AbstractFilter M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Base implementation of the filter interface.
AbstractFilter() AbstractFilter
AbstractGraph R extends GraphNode <K ,V >,K ,V > - Class in ubic.basecode.dataStructure.graph
AbstractGraph() AbstractGraph
AbstractGraph(Set<R>) AbstractGraph
Create a new graph from a set of nodes.
AbstractGraphNode K ,V > - Class in ubic.basecode.dataStructure.graph
AbstractGraphNode(K) AbstractGraphNode
Create a new node when given only a key.
AbstractGraphNode(K, V) AbstractGraphNode
AbstractLevelFilter R ,C > - Class in ubic.basecode.datafilter
Abstract class representing a filter that removes things from DoubleMatrixNamed matrices based on the values
themselves.
AbstractLevelFilter() AbstractLevelFilter
AbstractMatrix R ,C ,V > - Class in ubic.basecode.dataStructure.matrix
AbstractMatrix() AbstractMatrix
AbstractMatrix3D R ,C ,S ,V > - Class in ubic.basecode.dataStructure.matrix
TODO Document Me
AbstractMatrix3D() AbstractMatrix3D
AbstractMatrixReader M extends Matrix2D <String ,String ,V >,V > - Class in ubic.basecode.io.reader
Abstract class representing an object that can read in a
Matrix2Dfrom a file.
AbstractMatrixReader() AbstractMatrixReader
AbstractOntologyMemoryBackedService ubic.basecode.ontology.providers
This class has some stuff that's specific to in-memory ontologies.
AbstractOntologyMemoryBackedService() AbstractOntologyMemoryBackedService
AbstractOntologyResource ubic.basecode.ontology.model
AbstractOntologyResource() AbstractOntologyResource
AbstractOntologyService ubic.basecode.ontology.providers
AbstractOntologyService() AbstractOntologyService
AbstractRClient ubic.basecode.util.r
Base class for RClients
AbstractRClient() AbstractRClient
accept(HSSFSheet, int) SpreadSheetFilter
add(ObjectMatrix<String, String, Object>) DesignMatrix
Append additional factors/covariates to this
addChild(K) DirectedGraphNode
addChildTo(K, K) DirectedGraph
Add a child to a particular node identified by key; if the node is not in the graph, an exception is thrown.
addChildTo(K, K, V) DirectedGraph
Add a child to a particualar node identified by key.
addColumnName(C) AbstractMatrix
Add a column name when we don't care what the index will be.
addColumnName(C, int) AbstractMatrix3D
addColumnName(C) Matrix2D
Add a column name, to the end of the current column names.
addColumnName(C, int) Matrix3D
Add a column name associated with an index.
addDataExtension(String) FileTools
addImageExtension(String) FileTools
addInteraction() DesignMatrix
Add interaction term; only works if there exactly two factors so this can figure out which interaction to add.
addInteraction(String...) DesignMatrix
This will not add the interaction unless all of the terms are already part of the design, and interactions that
obviously can't be estimated will be dropped if possible, but otherwise this is fairly brain dead.
addNode(K, V) AbstractGraph
addNode(R) AbstractGraph
addNode(DirectedGraphNode<K, V>) DirectedGraph
addNode(K, V) DirectedGraph
Will not be attached to any other node.
addNode(K, V) Graph
addParamInstance(Map<String, String>) ParamKeeper
addParent(K) DirectedGraphNode
addParentTo(K, K) DirectedGraph
addParentTo(K, K, V) DirectedGraph
addPut(K, Double) DoubleAddingMap
adds the current value to the value of this key.
addPutAll(Map<? extends K, ? extends Double>) DoubleAddingMap
addRow(R, DoubleMatrix1D) SparseRaggedDoubleMatrix
addRow(R, IntArrayList, DoubleArrayList) SparseRaggedDoubleMatrix
addRowName(R) AbstractMatrix
Add a row name when we don't care what the index will be.
addRowName(R, int) AbstractMatrix3D
addRowName(R, int) Matrix3D
Add a row name associated with a row index.
addSliceName(S, int) AbstractMatrix3D
addSliceName(S, int) Matrix3D
Add a slice name
addStatement(CharacteristicStatement) ChainedStatementObject
AFFX AffymetrixProbeNameFilter
Filter probes that have the AFFX prefix.
AffymetrixProbeNameFilter M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Remove probes that have names meeting certain rules indicating they may have low reliability.
AffymetrixProbeNameFilter() AffymetrixProbeNameFilter
Filter probes with all criteria switched on.
AffymetrixProbeNameFilter(int[]) AffymetrixProbeNameFilter
AnnotationProperty ubic.basecode.ontology.model
AnnotationPropertyImpl ubic.basecode.ontology.model
Note that this is a concrete instance of the annotation.
