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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

## A

AFFX - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
  Filter probes that have the AFFX prefix.
AFFX - Static variable in class baseCode.dataFilter.RowAffyNameFilter
  Filter probes that have the AFFX prefix.
ASCENDING - Static variable in class baseCode.gui.table.TableSorter
AbstractFilter - class baseCode.dataFilter.AbstractFilter.
  Base implementation of the filter class.
AbstractFilter() - Constructor for class baseCode.dataFilter.AbstractFilter
AbstractGraph - class baseCode.dataStructure.graph.AbstractGraph.
  Copyright (c) Columbia University
AbstractGraph() - Constructor for class baseCode.dataStructure.graph.AbstractGraph
AbstractGraph(Set) - Constructor for class baseCode.dataStructure.graph.AbstractGraph
  Create a new graph from a set of nodes.
AbstractGraphNode - class baseCode.dataStructure.graph.AbstractGraphNode.
  Copyright (c) Columbia University
AbstractGraphNode(Object, Object, Graph) - Constructor for class baseCode.dataStructure.graph.AbstractGraphNode
  Create a new node with key and value given.
AbstractGraphNode(Object) - Constructor for class baseCode.dataStructure.graph.AbstractGraphNode
  Create a new node when given only a key.
AbstractLevelFilter - class baseCode.dataFilter.AbstractLevelFilter.
  Abstract class representing a filter that removes things from matrices based on the values themselves.
AbstractLevelFilter() - Constructor for class baseCode.dataFilter.AbstractLevelFilter
AbstractNamedDoubleMatrix - class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix.
AbstractNamedDoubleMatrix() - Constructor for class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
AbstractNamedMatrix - class baseCode.dataStructure.matrix.AbstractNamedMatrix.
  Copyright (c) 2004 Columbia University
AbstractNamedMatrix() - Constructor for class baseCode.dataStructure.matrix.AbstractNamedMatrix
AbstractNamedMatrixReader - class baseCode.io.reader.AbstractNamedMatrixReader.
  Abstract class representing an object that can read in a `NamedMatrix`from a file.
AbstractNamedMatrixReader() - Constructor for class baseCode.io.reader.AbstractNamedMatrixReader
AffymetrixProbeNameFilter - class baseCode.dataFilter.AffymetrixProbeNameFilter.
  Remove probes that have names meeting certain rules indicating they may have low reliability.
AffymetrixProbeNameFilter(int[]) - Constructor for class baseCode.dataFilter.AffymetrixProbeNameFilter
AffymetrixProbeNameFilter() - Constructor for class baseCode.dataFilter.AffymetrixProbeNameFilter
  Filter probes with all criteria switched on.
Algorithm - class baseCode.algorithm.Algorithm.
Algorithm() - Constructor for class baseCode.algorithm.Algorithm
AppDialog - class baseCode.gui.AppDialog.
  Title:
AppDialog() - Constructor for class baseCode.gui.AppDialog
AppDialog(JFrame, int, int) - Constructor for class baseCode.gui.AppDialog
AverageLinkageDistancer - class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer.
AverageLinkageDistancer() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer
accept(File) - Method in class baseCode.gui.file.DataFileFilter
accept(File) - Method in class baseCode.gui.file.ImageFileFilter
accept(File) - Method in class baseCode.gui.file.XMLFileFilter
actionButton - Variable in class baseCode.gui.AppDialog
actionButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.AppDialog
actionPerformed(ActionEvent) - Method in class baseCode.gui.JWebBrowser
addChild(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
addChildTo(Object, Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
  Add a child to a particualar node identified by key.
addChildTo(Object, Object) - Method in class 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.
addClass(String, String) - Method in class baseCode.bio.geneset.GONames
addClass(String, ArrayList) - Method in class baseCode.bio.geneset.GeneAnnotations
  Add a class
addColumnName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
  Add a column name when we don't care what the index will be.
addColumnName(String, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
addColumnName(String, int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Add a column name associated with an index.
addDataExtension(String) - Static method in class baseCode.util.FileTools
addHelp(String) - Method in class baseCode.gui.AppDialog
addHelp(String) - Method in class baseCode.gui.WizardStep
addImageExtension(String) - Static method in class baseCode.util.FileTools
addItem(Cluster) - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
addMain(JPanel) - Method in class baseCode.gui.AppDialog
addMain(JPanel) - Method in class baseCode.gui.WizardStep
addNode(GraphNode) - Method in class baseCode.dataStructure.graph.AbstractGraph
addNode(Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
addNode(Object, Object) - Method in interface baseCode.dataStructure.graph.Graph
addParent(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
addParentTo(Object, Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
addParentTo(Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
addRow(String, IntArrayList, DoubleArrayList) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
addRow(String, DoubleMatrix1D) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
addRowName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
  Add a row name when we don't care what the index will be.
addRowName(String, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
addRowName(String, int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Add a row name associated with a row index.
addStep(int, WizardStep) - Method in class baseCode.gui.Wizard
aroc(int, Set) - Static method in class baseCode.math.ROC
  Calculate area under ROC.
aroc(int, Set, int) - Static method in class baseCode.math.ROC
  Calculate area under ROC, up to a given number of False positives.
assign(DoubleFunction) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
  WARNING this only even assigns to the non-empty values, for performance reasons.
autoCorrelation(DoubleArrayList, int, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Not supported.

## B

BLACKBODY_COLORMAP - Static variable in class baseCode.gui.ColorMap
BenjaminiHochbergCut(DoubleArrayList, double) - Static method in class baseCode.math.MultipleTestCorrection
  Benjamini-Hochberg method.
BinaryTree - class baseCode.dataStructure.tree.BinaryTree.
BinaryTree(BinaryTreeNode) - Constructor for class baseCode.dataStructure.tree.BinaryTree
BinaryTree() - Constructor for class baseCode.dataStructure.tree.BinaryTree
BinaryTreeNode - class baseCode.dataStructure.tree.BinaryTreeNode.
BinaryTreeNode(Object) - Constructor for class baseCode.dataStructure.tree.BinaryTreeNode
BinaryTreeNode() - Constructor for class baseCode.dataStructure.tree.BinaryTreeNode
BonferroniCut(DoubleArrayList, double) - Static method in class baseCode.math.MultipleTestCorrection
  Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are independent).
BottomPanel - Variable in class baseCode.gui.Wizard
BottomPanelWrap - Variable in class baseCode.gui.Wizard
BrowserLauncher - class baseCode.util.BrowserLauncher.
  BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
ByteArrayConverter - class baseCode.io.ByteArrayConverter.
  Class to convert byte arrays (e.g., Blobs) to and from other types of arrays.
ByteArrayConverter() - Constructor for class baseCode.io.ByteArrayConverter
backButton - Variable in class baseCode.gui.Wizard
backButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
  Define what happens when the 'back' button is pressed
baseCode.algorithm - package baseCode.algorithm
baseCode.algorithm.learning.unsupervised - package baseCode.algorithm.learning.unsupervised
baseCode.algorithm.learning.unsupervised.cluster - package baseCode.algorithm.learning.unsupervised.cluster
baseCode.bio - package baseCode.bio
baseCode.bio.geneset - package baseCode.bio.geneset
baseCode.common - package baseCode.common
baseCode.dataFilter - package baseCode.dataFilter
baseCode.dataStructure - package baseCode.dataStructure
baseCode.dataStructure.graph - package baseCode.dataStructure.graph
baseCode.dataStructure.matrix - package baseCode.dataStructure.matrix
baseCode.dataStructure.tree - package baseCode.dataStructure.tree
baseCode.db - package baseCode.db
baseCode.graphics.text - package baseCode.graphics.text
baseCode.gui - package baseCode.gui
baseCode.gui.file - package baseCode.gui.file
baseCode.gui.table - package baseCode.gui.table
baseCode.io - package baseCode.io
baseCode.io.reader - package baseCode.io.reader
baseCode.io.writer - package baseCode.io.writer
baseCode.math - package baseCode.math
baseCode.math.distribution - package baseCode.math.distribution
baseCode.math.metaanalysis - package baseCode.math.metaanalysis
baseCode.misc - package baseCode.misc
baseCode.util - package baseCode.util
baseCode.xml - package baseCode.xml
best() - Method in class baseCode.algorithm.Ranker
byteArrayToAsciiString(byte[]) - Method in class baseCode.io.ByteArrayConverter
  Convert a byte array with one-byte-per-character ASCII encoding (aka ISO-8859-1).
byteArrayToChars(byte[]) - Method in class baseCode.io.ByteArrayConverter
byteArrayToDoubles(byte[]) - Method in class baseCode.io.ByteArrayConverter
byteArrayToInts(byte[]) - Method in class baseCode.io.ByteArrayConverter
byteArrayToLongs(byte[]) - Method in class baseCode.io.ByteArrayConverter
byteToCorrel(int) - Static method in class baseCode.math.CorrelationStats
byteToPvalue(int) - Static method in class baseCode.math.CorrelationStats

