.math.SpecFunc

trigammaInverse(DoubleMatrix1D) - Static method in class ubic.basecode.math.SpecFunc

Ported from limma

trimmedMean(DoubleArrayList, double, int, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the trimmed mean of a sorted data sequence.

trimToSize() - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

trimToSize() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix

twoSample(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.KSTest

twoSampleProbability(double, int, int) - Static method in class ubic.basecode.math.KSTest

twoSampleStatistic(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.KSTest

twoStringHashKey(String, String) - Static method in class ubic.basecode.util.StringUtil

twoWayAnova(double[], List<String>, List<String>, boolean) - Method in class ubic.basecode.util.r.AbstractRClient

twoWayAnova(double[], List<String>, List<String>, boolean) - Method in interface ubic.basecode.util.r.RClient

Lower-level access to two-way ANOVA

twoWayAnovaEval(String, boolean) - Method in class ubic.basecode.util.r.AbstractRClient

twoWayAnovaEval(String, boolean) - Method in interface ubic.basecode.util.r.RClient

Evaluates two way anova commands of the form

TwoWayAnovaResult - Class in ubic.basecode.util.r.type

Represents a two-way ANOVA table

TwoWayAnovaResult() - Constructor for class ubic.basecode.util.r.type.TwoWayAnovaResult

A null result.

TwoWayAnovaResult(REXP) - Constructor for class ubic.basecode.util.r.type.TwoWayAnovaResult

U

UberonOntologyService - Class in ubic.basecode.ontology.providers

Uberon multi-species anatomy ontology

UberonOntologyService() - Constructor for class ubic.basecode.ontology.providers.UberonOntologyService

ubic.basecode.datafilter - package ubic.basecode.datafilter

ubic.basecode.dataStructure - package ubic.basecode.dataStructure

ubic.basecode.dataStructure.graph - package ubic.basecode.dataStructure.graph

ubic.basecode.dataStructure.matrix - package ubic.basecode.dataStructure.matrix

ubic.basecode.dataStructure.params - package ubic.basecode.dataStructure.params

ubic.basecode.dataStructure.tree - package ubic.basecode.dataStructure.tree

ubic.basecode.graphics - package ubic.basecode.graphics

ubic.basecode.graphics.text - package ubic.basecode.graphics.text

ubic.basecode.io - package ubic.basecode.io

ubic.basecode.io.excel - package ubic.basecode.io.excel

ubic.basecode.io.reader - package ubic.basecode.io.reader

ubic.basecode.io.writer - package ubic.basecode.io.writer

ubic.basecode.math - package ubic.basecode.math

ubic.basecode.math.distribution - package ubic.basecode.math.distribution

ubic.basecode.math.linalg - package ubic.basecode.math.linalg

ubic.basecode.math.linearmodels - package ubic.basecode.math.linearmodels

ubic.basecode.math.metaanalysis - package ubic.basecode.math.metaanalysis

ubic.basecode.ontology - package ubic.basecode.ontology

ubic.basecode.ontology.jena - package ubic.basecode.ontology.jena

Implementation of OntologyService using Apache Jena.

ubic.basecode.ontology.model - package ubic.basecode.ontology.model

ubic.basecode.ontology.ncbo - package ubic.basecode.ontology.ncbo

ubic.basecode.ontology.providers - package ubic.basecode.ontology.providers

This package contains baseCode built-in ontologies and a GenericOntologyService to implement your own ontologies.

ubic.basecode.ontology.search - package ubic.basecode.ontology.search

ubic.basecode.util - package ubic.basecode.util

ubic.basecode.util.r - package ubic.basecode.util.r

ubic.basecode.util.r.type - package ubic.basecode.util.r.type

underflow() - Method in class ubic.basecode.math.distribution.Histogram

The height of the underflow bin.