AnnotationPropertyImpl(AnnotationProperty, RDFNode) AnnotationPropertyImpl
AnnotatorClient ubic.basecode.ontology.ncbo
Use the NCBO annotator to find ontology terms matching strings.
AnnotatorClient() AnnotatorClient
AnnotatorResponse ubic.basecode.ontology.ncbo
This represents an Ontology terms returned by the AnnotatorClient
AnnotatorResponse(String, String, String, Integer, Integer, String, String) AnnotatorResponse
anova() LeastSquaresFit
Compute ANOVA based on the model fit (Type I SSQ, sequential)
The idea is to add up the sums of squares (and dof) for all parameters associated with a particular factor.
AnovaEffect ubic.basecode.util.r.type
Represents one row of an ANOVA table
AnovaEffect(String, Double, Double, Double, Double, boolean) AnovaEffect
AnovaResult ubic.basecode.util.r.type
AnovaResult() AnovaResult
append(String, String, String) StringUtil
applyToIndicesMatchingCriteria(DoubleMatrix1D, DoubleFunction<Boolean>, DoubleFunction<Double>) MatrixUtil
aroc(int, List<Double>) ROC
Calculate area under ROC, up to a given number of False positives.
asArray() CompressedSparseDoubleMatrix
asArray() DenseDoubleMatrix
asArray() DoubleMatrix
asArray() FastRowAccessDoubleMatrix
asArray() SparseDoubleMatrix
asArray() SparseRaggedDoubleMatrix
asBools(byte[]) BitUtil
asDoubles() AbstractMatrix
asDoubles() Matrix2D
Attempt to coerce the entries into doubles.
asId(Object) SQLUtils
asProperty(OntProperty) PropertyFactory
Convert a Jena property.
asRestriction(Restriction) RestrictionFactory
assign(V) AbstractMatrix
assign(V) Matrix2D
Set all values in the matrix to the given value.
assign(double[]) RCDoubleMatrix1D
assign(DoubleFunction) RCDoubleMatrix1D
WARNING this only assigns to the non-empty values, for performance reasons.
assign(String, double[]) JRIClient
assign(String, int[]) JRIClient
assign(String, String) JRIClient
assign(String, String[]) JRIClient
assign(String, double[]) RClient
assign(String, int[]) RClient
assign(String, String) RClient
assign(String, String[]) RClient
assign(String, double[]) RServeClient
assign(String, int[]) RServeClient
assign(String, String) RServeClient
assign(String, String[]) RServeClient
assignFactor(List<String>) AbstractRClient
assignFactor(String, List<String>) AbstractRClient
assignFactor(List<String>) RClient
assignFactor(String, List<String>) RClient
assignMatrix(double[][]) AbstractRClient
assignMatrix(DoubleMatrix<?, ?>) AbstractRClient
assignMatrix(DoubleMatrix<?, ?>, Transformer) AbstractRClient
assignMatrix(double[][]) RClient
Assign a 2-d matrix.
assignMatrix(DoubleMatrix<?, ?>) RClient
Assign a 2-d matrix.
assignMatrix(DoubleMatrix<?, ?>, Transformer) RClient
Assign a 2-d matrix.
assignStringList(List<?>) AbstractRClient
assignStringList(List<?>) RClient
Define a variable corresponding to a character array in the R context, given a List of Strings.
asString(RDFNode) OntologyUtil
Use to pretty-print a RDFNode
autoCorrelation(DoubleArrayList, int, double, double) DescriptiveWithMissing
Not supported.
averagePrecision(List<Double>) PrecisionRecall
"Average Precision is the average of the precision value obtained for the set of top $k$ documents existing after
each relevant document is retrieved, and this value is then averaged over information needs".
cancelInitializationThread() AbstractOntologyService
Cancel the initialization thread.
cancelInitializationThread() OntologyService
cardinality() CompressedSparseDoubleMatrix
cardinality() SparseDoubleMatrix
cdf(DoubleArrayList) Stats
Convert an array into a cumulative density function (CDF).
CellLineOntologyService ubic.basecode.ontology.providers
See http://www.obofoundry.org/cgi-bin/detail.cgi?
CellLineOntologyService() CellLineOntologyService
CellTypeOntologyService ubic.basecode.ontology.providers
See http://www.obofoundry.org/cgi-bin/detail.cgi?
CellTypeOntologyService() CellTypeOntologyService
ChainedStatement ubic.basecode.ontology.model
ChainedStatementObject ubic.basecode.ontology.model
Acts as an 'anonymous' node in a statement
changeExtension(String, String) FileTools
CharacteristicStatement ubic.basecode.ontology.model
charArrayToBytes(char[]) ByteArrayConverter
ChebiOntologyService ubic.basecode.ontology.providers
Loads the CHEBI Ontology at startup in its own thread.