## C

COLORS - Static variable in class baseCode.gui.table.JBarGraphCellRenderer
COMPARABLE_COMAPRATOR - Static variable in class baseCode.gui.table.TableSorter
CV - Static variable in class baseCode.dataFilter.RowLevelFilter
  Use the coefficient of variation as the criterion
Cluster - class baseCode.algorithm.learning.unsupervised.cluster.Cluster.
Cluster() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.Cluster
Cluster(Object, Distancer) - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.Cluster
Cluster(Collection, Distancer) - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.Cluster
ClusteringAlgorithm - class baseCode.algorithm.learning.unsupervised.cluster.ClusteringAlgorithm.
ClusteringAlgorithm() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.ClusteringAlgorithm
ColorMap - class baseCode.gui.ColorMap.
  Title: ColorMap
ColorMap() - Constructor for class baseCode.gui.ColorMap
ColorMap(int) - Constructor for class baseCode.gui.ColorMap
ColorMap(Color[]) - Constructor for class baseCode.gui.ColorMap
ColorMap(int, Color[]) - Constructor for class baseCode.gui.ColorMap
  Pre-condition: suggestedNumberOfColors > colorMap.length
ColorMatrix - class baseCode.gui.ColorMatrix.
  Title: ColorMatrix
ColorMatrix(String) - Constructor for class baseCode.gui.ColorMatrix
ColorMatrix(DenseDoubleMatrix2DNamed) - Constructor for class baseCode.gui.ColorMatrix
ColorMatrix(String, Color[], Color) - Constructor for class baseCode.gui.ColorMatrix
ColorMatrix(AbstractNamedDoubleMatrix, Color[], Color) - Constructor for class baseCode.gui.ColorMatrix
Constants - class baseCode.math.Constants.
  Used in some ports of statistical code.
Constants() - Constructor for class baseCode.math.Constants
CorrelationEffectMetaAnalysis - class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis.
  Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of Research Synthesis".
CorrelationEffectMetaAnalysis(boolean, boolean) - Constructor for class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
CorrelationEffectMetaAnalysis() - Constructor for class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
CorrelationStats - class baseCode.math.CorrelationStats.
  Statistical evaluation and transformation tools for correlations.
CorrelationStats() - Constructor for class baseCode.math.CorrelationStats
callingframe - Variable in class baseCode.gui.AppDialog
callingframe - Variable in class baseCode.gui.Wizard
cancelButton - Variable in class baseCode.gui.AppDialog
cancelButton - Variable in class baseCode.gui.Wizard
cancelButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.AppDialog
cancelButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
  Define what happens when the 'cancel' button is pressed.
cancelSorting() - Method in class baseCode.gui.table.TableSorter
cardinality() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
cdf(DoubleArrayList) - Static method in class baseCode.math.Stats
  Convert an array into a cumulative density function (CDF).
changeExtension(String, String) - Static method in class baseCode.util.FileTools
charArrayToBytes(char[]) - Method in class baseCode.io.ByteArrayConverter
checkPathIsReadableFile(String) - Static method in class baseCode.util.FileTools
children - Variable in class baseCode.dataStructure.graph.DirectedGraphNode
chooserandom(double[], double[], int[], int, int) - Static method in class baseCode.math.RandomChooser
  Fill randomvals with random things from sourcedata, without replacement.
chooserandom(int[], int[], int, int) - Static method in class baseCode.math.RandomChooser
  choose n random integers from 0 to max without repeating
chooserandom(int[], boolean[], int, int) - Static method in class baseCode.math.RandomChooser
  choose n random integers from 0 to max without repeating
chooserandomWrep(int[], int, int) - Static method in class baseCode.math.RandomChooser
  Same as chooserandom, but with replacement -- that is, repeats are allowed.
clear() - Method in class baseCode.gui.StatusJlabel
clear() - Method in class baseCode.util.StatusDebugLogger
clear() - Method in class baseCode.util.StatusStderr
clear() - Method in interface baseCode.util.StatusViewer
  Clear the status dislay.
clearStatus() - Method in class baseCode.gui.Wizard
  Make the status bar empty.
clone() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Makes a copy of this node.
clone() - Method in class baseCode.gui.ColorMatrix
closeCon() - Method in class baseCode.db.Handle
  Close the database connection.
closeEnough(DoubleArrayList, DoubleArrayList, double) - Static method in class baseCode.util.RegressionTesting
  Test whether two DoubleArrayLists are 'close enough' to call equal.
closeEnough(AbstractNamedDoubleMatrix, AbstractNamedDoubleMatrix, double) - Static method in class baseCode.util.RegressionTesting
  Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.
closeEnough(DoubleMatrix2D, DoubleMatrix2D, double) - Static method in class baseCode.util.RegressionTesting
closeEnough(Object[], Object[]) - Static method in class baseCode.util.RegressionTesting
  Test whether two object arrays are the same.
collapseGeneSets(GeneAnnotations, StatusViewer) - Static method in class baseCode.bio.geneset.GeneSetMapTools
  Identify classes which are absoluely identical to others.
columns() - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
columns() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
columns() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
columns() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Get the number of columns the matrix has.
columns() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
columns() - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
columns() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
compare(double, int, double, int) - Static method in class baseCode.math.CorrelationStats
  Statistical comparison of two correlations.
compareTo(Object) - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
compareTo(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Uses the topological sort order.
compareTo(Object) - Method in class baseCode.dataStructure.graph.UndirectedGraphNode
compareTo(Object) - Method in class baseCode.dataStructure.tree.BinaryTreeNode
compareTo(Object) - Method in class baseCode.dataStructure.tree.TreeNode
computeRanking(AbstractNamedDoubleMatrix, AbstractNamedDoubleMatrix, int) - Method in class baseCode.algorithm.learning.unsupervised.RankProp
computeRanking(AbstractNamedDoubleMatrix, DoubleMatrix1D, int) - Method in class baseCode.algorithm.learning.unsupervised.RankProp
containsColumnName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
containsColumnName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
containsKey(Object) - Method in class baseCode.dataStructure.graph.AbstractGraph
containsKey(Object) - Method in interface baseCode.dataStructure.graph.Graph
containsRowName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
containsRowName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
containsSame(Collection, Collection) - Static method in class baseCode.util.RegressionTesting
  Test whether two collections contain the same items.
containsSame(Object[], Object[]) - Static method in class baseCode.util.RegressionTesting
  Test whether two object arrays contain the same items.
containsSame(double[], double[]) - Static method in class baseCode.util.RegressionTesting
  Test whether two double arrays contain the same items in any order (tolerance is ZERO)
copy() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
  Make a copy of a matrix.
correlAsByte(double) - Static method in class baseCode.math.CorrelationStats
correlation(DoubleArrayList, double, DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the correlation of two data sequences.
correlation(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Calculate the pearson correlation of two arrays.
correlationForPvalue(double, int) - Static method in class baseCode.math.CorrelationStats
  Find the approximate correlation required to meet a particular pvalue.
correlationMatrix(AbstractNamedDoubleMatrix) - Static method in class baseCode.math.MatrixStats
correlationMatrix(AbstractNamedDoubleMatrix, double) - Static method in class baseCode.math.MatrixStats
correlationOfStandardized(double[], double[]) - Static method in class baseCode.math.Distance
  Highly optimized implementation of the Pearson correlation.
correlationOfStandardized(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.Distance
  Like correlationofNormedFast, but takes DoubleArrayLists as inputs, handles missing values correctly, and does more error checking.
correlationTstat(double, int) - Static method in class baseCode.math.CorrelationStats
  Compute the t-statistic associated with a Pearson correlation.
countsNormalize(AbstractNamedDoubleMatrix, double) - Static method in class baseCode.math.MatrixStats
  Normalize a count matrix in place to be a transition matrix.
covariance(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the SAMPLE covariance of two data sequences.
createColorPalette(int, Color[]) - Method in class baseCode.gui.ColorMap
  Allocates colors across a range.
createEmptyRow(int) - Method in class baseCode.io.reader.DoubleMatrixReader
createMatrix(List, int, int, List, List) - Method in class baseCode.io.reader.DoubleMatrixReader
createRowKeys() - Method in class baseCode.gui.ColorMatrix
  To be able to sort the rows by an arbitrary key.
cumulate(DoubleArrayList) - Static method in class baseCode.math.Stats
  Convert an array into a cumulative array.
cumulateRight(DoubleArrayList) - Static method in class baseCode.math.Stats
  Convert an array into a cumulative array.
cv(DoubleArrayList) - Static method in class baseCode.math.Stats
  Compute the coefficient of variation of an array (standard deviation / mean)

## D

DARK_RED - Static variable in class baseCode.gui.ColorMap
DATA_EXTENSIONS - Static variable in class baseCode.util.FileTools
DEFAULT_DATA_EXTENSION - Static variable in class baseCode.util.FileTools
DEFAULT_IMAGE_EXTENSION - Static variable in class baseCode.util.FileTools
DEFAULT_XML_EXTENSION - Static variable in class baseCode.util.FileTools
DESCENDING - Static variable in class baseCode.gui.table.TableSorter
DataFileFilter - class baseCode.gui.file.DataFileFilter.
DataFileFilter() - Constructor for class baseCode.gui.file.DataFileFilter
DenseDoubleMatrix1D - class baseCode.dataStructure.matrix.DenseDoubleMatrix1D.
  Use this class when fast iteration over the matrix is of primary interest.
DenseDoubleMatrix1D(int, double[], int, int) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix1D(double[]) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix1D(int) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix2DNamed - class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed.
  A matrix of doubles that knows about row and column names.
DenseDoubleMatrix2DNamed(double[][]) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
DenseDoubleMatrix2DNamed(int, int) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
DensityGenerator - interface baseCode.math.distribution.DensityGenerator.
  An interface that describes a class that can produce values from a particular probability density.
DescriptiveWithMissing - class baseCode.math.DescriptiveWithMissing.
  Mathematical functions for statistics that allow missing values without scotching the calculations.
DirectedGraph - class baseCode.dataStructure.graph.DirectedGraph.
  A graph that contains DirectedGraphNodes.
DirectedGraph() - Constructor for class baseCode.dataStructure.graph.DirectedGraph
DirectedGraph(Set) - Constructor for class baseCode.dataStructure.graph.DirectedGraph
DirectedGraphNode - class baseCode.dataStructure.graph.DirectedGraphNode.
  A graph node that has the concept of parents and children.
DirectedGraphNode(Object, Object, Graph) - Constructor for class baseCode.dataStructure.graph.DirectedGraphNode
Dirichlet - class baseCode.math.distribution.Dirichlet.
Dirichlet(DoubleArrayList, RandomEngine) - Constructor for class baseCode.math.distribution.Dirichlet
Distance - class baseCode.math.Distance.
  Alternative distance and similarity metrics for vectors.
Distance() - Constructor for class baseCode.math.Distance
DistanceFactory - class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory.
DistanceFactory() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory
Distanceable - class baseCode.common.Distanceable.
  An object whose distance to other objects can be measured.
Distanceable() - Constructor for class baseCode.common.Distanceable
Distancer - interface baseCode.algorithm.learning.unsupervised.cluster.Distancer.
DoubleArrayToString(double[]) - Method in class baseCode.io.StringConverter
  Convert a double array to a delimited string.
DoubleMatrix2DNamedFactory - class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory.
  Use this factory to create matrices of type selected at runtime.
DoubleMatrix2DNamedFactory() - Constructor for class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory
DoubleMatrixReader - class baseCode.io.reader.DoubleMatrixReader.
  Reader for `DenseDoubleMatrix2DNamed`.
DoubleMatrixReader() - Constructor for class baseCode.io.reader.DoubleMatrixReader
dbinom(double, double, double) - Static method in class baseCode.math.SpecFunc
  See dbinom_raw.
dense(double[][]) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory
dense(int, int) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory
density(double) - Method in interface baseCode.math.distribution.DensityGenerator
density(double) - Method in class baseCode.math.distribution.UniformDensityComputer
dequeue() - Method in class baseCode.dataStructure.Queue
  Deprecated.
dhyper(int, int, int, int) - Static method in class baseCode.math.SpecFunc
  Ported from R (Catherine Loader)
distAlg - Variable in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
distance(Distanceable, Distanceable) - Method in class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer
distance(Distanceable, Distanceable) - Method in interface baseCode.algorithm.learning.unsupervised.cluster.Distancer
distanceTo(Distanceable) - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
distanceTo(Distanceable) - Method in class baseCode.common.Distanceable
doubleArrayToBytes(double[]) - Method in class baseCode.io.ByteArrayConverter
drawColumnNames(Graphics) - Method in class baseCode.gui.JMatrixDisplay
  Draws column names vertically (turned 90 degrees counter-clockwise)
drawMatrix(Graphics, boolean) - Method in class baseCode.gui.JMatrixDisplay
  Gets called from #paintComponent and #saveImage
drawRowNames(Graphics) - Method in class baseCode.gui.JMatrixDisplay
  Draws row names (horizontally)
drawVerticalString(Graphics, String, Font, int, int) - Static method in class baseCode.graphics.text.Util
  Draws a string vertically, turned 90 degrees counter-clockwise.
draws(int) - Method in class baseCode.math.distribution.Dirichlet
durbinWatson(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Durbin-Watson computation.

## E

EMPTY - Static variable in class baseCode.gui.JGradientBar
enqueue(Object) - Method in class baseCode.dataStructure.Queue
  Deprecated.
ensureCapacity(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
error(String, Exception) - Static method in class baseCode.gui.GuiUtil
error(String) - Static method in class baseCode.gui.GuiUtil
euclDistance(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.Distance
  Calculate the Euclidean distance between two vectors.