UndirectedGraphNode<K,V> - Class in ubic.basecode.dataStructure.graph

UndirectedGraphNode(K) - Constructor for class ubic.basecode.dataStructure.graph.UndirectedGraphNode

UndirectedGraphNode(K, V, Graph<UndirectedGraphNode<K, V>, K, V>) - Constructor for class ubic.basecode.dataStructure.graph.UndirectedGraphNode

unFisherTransform(double) - Static method in class ubic.basecode.math.CorrelationStats

Reverse the Fisher z-transform of Pearson correlations

unGzipFile(String) - Static method in class ubic.basecode.util.FileTools

Given the path to a gzipped-file, unzips it into the same directory.

UniformDensityComputer - Class in ubic.basecode.math.distribution

UniformDensityComputer() - Constructor for class ubic.basecode.math.distribution.UniformDensityComputer

Create a UniformDensityComputer where the density is defined over the unit inteval [0,1].

UniformDensityComputer(double, double) - Constructor for class ubic.basecode.math.distribution.UniformDensityComputer

Create a UniformDensityComputer where the density is defined over the interval given

UniformProbabilityComputer - Class in ubic.basecode.math.distribution

Generate probabilities from the uniform distribution.

UniformProbabilityComputer() - Constructor for class ubic.basecode.math.distribution.UniformProbabilityComputer

Create a UniformProbabilityComputer where the density is defined over the unit inteval [0,1].

UniformProbabilityComputer(double, double) - Constructor for class ubic.basecode.math.distribution.UniformProbabilityComputer

Create a UniformProbabilityComputer where the density is defined over the interval given

UnitsOntologyService - Class in ubic.basecode.ontology.providers

Units of measurement ontology

UnitsOntologyService() - Constructor for class ubic.basecode.ontology.providers.UnitsOntologyService

unLogTransform(DoubleMatrix<R, C>) - Static method in class ubic.basecode.math.MatrixStats

Undo log2 transform.

unMark() - Method in class ubic.basecode.dataStructure.graph.AbstractGraphNode

unMark() - Method in class ubic.basecode.dataStructure.Visitable

unmarkAll() - Method in class ubic.basecode.dataStructure.graph.AbstractGraph

Reset the 'visited' marks of the graph to false.

unmarkAll() - Method in interface ubic.basecode.dataStructure.graph.Graph

unset(int, int, int) - Method in class ubic.basecode.dataStructure.matrix.CompressedBitMatrix

unZipFiles(String) - Static method in class ubic.basecode.util.FileTools

useHighAsFraction - Variable in class ubic.basecode.datafilter.AbstractLevelFilter

useLowAsFraction - Variable in class ubic.basecode.datafilter.AbstractLevelFilter

Util - Class in ubic.basecode.graphics.text

Util() - Constructor for class ubic.basecode.graphics.text.Util

V

valueOf(String) - Static method in enum ubic.basecode.ontology.model.OntologyCardinalityRestriction.CardinalityType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ubic.basecode.ontology.providers.OntologyService.InferenceMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ubic.basecode.ontology.providers.OntologyService.LanguageLevel

Returns the enum constant of this type with the specified name.

values - Variable in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

values() - Method in class ubic.basecode.dataStructure.CountingMap

values() - Static method in enum ubic.basecode.ontology.model.OntologyCardinalityRestriction.CardinalityType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ubic.basecode.ontology.providers.OntologyService.InferenceMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ubic.basecode.ontology.providers.OntologyService.LanguageLevel

Returns an array containing the constants of this enum type, in the order they are declared.

variableIdentityNumber(Object) - Static method in class ubic.basecode.util.r.AbstractRClient

variance(int, double, double) - Static method in class ubic.basecode.math.DescriptiveWithMissing

variance(DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Provided for convenience!