ChebiOntologyService() ChebiOntologyService
checkColRange(int, int) AbstractMatrix
checkForFile(FTPClient, String) NetUtils
determine if a file exists on the remote server.
checkPathIsReadableFile(String) FileTools
checkRowRange(int, int) AbstractMatrix
children DirectedGraphNode
chol2inv() QRDecomposition
Used for computing standard errors of parameter estimates for least squares; copies functionality of R chol2inv.
chompExtension(String) FileTools
chooserandom(double[], int) RandomChooser
Random numbers from sourcedata, without replacement.
chooserandom(int, int) RandomChooser
choose n random integers from 0 (inclusive) to max (exclusive) without repeating
chooserandom(int[], int) RandomChooser
choose k random integers from 0 to max (exclusive) without repeating
chooserandom(List<? extends Object>, int) RandomChooser
chooseRandomSubset(int, Collection<? extends T>) RandomChooser
Select a random subset of size n from collection superSet
chooseRandomSubset(int, List<? extends T>) RandomChooser
Select a random subset of size n from List superSet
chooserandomWrep(int, int) RandomChooser
Same as chooserandom, but with replacement -- that is, repeats are allowed.
ClassStatement ubic.basecode.ontology.model
cleanForFileName(String) FileTools
Avoid getting file names with spaces, slashes, quotes, # etc; replace them with "_".
clear(byte[], int) BitUtil
Clear the bit at the specified position
clear() CountingMap
clear() StatusDebugLogger
clear() StatusStderr
clear() StatusViewer
Clear the status display.
clone() DirectedGraphNode
Makes a copy of this node.
clone() ColorMatrix
closeEnough(double[], double[], double) RegressionTesting
closeEnough(DoubleArrayList, DoubleArrayList, double) RegressionTesting
Test whether two DoubleArrayLists are 'close enough' to call equal.
closeEnough(DoubleMatrix<?, ?>, DoubleMatrix<?, ?>, double) RegressionTesting
Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.
closeEnough(DoubleMatrix1D, DoubleMatrix1D, double) RegressionTesting
closeEnough(DoubleMatrix2D, DoubleMatrix2D, double) RegressionTesting
closeEnough(Object[], Object[]) RegressionTesting
Test whether two object arrays are the same.
closeIndex() AbstractOntologyService
Do not do this except before re-indexing.
colaxpy_j(int, double, double[][], int, int, int) Blas
This method multiplies a constant times a portion of a column
of a matrix and adds the product to the corresponding portion
of another column of the matrix --- a portion of col2 is
replaced by the corresponding portion of a*col1 + col2.
coldot_j(int, double[][], int, int, int) Blas
This method calculates the dot product of portions of two
columns of a matrix.
colisamax_j(int, double[][], int, int, int) Blas
This method finds the index of the element of a portion of a
column of a matrix that has the maximum absolute value.
colMap AbstractMatrix3D
colNameMap MatrixWriter
colNames AbstractMatrix3D
colnrm2_j(int, double[][], int, int) Blas
This method calculates the Euclidean norm of a portion of a
column of a matrix.
ColorMap ubic.basecode.graphics
ColorMap() ColorMap
ColorMap(Color[]) ColorMap
ColorMap(int) ColorMap
ColorMap(int, Color[]) ColorMap
Pre-condition: suggestedNumberOfColors > colorMap.length
colorMap ColorMatrix
ColorMatrix A ,B > - Class in ubic.basecode.graphics
Creates a color matrix from a matrix of doubles
ColorMatrix(DoubleMatrix<A, B>) ColorMatrix
ColorMatrix(DoubleMatrix<A, B>, Color[], Color) ColorMatrix
colors ColorMatrix
colrot_j(int, double[][], int, int, double, double) Blas
This method "applies a plane rotation."
colscal_j(int, double, double[][], int, int) Blas
This method scales a portion of a column of a matrix by a constant.
colSums(DoubleMatrix<R, C>) MatrixStats
NaN values are omitted from calculations.
colswap_j(int, double[][], int, int) Blas
This method interchanges two columns of a matrix.
columns() AbstractMatrix3D
columns() CompressedBitMatrix
columns() CompressedSparseDoubleMatrix
columns() DenseDouble3dMatrix
columns() DenseDoubleMatrix
columns() DenseObject3DMatrix
columns() FastRowAccessDoubleMatrix
columns() IntegerMatrix
columns() Matrix2D
Get the number of columns the matrix has.
columns() Matrix3D
Get the number of columns the matrix has.
columns() ObjectMatrixImpl
columns() SparseDoubleMatrix
columns() SparseRaggedDoubleMatrix
Returns the size of the widest row.
columns() StringMatrix
colvaxpy_j(int, double, double[][], double[], int, int) Blas
This method multiplies a constant times a portion of a column
of a matrix x[ ][ ] and adds the product to the corresponding portion
of a vector y[ ] --- a portion of y[ ] is replaced by the corresponding
portion of ax[ ][j] + y[ ].