## F

F - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
  Filter probes that have the "_f_at" (family) tag.
F - Static variable in class baseCode.dataFilter.RowAffyNameFilter
  Filter probes that have the "_f_at" (family) tag.
FileTools - class baseCode.util.FileTools.
  Copyright (c) 2004 Columbia University
FileTools() - Constructor for class baseCode.util.FileTools
Filter - interface baseCode.dataFilter.Filter.
  An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented criteria.
filter(NamedMatrix) - Method in class baseCode.dataFilter.AffymetrixProbeNameFilter
filter(NamedMatrix) - Method in interface baseCode.dataFilter.Filter
  Filter the data
filter(NamedMatrix) - Method in class baseCode.dataFilter.ItemLevelFilter
filter(NamedMatrix) - Method in class baseCode.dataFilter.RowAbsentFilter
  The data is going to be filtered in accordance to strings in 'flags'.
filter(NamedMatrix) - Method in class baseCode.dataFilter.RowAffyNameFilter
filter(NamedMatrix) - Method in class baseCode.dataFilter.RowLevelFilter
filter(NamedMatrix) - Method in class baseCode.dataFilter.RowMissingFilter
filter(NamedMatrix) - Method in class baseCode.dataFilter.RowNameFilter
  Filter according to row names.
finishButton - Variable in class baseCode.gui.Wizard
finishButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
  Define what happens when the 'finish' button is pressed.
firePropertyChange(String, Object, Object) - Method in class baseCode.gui.table.JMatrixCellRenderer
firePropertyChange(String, boolean, boolean) - Method in class baseCode.gui.table.JMatrixCellRenderer
firePropertyChange(String, Object, Object) - Method in class baseCode.gui.table.JVerticalHeaderRenderer
firePropertyChange(String, boolean, boolean) - Method in class baseCode.gui.table.JVerticalHeaderRenderer
fisherCombineLogPvalues(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  Fisher's method for combining p values (Cooper and Hedges 15-8)
fisherCombinePvalues(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  Fisher's method for combining p values.
fisherTransform(double) - Static method in class baseCode.math.CorrelationStats
  Compute the Fisher z transform of the Pearson correlation.
fisherTransform(DoubleArrayList) - Static method in class baseCode.math.CorrelationStats
  Fisher-transform a list of correlations.
fisherTransformedSamplingVariance(double) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
  Equation 18-8 from CH.
fisherTransformedSamplingVariances(DoubleArrayList) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
  Run equation CH 18-8 on a list of sample sizes.
flowlayout1 - Variable in class baseCode.gui.Wizard
forEachNonZero(DoubleFunction) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
  Apply the given function to each element non-zero element in the matrix.

## G

G - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
  Filter probes that have the "_g_at" (group) tag.
G - Static variable in class baseCode.dataFilter.RowAffyNameFilter
  Filter probes that have the "_g_at" (group) tag.
GIF_EXTENSION - Static variable in class baseCode.util.FileTools
GOEntry - class baseCode.bio.GOEntry.
GOEntry(String, String, String, String) - Constructor for class baseCode.bio.GOEntry
GONames - class baseCode.bio.geneset.GONames.
  Rea data from GO XML file, store in easy-to-use data structure.
GONames(String) - Constructor for class baseCode.bio.geneset.GONames
GONames(InputStream) - Constructor for class baseCode.bio.geneset.GONames
GOParser - class baseCode.xml.GOParser.
  Read in the GO XML file provided by the Gene Ontology Consortium.
GOParser(InputStream) - Constructor for class baseCode.xml.GOParser
GOTermList - class baseCode.bio.GOTermList.
GOTermList() - Constructor for class baseCode.bio.GOTermList
GOTermProbability - class baseCode.bio.GOTermProbability.
GOTermProbability() - Constructor for class baseCode.bio.GOTermProbability
GREENRED_COLORMAP - Static variable in class baseCode.gui.ColorMap
GeneAnnotations - class baseCode.bio.geneset.GeneAnnotations.
  Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.
GeneAnnotations(String, StatusViewer) - Constructor for class baseCode.bio.geneset.GeneAnnotations
  This is for creating GeneAnnotations by reading from a file
GeneAnnotations(GeneAnnotations, Set) - Constructor for class baseCode.bio.geneset.GeneAnnotations
  This is for creating GeneAnnotations by pruning a copy.
GeneAnnotations(InputStream, Set, StatusViewer) - Constructor for class baseCode.bio.geneset.GeneAnnotations
  Make a new GeneAnnotations that only includes the probes in the parameter 'probes'.
GeneAnnotations(String, Set, StatusViewer) - Constructor for class baseCode.bio.geneset.GeneAnnotations
GeneSetMapTools - class baseCode.bio.geneset.GeneSetMapTools.
  Methods to 'clean' a set of geneSets - to remove redundancies, for example.
GeneSetMapTools() - Constructor for class baseCode.bio.geneset.GeneSetMapTools
Graph - interface baseCode.dataStructure.graph.Graph.
GraphNode - interface baseCode.dataStructure.graph.GraphNode.
GroupMap - class baseCode.misc.GroupMap.
  A data structure representing a map between items and a single set of keys.
GroupMap() - Constructor for class baseCode.misc.GroupMap
GuiUtil - class baseCode.gui.GuiUtil.
  Little oft-used functions.
GuiUtil() - Constructor for class baseCode.gui.GuiUtil
geneSetExists(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Returns true if the class is in the classToProbe map
geneSetSizeDistribution(GeneAnnotations, int, int, int) - Static method in class baseCode.bio.geneset.GeneSetMapTools
geneSetToRedundantMap() - Method in class baseCode.bio.geneset.GeneAnnotations
geometricMean(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the geometric mean of a data sequence.
get() - Method in class baseCode.dataStructure.Point
get(Object) - Method in class baseCode.dataStructure.graph.AbstractGraph
  Retrieve a node by key.
get(Object) - Method in interface baseCode.dataStructure.graph.Graph
get(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
get(int, int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
get(int, int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
get(int, int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
get(int, int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
getAllChildNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Get all the children of this node, recursively.
getAllParentNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Get all the parents of this node, recursively.
getAlpha() - Method in class baseCode.algorithm.learning.unsupervised.RankProp
getAspect() - Method in class baseCode.bio.GOEntry
getAspectForId(String) - Method in class baseCode.bio.geneset.GONames
  Get the aspect (molecular_function etc) for an id.
getBsv() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getBsv() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getChildGraph() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Get the subgraph starting from this node, including this node.
getChildKeys() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
getChildNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Get the immediate children of this node.
getChildren(String) - Method in class baseCode.bio.geneset.GONames
getClassToProbes(String) - Method in class baseCode.bio.geneset.GeneAnnotations
getCol(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
  Return a copy of a given column.
getCol(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
  Return a copy of a given column.
getCol(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
getColByName(String) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
  Return a copy of a given column.
getColIndexByName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getColIndexByName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Get the index of a column by name.
getColName(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getColName(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Gte the column name for an index.
getColNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getColNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
getColObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
getColObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getColObj(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
getColObj(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
getColObj(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
getColObj(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
getColObj(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
getColor(int) - Method in class baseCode.gui.ColorMap
getColor(int, int) - Method in class baseCode.gui.ColorMatrix
getColor(int, int) - Method in class baseCode.gui.JMatrixDisplay
getColorMap() - Method in class baseCode.gui.JMatrixDisplay
getColorMatrix() - Method in class baseCode.gui.JMatrixDisplay
getColumnClass(int) - Method in class baseCode.gui.table.TableSorter
getColumnCount() - Method in class baseCode.gui.ColorMatrix
getColumnCount() - Method in class baseCode.gui.JMatrixDisplay
getColumnCount() - Method in class baseCode.gui.table.TableSorter
getColumnName(int) - Method in class baseCode.gui.ColorMatrix
getColumnName(int) - Method in class baseCode.gui.JMatrixDisplay
getColumnName(int) - Method in class baseCode.gui.table.TableSorter
getColumnNames() - Method in class baseCode.gui.ColorMatrix
getColumnNames() - Method in class baseCode.gui.JMatrixDisplay
getComparator(int) - Method in class baseCode.gui.table.TableSorter
getComparator(Class) - Method in class baseCode.gui.table.TableSorter
getCon() - Method in class baseCode.db.Handle
getContents() - Method in class baseCode.dataStructure.tree.BinaryTreeNode
getDefinition() - Method in class baseCode.dataStructure.OntologyEntry
getDescription() - Method in class baseCode.gui.file.DataFileFilter
getDescription() - Method in class baseCode.gui.file.ImageFileFilter
getDescription() - Method in class baseCode.gui.file.XMLFileFilter
getDisplayMax() - Method in class baseCode.gui.ColorMatrix
getDisplayMax() - Method in class baseCode.gui.JMatrixDisplay
getDisplayMin() - Method in class baseCode.gui.ColorMatrix
getDisplayMin() - Method in class baseCode.gui.JMatrixDisplay
getDisplayRange() - Method in class baseCode.gui.JMatrixDisplay
getDistancer() - Method in class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory
getE() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getE() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getElement() - Method in class baseCode.dataStructure.tree.TreeNode
getExtension(String) - Static method in class baseCode.util.FileTools
  Returns the extension of a file.
getFirstChild() - Method in class baseCode.dataStructure.tree.TreeNode
getGONameMap() - Method in class baseCode.xml.GOParser
  Get a simple Map that contains keys that are the GO ids, values are the names.
getGeneProbeList(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get a list of the probes that correspond to a particular gene.
getGeneSetByIndex(int) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get a class by an integer index i from the sorted list.
getGeneSetToGeneMap() - Method in class baseCode.bio.geneset.GeneAnnotations
getGeneSetToProbeMap() - Method in class baseCode.bio.geneset.GeneAnnotations
getGeneToGeneSetMap() - Method in class baseCode.bio.geneset.GeneAnnotations
getGeneToProbeList() - Method in class baseCode.bio.geneset.GeneAnnotations
getGraph() - Method in class baseCode.bio.geneset.GONames
  Get the graph representation of the GO hierarchy.
getGraph() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
getGraph() - Method in interface baseCode.dataStructure.graph.GraphNode
getGraph() - Method in class baseCode.xml.GOParser
  Get the graph that was created.
getHeaderRendererIcon(int, int) - Method in class baseCode.gui.table.TableSorter
getId() - Method in class baseCode.dataStructure.OntologyEntry
getItem() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
  Get the actual contents of the node.
getItem() - Method in interface baseCode.dataStructure.graph.GraphNode
getItems() - Method in class baseCode.dataStructure.graph.AbstractGraph
getKey() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
  Get the key for the node.
getKey() - Method in interface baseCode.dataStructure.graph.GraphNode
getLeft() - Method in class baseCode.dataStructure.tree.BinaryTree
getLeft() - Method in class baseCode.dataStructure.tree.BinaryTreeNode
getMap() - Method in class baseCode.bio.geneset.GONames
  Get the Map representation of the GO id - name associations.
getMatrix() - Method in class baseCode.gui.ColorMatrix
getMatrix() - Method in class baseCode.gui.JMatrixDisplay
getMax() - Method in class baseCode.gui.JMatrixDisplay
getMaxIter() - Method in class baseCode.algorithm.learning.unsupervised.RankProp
  Maximum iterations before stopping.
getMin() - Method in class baseCode.gui.JMatrixDisplay
getMissingColor() - Method in class baseCode.gui.JMatrixDisplay
getN() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getN() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getName() - Method in class baseCode.dataStructure.OntologyEntry
getNameForId(String) - Method in class baseCode.bio.geneset.GONames
getNewGeneSets() - Method in class baseCode.bio.geneset.GONames
  Return the Set of all new gene sets (ones which were added after loading the file)
getNextSibling() - Method in class baseCode.dataStructure.tree.TreeNode
getNodeContents(Object) - Method in class baseCode.dataStructure.graph.AbstractGraph
  Retrieve the contents of a node by key.
getNodeContents(Object) - Method in interface baseCode.dataStructure.graph.Graph
getOutputMatrix(NamedMatrix, int, int) - Method in class baseCode.dataFilter.AbstractFilter
getP() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getP() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getPalette() - Method in class baseCode.gui.ColorMap
getPaletteSize() - Method in class baseCode.gui.ColorMap
getParentKeys() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
getParentNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Get the immediate parents of this node.
getParents(String) - Method in class baseCode.bio.geneset.GONames
getPreferredSize() - Method in class baseCode.gui.table.JVerticalHeaderRenderer
getProbeDescription(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get the description for a gene.
getProbeGeneName(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get the gene that a probe belongs to.
getProbeToGeneMap() - Method in class baseCode.bio.geneset.GeneAnnotations
getProbeToGeneSetMap() - Method in class baseCode.bio.geneset.GeneAnnotations
getQ() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getQ() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getQuick(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
getQuick(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
  This is an optimized version of getQuick.
getQuick(int, int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
getQuick(int) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
getQuick(int, int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
getQuick(int, int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
getQuick(int, int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
getRedundancies(String, Map) - Static method in class baseCode.bio.geneset.GeneSetMapTools
getRedundanciesString(String, Map) - Method in class baseCode.bio.geneset.GeneSetMapTools
getResults() - Method in class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer
getRight() - Method in class baseCode.dataStructure.tree.BinaryTree
getRight() - Method in class baseCode.dataStructure.tree.BinaryTreeNode
getRoot() - Method in class baseCode.dataStructure.tree.BinaryTree
getRow(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
getRow(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
  Return a reference to a specific row.
getRow(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
  Return a reference to a specific row.
getRow(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
getRow(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
getRow(int) - Method in class baseCode.gui.ColorMatrix
getRow(int) - Method in class baseCode.gui.JMatrixDisplay
getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
  This gives just the list of values in the row - make sure this is what you want.
getRowByName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
getRowByName(String) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
  Return a reference to a specific row.
getRowByName(String) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
getRowByName(String) - Method in class baseCode.gui.ColorMatrix
getRowByName(String) - Method in class baseCode.gui.JMatrixDisplay
getRowCount() - Method in class baseCode.gui.ColorMatrix
getRowCount() - Method in class baseCode.gui.JMatrixDisplay
getRowCount() - Method in class baseCode.gui.table.TableSorter
getRowHeight() - Method in class baseCode.gui.JMatrixDisplay
getRowIndexByName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getRowIndexByName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Get the index of a row by name..
getRowIndexByName(String) - Method in class baseCode.gui.ColorMatrix
getRowIndexByName(String) - Method in class baseCode.gui.JMatrixDisplay
getRowName(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getRowName(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Get the row name for an index
getRowName(int) - Method in class baseCode.gui.ColorMatrix
getRowName(int) - Method in class baseCode.gui.JMatrixDisplay
getRowNameMapIterator() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getRowNameMapIterator() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
getRowNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getRowNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
getRowNames() - Method in class baseCode.gui.ColorMatrix
getRowNames() - Method in class baseCode.gui.JMatrixDisplay
getRowObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
getRowObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
getRowObj(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
getRowObj(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Get a row in the matrix as a generic Object[].
getRowObj(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
getRowObj(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
getRowObj(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
getScores() - Method in class baseCode.algorithm.Ranker
getSelectedProbes() - Method in class baseCode.bio.geneset.GeneAnnotations
getSelectedSets() - Method in class baseCode.bio.geneset.GeneAnnotations
getSimilarities(String, Map) - Static method in class baseCode.bio.geneset.GeneSetMapTools
getSize(boolean) - Method in class baseCode.gui.JMatrixDisplay
getSortingStatus(int) - Method in class baseCode.gui.table.TableSorter
getStandardizedEnabled() - Method in class baseCode.gui.JMatrixDisplay
getStepSize(int, int, int) - Method in class baseCode.gui.ColorMap
  Calculate how fast we have to change color components.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class baseCode.gui.table.JBarGraphCellRenderer
  This method is called each time a cell in a column using this renderer needs to be rendered.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class baseCode.gui.table.JMatrixCellRenderer
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class baseCode.gui.table.JVerticalHeaderRenderer
getTableHeader() - Method in class baseCode.gui.table.TableSorter
getTableModel() - Method in class baseCode.gui.table.TableSorter
getTopoSortOrder() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
getTrueRowIndex(int) - Method in class baseCode.gui.ColorMatrix
getURL() - Method in class baseCode.gui.JLinkLabel
getUniqueItems() - Method in class baseCode.misc.GroupMap
getV() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getV() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getValue(int, int) - Method in class baseCode.gui.ColorMatrix
getValue(int, int) - Method in class baseCode.gui.JMatrixDisplay
getValueAt(int, int) - Method in class baseCode.gui.table.TableSorter
getWeight() - Method in class baseCode.dataStructure.Link
getWithoutExtension(String) - Static method in class baseCode.util.FileTools
getZ() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
getZ() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
getx() - Method in class baseCode.dataStructure.Point
gety() - Method in class baseCode.dataStructure.Point
graph - Variable in class baseCode.dataStructure.graph.AbstractGraphNode