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix

viewColumn(int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix

viewRow(int) - Method in class ubic.basecode.dataStructure.matrix.StringMatrix

viewSelectionLike(int[]) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

viewSlice(int) - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix

viewSlice(int) - Method in class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

Visitable - Class in ubic.basecode.dataStructure

Visitable() - Constructor for class ubic.basecode.dataStructure.Visitable

visited - Variable in class ubic.basecode.dataStructure.graph.AbstractGraphNode

voidEval(String) - Method in class ubic.basecode.util.r.JRIClient

voidEval(String) - Method in interface ubic.basecode.util.r.RClient

voidEval(String) - Method in class ubic.basecode.util.r.RServeClient

W

waitForInitializationThread() - Method in class ubic.basecode.ontology.jena.AbstractOntologyService

waitForInitializationThread() - Method in interface ubic.basecode.ontology.providers.OntologyService

Wait for the initialization thread to finish.

weightedMean(DoubleArrayList, DoubleArrayList) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the weighted mean of a data sequence.

weightedMean(DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis

General formula for weighted mean of effect sizes.

weightedMean(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.basecode.math.metaanalysis.MetaAnalysis

General formula for weighted mean of effect sizes including quality index scores for each value.

whereIs(String) - Method in class ubic.basecode.dataStructure.StringToStringSetMap

Wilcoxon - Class in ubic.basecode.math

Implements methods from supplementary file I of "Comparing functional annotation analyses with Catmap", Thomas Breslin, Patrik Ed�n and Morten Krogh, BMC Bioinformatics 2004, 5:193 doi:10.1186/1471-2105-5-193

Wilcoxon() - Constructor for class ubic.basecode.math.Wilcoxon

wilcoxonP(int, int, long) - Static method in class ubic.basecode.math.Wilcoxon

Only use when you know there are no ties.

wilcoxonP(int, int, long, boolean) - Static method in class ubic.basecode.math.Wilcoxon

wilcoxonP(int, List<Double>) - Static method in class ubic.basecode.math.Wilcoxon

winsorizedMean(DoubleArrayList, double, int, int) - Static method in class ubic.basecode.math.DescriptiveWithMissing

Returns the winsorized mean of a sorted data sequence.

Wishart - Class in ubic.basecode.math.distribution

Wishart distribution, used to simulate covariance matrices.

Wishart(double, DoubleMatrix2D, RandomEngine) - Constructor for class ubic.basecode.math.distribution.Wishart

workbook - Variable in class ubic.basecode.io.excel.CreateSpreadSheet

write(IHistogram1D, OutputStream) - Method in class ubic.basecode.io.writer.HistogramWriter

Print to a stream.

write(IHistogram1D, Writer) - Method in class ubic.basecode.io.writer.HistogramWriter

Print out a IHistogram1D object.

writeExcel(String) - Method in class ubic.basecode.dataStructure.params.ParamKeeper

writeMatrix(DoubleMatrix1D) - Method in class ubic.basecode.io.writer.MatrixWriter

Write a bare 1D matrix (one value per line)

writeMatrix(DoubleMatrix2D) - Method in class ubic.basecode.io.writer.MatrixWriter

Write a bare matrix without row names or columns

writeMatrix(Matrix2D<R, C, V>, boolean) - Method in class ubic.basecode.io.writer.MatrixWriter

writeMatrix(Matrix3D<R, C, S, V>, boolean) - Method in class ubic.basecode.io.writer.MatrixWriter

Writes a 3d matrix, collapsing the rows and columns

writeTestResult(String, String) - Static method in class ubic.basecode.util.RegressionTesting

writeToFile(FileWriter) - Method in class ubic.basecode.math.distribution.Histogram

Write the histogram to a file.

writeToPng(ColorMatrix<R, C>, OutputStream, boolean, boolean) - Method in class ubic.basecode.graphics.MatrixDisplay

X

X - Static variable in class ubic.basecode.datafilter.AffymetrixProbeNameFilter

Filter probes that have the "_x_at" tag.

XML_EXTENSIONS - Static variable in class ubic.basecode.util.FileTools

Z

zDotProduct(DoubleMatrix1D) - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

zSum() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

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