## H

Handle - class baseCode.db.Handle.
  Database handle container and query convenience functions.
Handle(String, String, String, String) - Constructor for class baseCode.db.Handle
Handle() - Constructor for class baseCode.db.Handle
Handle(String, String) - Constructor for class baseCode.db.Handle
HierarchicalClusterer - class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer.
  Start with all items in separate clusters.
HierarchicalClusterer(ObjectArrayList) - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer
HistogramWriter - class baseCode.io.writer.HistogramWriter.
  Print an `hep.aidia.IHistogram1D`object to a text file.
HistogramWriter() - Constructor for class baseCode.io.writer.HistogramWriter
hasChild(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Check to see if this node has a particular immediate child.
hasColNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
hasColNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Check if this matrix has a valid set of column names.
hasDataExtension(String) - Static method in class baseCode.util.FileTools
hasDuplicates(String) - Method in class baseCode.misc.GroupMap
  For a given key, return true if it has duplicates.
hasImageExtension(String) - Static method in class baseCode.util.FileTools
hasParent(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Check to see if this node has a particular immediate parent.
hasRow(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
hasRow(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
hasRowNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
hasRowNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
hasXMLExtension(String) - Static method in class baseCode.util.FileTools
helpButton - Variable in class baseCode.gui.AppDialog
helpButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.AppDialog
highCut - Variable in class baseCode.dataFilter.AbstractLevelFilter
hyperlinkUpdate(HyperlinkEvent) - Method in class baseCode.gui.JWebBrowser

## I

IMAGE_EXTENSIONS - Static variable in class baseCode.util.FileTools
ImageFileFilter - class baseCode.gui.file.ImageFileFilter.
ImageFileFilter() - Constructor for class baseCode.gui.file.ImageFileFilter
ItemLevelFilter - class baseCode.dataFilter.ItemLevelFilter.
  Filter that remove individual values that are outside of a range.
ItemLevelFilter() - Constructor for class baseCode.dataFilter.ItemLevelFilter
ignoreSimilar(double, GeneAnnotations, StatusViewer, int, int, double) - Static method in class baseCode.bio.geneset.GeneSetMapTools
  Remove classes which are too similar to some other class.
inDegree() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
incrementalUpdate(DoubleArrayList, int, int, double[]) - Static method in class baseCode.math.DescriptiveWithMissing
  Not supported.
incrementalUpdateSumsOfPowers(DoubleArrayList, int, int, int, int, double[]) - Static method in class baseCode.math.DescriptiveWithMissing
  Not supported.
incrementalWeightedUpdate(DoubleArrayList, DoubleArrayList, int, int, double[]) - Static method in class baseCode.math.DescriptiveWithMissing
  Not supported.
indexes - Variable in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
init(AbstractNamedDoubleMatrix) - Method in class baseCode.gui.ColorMatrix
init(ColorMatrix) - Method in class baseCode.gui.JMatrixDisplay
init(long) - Static method in class baseCode.math.RandomChooser
  Initialized the random number generator witha given seed.
initSize() - Method in class baseCode.gui.JMatrixDisplay
  Sets the display size
insertLeft(BinaryTreeNode, Object) - Method in class baseCode.dataStructure.tree.BinaryTree
insertRight(BinaryTreeNode, Object) - Method in class baseCode.dataStructure.tree.BinaryTree
intArrayToBytes(int[]) - Method in class baseCode.io.ByteArrayConverter
isCellEditable(int, int) - Method in class baseCode.gui.table.TableSorter
isCompound() - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
isEmpty() - Method in class baseCode.dataStructure.Queue
  Deprecated.
isEmpty() - Method in class baseCode.dataStructure.Stack
  Deprecated.
isEmpty() - Method in class baseCode.dataStructure.tree.BinaryTree
isFull() - Method in class baseCode.dataStructure.Queue
  Deprecated.
isFull() - Method in class baseCode.dataStructure.Stack
  Deprecated.
isLeaf() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
isLeaf() - Method in class baseCode.dataStructure.tree.BinaryTreeNode
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
isMissing(int, int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Check if the value at a given index is missing.
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
  (non-Javadoc) Note that in a sparse matrix, zero values are considered "missing"!
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
isReady() - Method in class baseCode.gui.WizardStep
isSorting() - Method in class baseCode.gui.table.TableSorter
isValidFraction(double) - Static method in class baseCode.math.Stats
  Test whether a value is a valid fractional or probability value.
isValidPearsonCorrelation(double) - Static method in class 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 baseCode.common.Visitable
isVisited() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
item - Variable in class baseCode.dataStructure.graph.AbstractGraphNode
items - Variable in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
items - Variable in class baseCode.dataStructure.graph.AbstractGraph

## J

JBarGraphCellRenderer - class baseCode.gui.table.JBarGraphCellRenderer.
JBarGraphCellRenderer() - Constructor for class baseCode.gui.table.JBarGraphCellRenderer
JGradientBar - class baseCode.gui.JGradientBar.
  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 baseCode.gui.JGradientBar
  Creates a new instance of JGradientBar
JLinkLabel - class baseCode.gui.JLinkLabel.
  A clickable link label that contains a URL.
JLinkLabel() - Constructor for class baseCode.gui.JLinkLabel
  Creates a new instance of JLinkLabel
JLinkLabel(String) - Constructor for class baseCode.gui.JLinkLabel
JLinkLabel(String, String) - Constructor for class baseCode.gui.JLinkLabel
JMatrixCellRenderer - class baseCode.gui.table.JMatrixCellRenderer.
JMatrixCellRenderer(JMatrixDisplay) - Constructor for class baseCode.gui.table.JMatrixCellRenderer
JMatrixDisplay - class baseCode.gui.JMatrixDisplay.
  Title: JMatrixDisplay
JMatrixDisplay(String) - Constructor for class baseCode.gui.JMatrixDisplay
JMatrixDisplay(DenseDoubleMatrix2DNamed) - Constructor for class baseCode.gui.JMatrixDisplay
JMatrixDisplay(ColorMatrix) - Constructor for class baseCode.gui.JMatrixDisplay
JVerticalHeaderRenderer - class baseCode.gui.table.JVerticalHeaderRenderer.
JVerticalHeaderRenderer() - Constructor for class baseCode.gui.table.JVerticalHeaderRenderer
JWebBrowser - class baseCode.gui.JWebBrowser.
JWebBrowser(String) - Constructor for class baseCode.gui.JWebBrowser
jLabelStatus - Variable in class baseCode.gui.Wizard
jPanelStatus - Variable in class baseCode.gui.Wizard
jbInit() - Method in class baseCode.gui.WizardStep

## K

KSTest - class baseCode.math.KSTest.
  Class to perform the Kolmogorov-Smirnov test.
KSTest() - Constructor for class baseCode.math.KSTest
key - Variable in class baseCode.dataStructure.graph.AbstractGraphNode
kurtosis(double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the kurtosis (aka excess) of a data sequence.
kurtosis(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the kurtosis (aka excess) of a data sequence, which is `-3 + moment(data,4,mean) / standardDeviation4`.

## L

LEXICAL_COMPARATOR - Static variable in class baseCode.gui.table.TableSorter
LINE_WIDTH - Static variable in class baseCode.gui.table.JBarGraphCellRenderer
Link - class baseCode.dataStructure.Link.
  Title:
Link(int, int, double) - Constructor for class baseCode.dataStructure.Link
lag1(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Not supported.
like(int) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
like2D(int, int) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
loadMatrixFromFile(String) - Method in class baseCode.gui.ColorMatrix
  A convenience method for loading data files
log - Static variable in class baseCode.algorithm.Algorithm
log - Static variable in class baseCode.dataFilter.AbstractFilter
log - Static variable in class baseCode.dataStructure.graph.AbstractGraphNode
log - Static variable in class baseCode.gui.GuiUtil
log - Static variable in class baseCode.io.reader.AbstractNamedMatrixReader
log - Static variable in class baseCode.util.StatusDebugLogger
lowCut - Variable in class baseCode.dataFilter.AbstractLevelFilter

## M

MAX - Static variable in class baseCode.dataFilter.RowLevelFilter
  Use the maximum of the row as the criterion.
MEAN - Static variable in class baseCode.dataFilter.RowLevelFilter
  Use the mean as the criterion.
MEDIAN - Static variable in class baseCode.dataFilter.RowLevelFilter
  Use the median as the criterion.
MIN - Static variable in class baseCode.dataFilter.RowLevelFilter
  Use the minimum of the row as the criterion.
M_1_PI - Static variable in class baseCode.math.Constants
M_1_SQRT_2 - Static variable in class baseCode.math.Constants
M_1_SQRT_2PI - Static variable in class baseCode.math.Constants
M_LN_2 - Static variable in class baseCode.math.Constants
M_LN_SQRT_2PI - Static variable in class baseCode.math.Constants
M_LN_SQRT_PI - Static variable in class baseCode.math.Constants
M_LN_SQRT_PId2 - Static variable in class baseCode.math.Constants
M_LOG10_2 - Static variable in class baseCode.math.Constants
M_PI_2 - Static variable in class baseCode.math.Constants
M_PI_4 - Static variable in class baseCode.math.Constants
M_PI_half - Static variable in class baseCode.math.Constants
M_SQRT_2 - Static variable in class baseCode.math.Constants
M_SQRT_2dPI - Static variable in class baseCode.math.Constants
M_SQRT_PI - Static variable in class baseCode.math.Constants
MapReader - class baseCode.io.reader.MapReader.
  Reads a tab-delimited file with lines of the format Key Value.
MapReader() - Constructor for class baseCode.io.reader.MapReader
MatrixRowStats - class baseCode.math.MatrixRowStats.
  Convenience functions for getting row statistics from matrices.
MatrixStats - class baseCode.math.MatrixStats.
MatrixStats() - Constructor for class baseCode.math.MatrixStats
MeanDifferenceMetaAnalysis - class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis.
  Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
MeanDifferenceMetaAnalysis(boolean) - Constructor for class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
MetaAnalysis - class baseCode.math.metaanalysis.MetaAnalysis.
  Statistics for meta-analysis.
MetaAnalysis() - Constructor for class baseCode.math.metaanalysis.MetaAnalysis
MultipleTestCorrection - class baseCode.math.MultipleTestCorrection.
  Methods for p-value correction of sets of hypothesis tests.
MultipleTestCorrection() - Constructor for class baseCode.math.MultipleTestCorrection
m_cellSize - Variable in class baseCode.gui.JMatrixDisplay
m_colorMap - Variable in class baseCode.gui.ColorMatrix
m_colorPalette - Variable in class baseCode.gui.ColorMap
m_colors - Variable in class baseCode.gui.ColorMatrix
m_columnLabelHeight - Variable in class baseCode.gui.JMatrixDisplay
m_currentColorMap - Variable in class baseCode.gui.ColorMap
m_customColorMap - Variable in class baseCode.gui.ColorMap
m_defaultResolution - Variable in class baseCode.gui.JMatrixDisplay
m_defaultSuggestedNumberOfColors - Static variable in class baseCode.gui.ColorMap
m_displayMax - Variable in class baseCode.gui.ColorMatrix
m_displayMin - Variable in class baseCode.gui.ColorMatrix
  Min and max values to display, which might not be the actual min and max values in the matrix.
m_fontGutter - Variable in class baseCode.gui.JMatrixDisplay
m_fontSize - Variable in class baseCode.gui.JMatrixDisplay
m_gradient - Variable in class baseCode.gui.JGradientBar
m_image - Variable in class baseCode.gui.JMatrixDisplay
m_isBarGraph - Variable in class baseCode.gui.table.JBarGraphCellRenderer
m_isSelected - Variable in class baseCode.gui.table.JBarGraphCellRenderer
m_isShowLabels - Variable in class baseCode.gui.JMatrixDisplay
m_labelFont - Variable in class baseCode.gui.JMatrixDisplay
m_labelGutter - Variable in class baseCode.gui.JMatrixDisplay
m_matrix - Variable in class baseCode.gui.ColorMatrix
m_matrixReader - Variable in class baseCode.gui.ColorMatrix
m_max - Variable in class baseCode.gui.ColorMatrix
m_max - Variable in class baseCode.gui.JGradientBar
m_maxColor - Variable in class baseCode.gui.ColorMap
  last color in the current color map
m_maxFontSize - Variable in class baseCode.gui.JMatrixDisplay
m_min - Variable in class baseCode.gui.ColorMatrix
m_min - Variable in class baseCode.gui.JGradientBar
m_minColor - Variable in class baseCode.gui.ColorMap
  first color in the current color map
m_missingColor - Variable in class baseCode.gui.ColorMatrix
m_noFocusBorder - Static variable in class baseCode.gui.table.JBarGraphCellRenderer
m_ratioWidth - Variable in class baseCode.gui.JMatrixDisplay
m_resolution - Variable in class baseCode.gui.JMatrixDisplay
m_rowKeys - Variable in class baseCode.gui.ColorMatrix
  to be able to sort the rows by an arbitrary key
m_rowLabelWidth - Variable in class baseCode.gui.JMatrixDisplay
m_selectionBackground - Static variable in class baseCode.gui.table.JBarGraphCellRenderer
m_text - Variable in class baseCode.gui.JLinkLabel
m_textSize - Variable in class baseCode.gui.JMatrixDisplay
m_totalColumns - Variable in class baseCode.gui.ColorMatrix
m_totalRows - Variable in class baseCode.gui.ColorMatrix
m_url - Variable in class baseCode.gui.JLinkLabel
m_values - Variable in class baseCode.gui.table.JBarGraphCellRenderer
main(String[]) - Static method in class baseCode.gui.JWebBrowser
mainPanel - Variable in class baseCode.gui.Wizard
makeEmpty() - Method in class baseCode.dataStructure.Queue
  Deprecated.
manhattanDistance(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.Distance
  Calculate the Manhattan distance between two vectors.
mapValuesToColors() - Method in class baseCode.gui.ColorMatrix
mark() - Method in class baseCode.common.Visitable
mark() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
max(AbstractNamedDoubleMatrix) - Static method in class baseCode.math.MatrixStats
  Compute the maximum value in the matrix.
maxStringPixelWidth(String[], Font, Component) - Static method in class baseCode.graphics.text.Util
mean(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
mean(DoubleArrayList, int) - Static method in class baseCode.math.DescriptiveWithMissing
  Special mean calculation where we use the effective size as an input.
mean(double[], int) - Static method in class baseCode.math.DescriptiveWithMissing
  Special mean calculation where we use the effective size as an input.
meanAboveQuantile(int, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Calculate the mean of the values above a particular quantile of an array.
meanAboveQuantile(int, double[], int) - Static method in class baseCode.math.Stats
  calculate the mean of the values above (NOT greater or equal to) a particular index rank of an array.
meanGeneSetSize(GeneAnnotations, boolean) - Static method in class baseCode.bio.geneset.GeneSetMapTools
meanSetsPerGene(GeneAnnotations, boolean) - Static method in class baseCode.bio.geneset.GeneSetMapTools
means(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
  Calculates the means of a matrix's rows.
median(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the median of a sorted data sequence.
metaFEWeights(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  Weights under a fixed effects model.
metaRESampleVariance(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  CH sample variance under random effects model, equation 18-20
metaREVariance(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  CH equation 18-23.
metaREWeights(DoubleArrayList, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  Under a random effects model, CH eqn.
metaVariance(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  CH 18-3.
metaVariance(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  CH 18-3 version 2 for quality weighted.
metaZscore(double, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  Test statistic for H0: effectSize == 0.
min(AbstractNamedDoubleMatrix) - Static method in class baseCode.math.MatrixStats
  Find the minimum of the entire matrix.
modelIndex(int) - Method in class baseCode.gui.table.TableSorter
modifyClass(String, String) - Method in class baseCode.bio.geneset.GONames
modifyClass(String, ArrayList) - Method in class baseCode.bio.geneset.GeneAnnotations
  Redefine a class.
moment(DoubleArrayList, int, double) - Static method in class 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()`.
mouseButton_actionPerformed(MouseEvent) - Method in class baseCode.gui.AppDialog
mouseClicked(MouseEvent) - Method in class baseCode.gui.JLinkLabel
mouseEntered(MouseEvent) - Method in class baseCode.gui.JLinkLabel
mouseExited(MouseEvent) - Method in class baseCode.gui.JLinkLabel
mousePressed(MouseEvent) - Method in class baseCode.gui.JLinkLabel
mouseReleased(MouseEvent) - Method in class baseCode.gui.JLinkLabel

## N

NOT_SORTED - Static variable in class baseCode.gui.table.TableSorter
NamedMatrix - interface baseCode.dataStructure.matrix.NamedMatrix.
  Copyright (c) 2004
NormalProbabilityComputer - class baseCode.math.distribution.NormalProbabilityComputer.
NormalProbabilityComputer(double, double) - Constructor for class baseCode.math.distribution.NormalProbabilityComputer
newSet(String) - Method in class baseCode.bio.geneset.GONames
  Check if a gene set is already defined.
newStatement() - Method in class baseCode.db.Handle
nextButton - Variable in class baseCode.gui.Wizard
nextButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
  Define what happens when the 'next' button is pressed
nextDouble() - Method in class baseCode.math.distribution.Dirichlet
nextDoubleMatrix() - Method in class baseCode.math.distribution.Wishart
  Based on R code from Francesca Dominici, http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html
normalize(DoubleArrayList, double) - Static method in class baseCode.math.Stats
  Divide the elements of an array by a given factor.
normalize(DoubleArrayList) - Static method in class baseCode.math.Stats
  Adjust the elements of an array so they total to 1.0.
numAnnotatedGenes() - Method in class baseCode.bio.geneset.GeneAnnotations
  Compute how many genes have Gene set annotations.
numChildren() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
numDuplicates(String) - Method in class baseCode.misc.GroupMap
  For a given key, return the number of duplicates it has (not counting itself).
numGeneSets() - Method in class baseCode.bio.geneset.GeneAnnotations
  Get the number of classes.
numGenes() - Method in class baseCode.bio.geneset.GeneAnnotations
  How many genes are in the file?
numGenesInGeneSet(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get the number of genes in a gene set, identified by id.
numMissing() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
numMissing() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Return the number of missing values in the matrix.
numNeighbors() - Method in class baseCode.dataStructure.graph.UndirectedGraphNode
numParents() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
numProbesForGene(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get how many probes point to the same gene.
numProbesInGeneSet(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Get the number of probes in a gene set, identified by id.

## O

OntologyEntry - class baseCode.dataStructure.OntologyEntry.
  A class representing a descriptive term that can be associated with things.
OntologyEntry(String) - Constructor for class baseCode.dataStructure.OntologyEntry
OntologyEntry(String, String, String) - Constructor for class baseCode.dataStructure.OntologyEntry
oneSample(DoubleArrayList, ProbabilityComputer) - Static method in class baseCode.math.KSTest
openURL(String) - Static method in class baseCode.util.BrowserLauncher
  Attempts to open the default web browser to the given URL.
order(DoubleArrayList) - Static method in class baseCode.math.Rank
  Return a permutation which puts the array in sorted order.
outDegree() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

## P

PNG_EXTENSION - Static variable in class baseCode.util.FileTools
Point - class baseCode.dataStructure.Point.
  Title:
Point(int, int) - Constructor for class baseCode.dataStructure.Point
ProbabilityComputer - interface baseCode.math.distribution.ProbabilityComputer.
  An interface that describes objects that can produce probabilities according to some distribution.
paintBackground(Graphics) - Method in class baseCode.gui.table.JBarGraphCellRenderer
paintComponent(Graphics) - Method in class baseCode.gui.JMatrixDisplay
  `JComponent` method used to render this component
paintComponent(Graphics) - Method in class baseCode.gui.table.JBarGraphCellRenderer
paintComponent(Graphics) - Method in class baseCode.gui.table.JVerticalHeaderRenderer
parents - Variable in class baseCode.dataStructure.graph.DirectedGraphNode
phyper(int, int, int, int, boolean) - Static method in class baseCode.math.SpecFunc
  Ported from R phyper.c
pop() - Method in class baseCode.dataStructure.Stack
  Deprecated. Remove the most recently added item.
prepareStatement(String) - Method in class baseCode.db.Handle
print(Writer) - Method in class baseCode.bio.geneset.GeneAnnotations
  Print out the gene annotations in the same format we got them in, but if the gene sets have been modified, this will be reflected.
probability(double) - Method in class baseCode.math.distribution.NormalProbabilityComputer
probability(double, boolean) - Method in class baseCode.math.distribution.NormalProbabilityComputer
probability(double) - Method in interface baseCode.math.distribution.ProbabilityComputer
  Return the probability associated with a certain value.The upper tail of the associated distribution is returned.
probability(double, boolean) - Method in interface baseCode.math.distribution.ProbabilityComputer
  Return the probability associated with a certain value, with choice of tail.
probability(double) - Method in class baseCode.math.distribution.UniformProbabilityComputer
probability(double, boolean) - Method in class baseCode.math.distribution.UniformProbabilityComputer
product(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the product of a data sequence, which is `Prod( data[i] )`.
prune() - Method in class baseCode.dataStructure.graph.DirectedGraph
  Remove vertices to nodes that aren't in the graph.
prune() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
  Remove connections that are to nodes not contained in this graph
push(Object) - Method in class baseCode.dataStructure.Stack
  Deprecated. Add an item to the stack.
pvalue(double, int) - Static method in class baseCode.math.CorrelationStats
pvalueAsByte(double, int) - Static method in class baseCode.math.CorrelationStats
  Conver a correlation p value into a value between 0 and 255 inclusive.

## Q

Queue - class baseCode.dataStructure.Queue.
  Deprecated. -- use java.util.List instead.
Queue() - Constructor for class baseCode.dataStructure.Queue
  Deprecated.
Queue(int) - Constructor for class baseCode.dataStructure.Queue
  Deprecated.
qStatistic(DoubleArrayList, DoubleArrayList, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  The "Q" statistic used to test homogeneity of effect sizes.
qTest(double, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  Test for statistical significance of Q.
quantile(DoubleArrayList, double) - Static method in class 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`.
quantile(int, double[], int) - Static method in class baseCode.math.Stats
  Given a double array, calculate the quantile requested.
quantileInverse(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns how many percent of the elements contained in the receiver are `<= element`.
quantiles(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the quantiles of the specified percentages.
queryToDouble(String) - Method in class baseCode.db.Handle
queryToInt(String) - Method in class baseCode.db.Handle
queryToList(String) - Method in class baseCode.db.Handle
queryToMap(String) - Method in class baseCode.db.Handle
queryToSet(String) - Method in class baseCode.db.Handle
queryToString(String) - Method in class baseCode.db.Handle
quote(String) - Method in class baseCode.db.Handle

## R

RANGE - Static variable in class baseCode.dataFilter.RowLevelFilter
  Use the range as the criterion
RCDoubleMatrix1D - class baseCode.dataStructure.matrix.RCDoubleMatrix1D.
  A row-compressed 1D matrix.
RCDoubleMatrix1D(double[]) - Constructor for class baseCode.dataStructure.matrix.RCDoubleMatrix1D
RCDoubleMatrix1D(int) - Constructor for class baseCode.dataStructure.matrix.RCDoubleMatrix1D
RCDoubleMatrix1D(IntArrayList, DoubleArrayList) - Constructor for class baseCode.dataStructure.matrix.RCDoubleMatrix1D
REDGREEN_COLORMAP - Static variable in class baseCode.gui.ColorMap
ROC - class baseCode.math.ROC.
  Functions for calculating Receiver operator characteristics.
ROC() - Constructor for class baseCode.math.ROC
RandomChooser - class baseCode.math.RandomChooser.
  Fill arrays with random values given a source of values.
Rank - class baseCode.math.Rank.
  Calculate rank statistics for arrays.
Rank() - Constructor for class baseCode.math.Rank
RankProp - class baseCode.algorithm.learning.unsupervised.RankProp.
  Implementation of RankProp, as described in Weston et al.
RankProp() - Constructor for class baseCode.algorithm.learning.unsupervised.RankProp
Ranker - class baseCode.algorithm.Ranker.
Ranker() - Constructor for class baseCode.algorithm.Ranker
RegressionTesting - class baseCode.util.RegressionTesting.
  Tools to help make regression testing easier.
RowAbsentFilter - class baseCode.dataFilter.RowAbsentFilter.
  Filter a data matrix according to flags given in a separate matrix.
RowAbsentFilter() - Constructor for class baseCode.dataFilter.RowAbsentFilter
RowAffyNameFilter - class baseCode.dataFilter.RowAffyNameFilter.
  Remove probes that have names meeting certain rules indicating they may have low reliability.
RowAffyNameFilter(int[]) - Constructor for class baseCode.dataFilter.RowAffyNameFilter
RowLevelFilter - class baseCode.dataFilter.RowLevelFilter.
  Remove rows from a matrix based on some row-based statistic.
RowLevelFilter() - Constructor for class baseCode.dataFilter.RowLevelFilter
RowMissingFilter - class baseCode.dataFilter.RowMissingFilter.
  Remove rows from a matrix that are missing too many points.
RowMissingFilter() - Constructor for class baseCode.dataFilter.RowMissingFilter
RowNameFilter - class baseCode.dataFilter.RowNameFilter.
  Remove or retain rows that are on a list.
RowNameFilter(Set, boolean) - Constructor for class baseCode.dataFilter.RowNameFilter
RowNameFilter(Set) - Constructor for class baseCode.dataFilter.RowNameFilter
RowNameFilter() - Constructor for class baseCode.dataFilter.RowNameFilter
range(DoubleArrayList) - Static method in class baseCode.math.Stats
  Compute the range of an array.
rankInterpolated(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the linearly interpolated number of elements in a list less or equal to a given element.
rankTransform(DoubleArrayList) - Static method in class baseCode.math.Rank
  Rank transform an array.
rankTransform(Map) - Static method in class baseCode.math.Rank
  Rank transform a map, where the values are numerical (java.lang.Double) values we wish to rank.
rbfNormalize(AbstractNamedDoubleMatrix, double) - Static method in class baseCode.math.MatrixStats
  Normalize a matrix in place to be a transition matrix.
read(String) - Method in class baseCode.io.reader.AbstractNamedMatrixReader
read(InputStream) - Method in class baseCode.io.reader.AbstractNamedMatrixReader
read(String) - Method in class baseCode.io.reader.DoubleMatrixReader
read(InputStream) - Method in class baseCode.io.reader.DoubleMatrixReader
read(InputStream, Set) - Method in class baseCode.io.reader.DoubleMatrixReader
read(InputStream, Set, boolean) - Method in class baseCode.io.reader.DoubleMatrixReader
read(String, Set) - Method in class baseCode.io.reader.DoubleMatrixReader
  Read a matrix from a file, subject to filtering criteria.
read(String) - Method in class baseCode.io.reader.MapReader
read(InputStream) - Method in class baseCode.io.reader.MapReader
read(String, boolean) - Method in class baseCode.io.reader.MapReader
read(InputStream, boolean) - Method in class baseCode.io.reader.MapReader
read(String) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
read(InputStream) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
read(String, Set) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
  Read a matrix from a file, subject to filtering criteria.
read(InputStream, Set) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
  Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
read(String) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
read(InputStream) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
  Read an entire sparse matrix from a stream (JW format).
read(InputStream, int) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
  Read an entire sparse matrix from a stream (JW format).
read(String) - Method in class baseCode.io.reader.StringMatrixReader
read(InputStream) - Method in class baseCode.io.reader.StringMatrixReader
  Missing values are entered as an empty string.
read(String, DenseDoubleMatrix2DNamed) - Method in class baseCode.misc.GroupMap
  The input file format is that used by `MapReader`.
readFromAdjList(String) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
  Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
readFromAdjList(InputStream) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
readHeader(BufferedReader) - Method in class baseCode.io.reader.AbstractNamedMatrixReader
readJW(InputStream) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
  Read a sparse matrix in "JW" (Jason Weston) format.
readOneRow(BufferedReader) - Method in class baseCode.io.reader.AbstractNamedMatrixReader
readOneRow(BufferedReader) - Method in class baseCode.io.reader.DoubleMatrixReader
readOneRow(BufferedReader) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
readOneRow(BufferedReader) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
readOneRow(BufferedReader, int) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
  Use this to read one row from a matrix (JW format).
readOneRow(BufferedReader) - Method in class baseCode.io.reader.StringMatrixReader
readTestResult(InputStream) - Static method in class baseCode.util.RegressionTesting
readTestResult(String) - Static method in class baseCode.util.RegressionTesting
readTestResultFromFile(String) - Static method in class baseCode.util.RegressionTesting
removeAspect(GeneAnnotations, GONames, StatusViewer, String) - Static method in class baseCode.bio.geneset.GeneSetMapTools
removeBySize(GeneAnnotations, StatusViewer, int, int) - Static method in class baseCode.bio.geneset.GeneSetMapTools
  Remove gene sets that don't meet certain criteria.
removeClassFromMaps(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Remove a gene set (class) from all the maps that reference it.
repaint(long, int, int, int, int) - Method in class baseCode.gui.table.JBarGraphCellRenderer
repaint(Rectangle) - Method in class baseCode.gui.table.JBarGraphCellRenderer
resetRowKeys() - Method in class baseCode.gui.ColorMatrix
resetRowKeys() - Method in class baseCode.gui.JMatrixDisplay
resetSelectedProbes() - Method in class baseCode.bio.geneset.GeneAnnotations
  Set the selected gene set to be the entire set.
resetSelectedSets() - Method in class baseCode.bio.geneset.GeneAnnotations
  Set the selected gene set to be the entire set.
revalidate() - Method in class baseCode.gui.table.JBarGraphCellRenderer
revalidate() - Method in class baseCode.gui.table.JMatrixCellRenderer
revalidate() - Method in class baseCode.gui.table.JVerticalHeaderRenderer
rocpval(int, double) - Static method in class baseCode.math.ROC
  For an AROC value, calculates a p value based on approximation for calculating the stanadard deviation.
rows() - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
rows() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
rows() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
rows() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Get the number of rows the matrix has
rows() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
rows() - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
rows() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
run() - Method in class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer
  Perform a hierarchical clustering on the objects.
run(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
  Following CH section 2.2.
run(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
run(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
runQuery(String) - Method in class baseCode.db.Handle
runUpdateQuery(String) - Method in class baseCode.db.Handle

## S

SMALL - Static variable in class baseCode.math.Constants
ST - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
  Filter probes that contain the '_st' (sense strand) tag
ST - Static variable in class baseCode.dataFilter.RowAffyNameFilter
  Filter probes that contain the '_st' (sense strand) tag
Similarity - interface baseCode.algorithm.learning.unsupervised.cluster.Similarity.
SparseDoubleMatrix2DNamed - class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed.
  Title: SparseDoubleMatrix2DNamed
SparseDoubleMatrix2DNamed(double[][]) - Constructor for class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
SparseDoubleMatrix2DNamed(int, int) - Constructor for class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
SparseDoubleMatrixReader - class baseCode.io.reader.SparseDoubleMatrixReader.
SparseDoubleMatrixReader() - Constructor for class baseCode.io.reader.SparseDoubleMatrixReader
SparseRaggedDouble2DNamedMatrixReader - class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader.
  Best data structure for reading really big, really sparse matrices when a matrix represetation is needed.
SparseRaggedDouble2DNamedMatrixReader() - Constructor for class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
SparseRaggedDoubleMatrix2DNamed - class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed.
  A sparse matrix class where the rows are ragged and compressed.
SparseRaggedDoubleMatrix2DNamed() - Constructor for class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
SpecFunc - class baseCode.math.SpecFunc.
  Assorted special functions, primarily concerning probability distributions.
SpecFunc() - Constructor for class baseCode.math.SpecFunc
Stack - class baseCode.dataStructure.Stack.
  Deprecated. -- use java.util.List instead.
Stack() - Constructor for class baseCode.dataStructure.Stack
  Deprecated. Build a stack with the default capacity.
Stack(int) - Constructor for class baseCode.dataStructure.Stack
  Deprecated. Build a stack with a given capacity.
Stats - class baseCode.math.Stats.
  Miscellaneous functions used for statistical analysis.
StatusDebugLogger - class baseCode.util.StatusDebugLogger.
  Copyright (c) 2004 Columbia University
StatusDebugLogger() - Constructor for class baseCode.util.StatusDebugLogger
StatusJlabel - class baseCode.gui.StatusJlabel.
  Title:
StatusJlabel(JLabel) - Constructor for class baseCode.gui.StatusJlabel
StatusStderr - class baseCode.util.StatusStderr.
  Prints status info to stderr
StatusStderr() - Constructor for class baseCode.util.StatusStderr
StatusViewer - interface baseCode.util.StatusViewer.
  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).
StringArrayToBytes(String[]) - Method in class baseCode.io.StringConverter
  FIXME this is broken.
StringConverter - class baseCode.io.StringConverter.
StringConverter() - Constructor for class baseCode.io.StringConverter
StringMatrix2DNamed - class baseCode.dataStructure.matrix.StringMatrix2DNamed.
  A NamedMatrix containing String objects.
StringMatrix2DNamed(int, int) - Constructor for class baseCode.dataStructure.matrix.StringMatrix2DNamed
StringMatrixReader - class baseCode.io.reader.StringMatrixReader.
  Reader for `StringMatrix2DNamed`
StringMatrixReader() - Constructor for class baseCode.io.reader.StringMatrixReader
StringToDoubles(String) - Method in class baseCode.io.StringConverter
sampleKurtosis(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sample kurtosis (aka excess) of a data sequence.
sampleSkew(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sample skew of a data sequence.
sampleStandardDeviation(int, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sample standard deviation.
sampleStandardDeviations(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
  Calculates the sample standard deviation of each row of a matrix
sampleVariance(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sample variance of a data sequence.
samplingVariance(double, double) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
  Equation 18-10 from CH.
samplingVariance(double, double, double) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
  CH eqn 18-7
samplingVariances(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
  Run equation CH 18-10 on a list of sample sizes and effects.
samplingVariances(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
  Run eqn 18-7 on a set of effect sizes.
saveImage(String) - Method in class baseCode.gui.JMatrixDisplay
  Saves the image to a png file.
saveImage(String, boolean) - Method in class baseCode.gui.JMatrixDisplay
saveImage(String, boolean, boolean) - Method in class baseCode.gui.JMatrixDisplay
selectProbes(String) - Method in class baseCode.bio.geneset.GeneAnnotations
  Create a selected probes list based on a search string.
selectSets(String, GONames) - Method in class baseCode.bio.geneset.GeneAnnotations
selectedProbes() - Method in class baseCode.bio.geneset.GeneAnnotations
selectedSets() - Method in class baseCode.bio.geneset.GeneAnnotations
set(int, int) - Method in class baseCode.dataStructure.Point
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
set(int, int, double) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
set(int, int, double) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
set(int, int, Object) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
  Set a value in the matrix.
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
set(int, int, double) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
set(int, int, double) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
setActionButtonText(String) - Method in class baseCode.gui.AppDialog
setAlpha(double) - Method in class baseCode.algorithm.learning.unsupervised.RankProp
  controls amount of "clustering"
setAspect(String) - Method in class baseCode.bio.GOEntry
setCancelButtonText(String) - Method in class baseCode.gui.AppDialog
setCellSize(Dimension) - Method in class baseCode.gui.JMatrixDisplay
setColor(int, int, Color) - Method in class baseCode.gui.ColorMatrix
setColorMap(Color[]) - Method in class baseCode.gui.ColorMatrix
setColorMap(Color[]) - Method in class baseCode.gui.JGradientBar
setColorMap(Color[]) - Method in class baseCode.gui.JMatrixDisplay
setColumnComparator(Class, Comparator) - Method in class baseCode.gui.table.TableSorter
setColumnNames(List) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
setColumnNames(List) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
setContents(Object) - Method in class baseCode.dataStructure.tree.BinaryTreeNode
setDefinition(String) - Method in class baseCode.dataStructure.OntologyEntry
setDelimiter(String) - Method in class baseCode.io.StringConverter
setDisplayRange(double, double) - Method in class baseCode.gui.ColorMatrix
setDisplayRange(double, double) - Method in class baseCode.gui.JMatrixDisplay
setElement(Object) - Method in class baseCode.dataStructure.tree.TreeNode
setError(String) - Method in class baseCode.gui.StatusJlabel
setError(String) - Method in class baseCode.util.StatusDebugLogger
setError(String) - Method in class baseCode.util.StatusStderr
setError(String) - Method in interface baseCode.util.StatusViewer
  Print an error status messge.
setFilterNames(Set, boolean) - Method in class baseCode.dataFilter.RowNameFilter
setFinishDisabled() - Method in class baseCode.gui.Wizard
  Disable the "finish" button, indicating the user has some steps to do yet.
setFinishEnabled() - Method in class baseCode.gui.Wizard
  Enable the "finish" button, indicating the user can get out of the wizard at this stage.
setFirstChild(TreeNode) - Method in class baseCode.dataStructure.tree.TreeNode
setFixed(boolean) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
setFlagMatrix(StringMatrix2DNamed) - Method in class baseCode.dataFilter.RowAbsentFilter
setGraph(Graph) - Method in class baseCode.dataStructure.graph.AbstractGraphNode
  Set the graph this belongs to.
setGraph(Graph) - Method in interface baseCode.dataStructure.graph.GraphNode
setHelpButtonText(String) - Method in class baseCode.gui.AppDialog
setHighCut(double) - Method in class baseCode.dataFilter.AbstractLevelFilter
  Set the high threshold for removal.
setHighCut(double, boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter
setItem(Object) - Method in class baseCode.dataStructure.graph.AbstractGraphNode
setItem(Object) - Method in interface baseCode.dataStructure.graph.GraphNode
  Set the contents of the node.
setKeepMarginal(boolean) - Method in class baseCode.dataFilter.RowAbsentFilter
setLabels(double, double) - Method in class baseCode.gui.JGradientBar
setLabelsVisible(boolean) - Method in class baseCode.gui.JMatrixDisplay
  If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
setLeft(BinaryTreeNode) - Method in class baseCode.dataStructure.tree.BinaryTreeNode
setLowCut(double) - Method in class baseCode.dataFilter.AbstractLevelFilter
  Set the low threshold for removal.
setLowCut(double, boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter
setMatrix(ColorMatrix) - Method in class baseCode.gui.JMatrixDisplay
setMaxFractionRemoved(double) - Method in class baseCode.dataFilter.RowMissingFilter
  Set the maximum fraction of rows which will be removed from the data set.
setMaxIter(int) - Method in class baseCode.algorithm.learning.unsupervised.RankProp
  Maximum iterations before stopping.
setMethod(int) - Method in class baseCode.dataFilter.RowLevelFilter
  Choose the method that will be used for filtering.
setMinPresentCount(int) - Method in class baseCode.dataFilter.RowAbsentFilter
setMinPresentCount(int) - Method in class baseCode.dataFilter.RowMissingFilter
  Set the minimum number of values that must be present in each row.
setMinPresentFraction(double) - Method in class baseCode.dataFilter.RowAbsentFilter
setMinPresentFraction(double) - Method in class baseCode.dataFilter.RowMissingFilter
setName(String) - Method in class baseCode.dataStructure.OntologyEntry
setNextSibling(TreeNode) - Method in class baseCode.dataStructure.tree.TreeNode
setQuick(int, int, double) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
setQuick(int, double) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
setQuick(int, int, double) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
setQuick(int, int, Object) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
setRemoveAllNegative(boolean) - Method in class baseCode.dataFilter.RowLevelFilter
  Set the filter to remove all rows that have only negative values.
setRight(BinaryTreeNode) - Method in class baseCode.dataStructure.tree.BinaryTreeNode
setRoot(BinaryTreeNode) - Method in class baseCode.dataStructure.tree.BinaryTree
setRow(int, double[]) - Method in class baseCode.gui.ColorMatrix
  Changes values in a row, clipping if there are more values than columns.
setRowHeight(int) - Method in class baseCode.gui.JMatrixDisplay
setRowKeys(int[]) - Method in class baseCode.gui.ColorMatrix
setRowKeys(int[]) - Method in class baseCode.gui.JMatrixDisplay
setRowNames(List) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
setRowNames(List) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
setSortingStatus(int, int) - Method in class baseCode.gui.table.TableSorter
setStandardizedEnabled(boolean) - Method in class baseCode.gui.JMatrixDisplay
setStatus(String) - Method in class baseCode.gui.StatusJlabel
setStatus(String) - Method in class baseCode.util.StatusDebugLogger
setStatus(String) - Method in class baseCode.util.StatusStderr
setStatus(String) - Method in interface baseCode.util.StatusViewer
  Print the status to the location appropriate for this application.
setTableHeader(JTableHeader) - Method in class baseCode.gui.table.TableSorter
setTableModel(TableModel) - Method in class baseCode.gui.table.TableSorter
setText(String) - Method in class baseCode.gui.JLinkLabel
setText(String, String) - Method in class baseCode.gui.JLinkLabel
setTopoSortOrder(int) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
setTransform(boolean) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
setURL(String) - Method in class baseCode.gui.JLinkLabel
setUseAsFraction(boolean) - Method in class 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 baseCode.dataFilter.AbstractLevelFilter
setUseLowCutAsFraction(boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter
setValue(Object, Object) - Method in class baseCode.dataStructure.graph.AbstractGraphNode
setValue(Object, Object) - Method in interface baseCode.dataStructure.graph.GraphNode
  Set the key and value associated with this node.
setValueAt(Object, int, int) - Method in class baseCode.gui.table.TableSorter
showDialog() - Method in class baseCode.gui.AppDialog
showError(String) - Method in class baseCode.gui.Wizard
  Print an error message to the status bar.
showError(String) - Method in class baseCode.gui.WizardStep
  Print an error message to the status bar.
showStatus(String) - Method in class baseCode.gui.Wizard
  Print a message to the status bar.
showStatus(String) - Method in class baseCode.gui.WizardStep
  Print a message to the status bar.
showWizard() - Method in class baseCode.gui.Wizard
similarity() - Method in interface baseCode.algorithm.learning.unsupervised.cluster.Similarity
size() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
size() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
size() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
sizeWithoutMissingValues(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Return the size of the list, ignoring missing values.
skew(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the skew of a data sequence, which is `moment(data,3,mean) / standardDeviation3`.
sortGeneSets() - Method in class baseCode.bio.geneset.GeneAnnotations
  Sort the gene sets, filling out the sortedGeneSets.
sortGeneSetsBySize() - Method in class baseCode.bio.geneset.GeneAnnotations
sparse(double[][]) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory
sparse(int, int) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory
spearmanRankCorrelation(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.Distance
  Spearman Rank Correlation.
standardize() - Method in class baseCode.gui.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, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
  Modifies a data sequence to be standardized.
standardize(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Standardize.
stringPixelWidth(String, Font, Component) - Static method in class baseCode.graphics.text.Util
sum(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sum of a data sequence.
sumOfInversions(DoubleArrayList, int, int) - Static method in class 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 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 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 baseCode.math.DescriptiveWithMissing
  Returns `Sum( (data[i]-c)k )` for all `i = from ..`
sumOfPowers(DoubleArrayList, int) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sum of powers of a data sequence, which is `Sum ( data[i]k )`.
sumOfSquaredDeviations(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Compute the sum of the squared deviations from the mean of a data sequence.
sumOfSquares(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the sum of squares of a data sequence.
sumOfSquares(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
  Calculates the sum of squares for each row of a matrix
sums(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
  Calculate the sums of a matrix's rows.

## T

TINY - Static variable in class baseCode.math.Constants
TXT_EXTENSION - Static variable in class baseCode.util.FileTools
TableSorter - class baseCode.gui.table.TableSorter.
  TableSorter is a decorator for TableModels; adding sorting functionality to a supplied TableModel.
TableSorter() - Constructor for class baseCode.gui.table.TableSorter
TableSorter(TableModel) - Constructor for class baseCode.gui.table.TableSorter
TableSorter(TableModel, JTableHeader) - Constructor for class baseCode.gui.table.TableSorter
TableSorter(TableModel, JMatrixDisplay) - Constructor for class baseCode.gui.table.TableSorter
Tree - class baseCode.dataStructure.tree.Tree.
Tree() - Constructor for class baseCode.dataStructure.tree.Tree
TreeNode - class baseCode.dataStructure.tree.TreeNode.
TreeNode(Object) - Constructor for class baseCode.dataStructure.tree.TreeNode
TreePanel - class baseCode.gui.TreePanel.
  Copyright (c) Columbia University
TreePanel(JTree) - Constructor for class baseCode.gui.TreePanel
tableModel - Variable in class baseCode.gui.table.TableSorter
testDir(String) - Static method in class baseCode.gui.GuiUtil
testDir(String) - Static method in class baseCode.util.FileTools
testFile(String) - Static method in class baseCode.gui.GuiUtil
testFile(String) - Static method in class baseCode.util.FileTools
testFile(File) - Static method in class baseCode.util.FileTools
toArray() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
  WARNING unlike the superclass, this returns the actual underlying array, not a copy.
toArray() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
toCollection() - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
toCollection() - Method in class baseCode.common.Distanceable
  Return a collections view of the object.
toString() - Method in class baseCode.dataStructure.Link
toString() - Method in class baseCode.dataStructure.OntologyEntry
toString() - Method in class baseCode.dataStructure.Point
toString() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
toString() - Method in class baseCode.dataStructure.graph.DirectedGraph
  Shows the tree as a tabbed list.
toString() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
toString() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
toString() - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
toString() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
toString() - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
toString() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
toString() - Method in class baseCode.gui.JLinkLabel
toTableModel() - Method in class baseCode.bio.geneset.GeneAnnotations
top() - Method in class baseCode.dataStructure.Stack
  Deprecated. Get the most recently added item, without removing it.
topoSort() - Method in class baseCode.dataStructure.graph.DirectedGraph
  Fills in the topoSortOrder for each node.
topoSortOrder - Variable in class baseCode.dataStructure.graph.DirectedGraphNode
treeView() - Method in class baseCode.dataStructure.graph.DirectedGraph
  Generate a JTree corresponding to this graph.
trimToSize() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
trimmedMean(DoubleArrayList, double, int, int) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the trimmed mean of a sorted data sequence.
twoSample(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.KSTest

## U

UndirectedGraphNode - class baseCode.dataStructure.graph.UndirectedGraphNode.
  Copyright (c) Columbia University
UndirectedGraphNode(Object, Object, AbstractGraph) - Constructor for class baseCode.dataStructure.graph.UndirectedGraphNode
UndirectedGraphNode(Object) - Constructor for class baseCode.dataStructure.graph.UndirectedGraphNode
UniformDensityComputer - class baseCode.math.distribution.UniformDensityComputer.
UniformDensityComputer() - Constructor for class baseCode.math.distribution.UniformDensityComputer
  Create a UniformDensityComputer where the density is defined over the unit inteval [0,1].
UniformDensityComputer(double, double) - Constructor for class baseCode.math.distribution.UniformDensityComputer
  Create a UniformDensityComputer where the density is defined over the interval given
UniformProbabilityComputer - class baseCode.math.distribution.UniformProbabilityComputer.
  Generate probabilities from the uniform distribution.
UniformProbabilityComputer() - Constructor for class baseCode.math.distribution.UniformProbabilityComputer
  Create a UniformProbabilityComputer where the density is defined over the unit inteval [0,1].
UniformProbabilityComputer(double, double) - Constructor for class baseCode.math.distribution.UniformProbabilityComputer
  Create a UniformProbabilityComputer where the density is defined over the interval given
Util - class baseCode.graphics.text.Util.
Util() - Constructor for class baseCode.graphics.text.Util
unFisherTransform(double) - Static method in class baseCode.math.CorrelationStats
  Reverse the Fisher z-transform of correlations.
unMark() - Method in class baseCode.common.Visitable
unMark() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
unmarkAll() - Method in class baseCode.dataStructure.graph.AbstractGraph
  Reset the 'visited' marks of the graph to false.
unmarkAll() - Method in interface baseCode.dataStructure.graph.Graph
useHighAsFraction - Variable in class baseCode.dataFilter.AbstractLevelFilter
useLowAsFraction - Variable in class baseCode.dataFilter.AbstractLevelFilter

## V

Visitable - class baseCode.common.Visitable.
Visitable() - Constructor for class baseCode.common.Visitable
validate() - Method in class baseCode.gui.table.JBarGraphCellRenderer
validate() - Method in class baseCode.gui.table.JMatrixCellRenderer
validate() - Method in class baseCode.gui.table.JVerticalHeaderRenderer
valueChanged(TreeSelectionEvent) - Method in class baseCode.gui.TreePanel
values - Variable in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
variance(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Provided for convenience!
viewColumn(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
viewColumn(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
viewColumn(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
viewRow(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
viewRow(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
viewRow(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
viewRow(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
viewRow(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed
viewSelectionLike(int[]) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
visited - Variable in class baseCode.dataStructure.graph.AbstractGraphNode

## W

Wishart - class baseCode.math.distribution.Wishart.
  Wishart distribution, used to simulate covariance matrices.
Wishart(double, DoubleMatrix2D, RandomEngine) - Constructor for class baseCode.math.distribution.Wishart
Wizard - class baseCode.gui.Wizard.
Wizard(JFrame, int, int) - Constructor for class baseCode.gui.Wizard
WizardStep - class baseCode.gui.WizardStep.
  Title:
WizardStep(Wizard) - Constructor for class baseCode.gui.WizardStep
weightedMean(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
  Returns the weighted mean of a data sequence.
weightedMean(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  General formula for weighted mean of effect sizes.
weightedMean(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
  General formula for weighted mean of effect sizes including quality index scores for each value.
winsorizedMean(DoubleArrayList, double, int, int) - Static method in class baseCode.math.DescriptiveWithMissing
  Not supported.
worst() - Method in class baseCode.algorithm.Ranker
write(IHistogram1D, Writer) - Method in class baseCode.io.writer.HistogramWriter
  Print out a IHistogram1D object.
write(IHistogram1D, OutputStream) - Method in class baseCode.io.writer.HistogramWriter
  Print to a stream.
writeTestResult(String, String) - Static method in class baseCode.util.RegressionTesting

## X

X - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
  Filter probes that have the "_x_at" tag.
X - Static variable in class baseCode.dataFilter.RowAffyNameFilter
  Filter probes that have the "_x_at" tag.
XMLFileFilter - class baseCode.gui.file.XMLFileFilter.
XMLFileFilter() - Constructor for class baseCode.gui.file.XMLFileFilter
XML_EXTENSIONS - Static variable in class baseCode.util.FileTools

## Z

zDotProduct(DoubleMatrix1D) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
zSum() - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D

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