colvdot_j(int, double[][], double[], int, int) Blas
This method calculates the dot product of a portion of a
column of a matrix and the corresponding portion of a
vector.
colvraxpy_j(int, double, double[], double[][], int, int) Blas
This method multiplies a constant times a portion of a vector y[ ]
and adds the product to the corresponding portion
of a column of a matrix x[ ][ ] --- a portion of column j of x[ ][ ]
is replaced by the corresponding
portion of ay[ ] + x[ ][j].
commonPrefix(Collection<String>) StringUtil
Given a set of strings, identify any prefix they have in common.
commonSuffix(Collection<String>) StringUtil
Given a set of strings, identify any suffix they have in common.
compare(double, int, double, int) CorrelationStats
Statistical comparison of two Pearson correlations.
compareTo(DirectedGraphNode<K, V>) DirectedGraphNode
Uses the topological sort order.
compareTo(UndirectedGraphNode<K, V>) UndirectedGraphNode
compareTo(Link) Link
compareTo(OntologyResource) AbstractOntologyResource
compareTo(AnnotatorResponse) AnnotatorResponse
CompressedBitMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
Named compressed sparse bit matrix.
CompressedBitMatrix(int, int, int) CompressedBitMatrix
Constructs a matrix with specified rows, columns, and total bits per cell
Implementation note: this is created by maintaining one or more Double matrices; the Doubles are used as bit
fields.
compressedsparse(int, int) DoubleMatrixFactory
CompressedSparseDoubleMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
Supports sparse matrices (where sparse means most values are zero, not that they are missing).
CompressedSparseDoubleMatrix(double[][]) CompressedSparseDoubleMatrix
CompressedSparseDoubleMatrix(int, int) CompressedSparseDoubleMatrix
computeSize(boolean, boolean) MatrixDisplay
compute the size of the matrix in pixels.
cond() SingularValueDecomposition
Configuration ubic.basecode.util
Configuration of ontology services and other things.
Configuration() Configuration
ConfigUtils ubic.basecode.util
Convenience methods for loading configurations
ConfigUtils() ConfigUtils
conjunction(BooleanArrayList, BooleanArrayList) MatrixUtil
Compute the conjuction (logical 'and') of two boolean vectors
connect(int, String, String, String) NetUtils
Convenient method to get a FTP connection.
connect() RServeClient
Constants ubic.basecode.math
Used in some ports of statistical code.
Constants() Constants
containsColumnName(C) AbstractMatrix
containsColumnName(Object) AbstractMatrix3D
containsColumnName(C) Matrix2D
containsColumnName(C) Matrix3D
Check if the matrix contains a column name
containsKey(Object) CountingMap
containsKey(K) AbstractGraph
containsKey(K) DirectedGraph
containsKey(K) Graph
containsNearlyZeros(DoubleMatrix1D) MatrixUtil
containsRowName(R) AbstractMatrix
containsRowName(Object) AbstractMatrix3D
containsRowName(R) Matrix2D
containsRowName(R) Matrix3D
Check if the matrix contains a row name
containsSame(Collection<? extends Object>, Collection<? extends Object>) RegressionTesting
Test whether two collections contain the same items.
containsSame(double[], double[]) RegressionTesting
Test whether two double arrays contain the same items in any order (tolerance is ZERO)
containsSame(Object[], Object[]) RegressionTesting
Test whether two object arrays contain the same items in any order.
containsSliceName(Object) AbstractMatrix3D
containsSliceName(S) Matrix3D
Check if the matrix contains a slice name
containsValidCharacter(String) StringUtil
Checks a string to find "strange" character, used by phenocarta to check evidence description
containsValue(Object) CountingMap
convertDateToString(Date) DateUtil
This method generates a string representation of a date based on the System Property 'dateFormat' in the format
you specify on input
convertStringToDate(String, String) DateUtil
This method generates a string representation of a date/time in the format you specify on input
convertToLog2(DoubleMatrix<R, C>, double) MatrixStats
Convert a log_b-transformed data set to log 2.
convertToLog2Cpm(DoubleMatrix<R, C>, DoubleMatrix1D) MatrixStats
Convert a count matrix to log2 counts per million.
convertType(DatatypeProperty) PropertyFactory
copy() CompressedSparseDoubleMatrix
copy() DenseDoubleMatrix
copy() DoubleMatrix
Create a deep copy of this
copy() FastRowAccessDoubleMatrix
copy() SparseDoubleMatrix
copy() SparseRaggedDoubleMatrix
copy(InputStream, OutputStream) FileTools
On completion streams are closed.
copyPlainOrCompressedFile(String, String) FileTools
correl(double[], double[]) CorrelationStats
Compute the Pearson correlation, missing values are permitted.
correlAsByte(double) CorrelationStats
correlation(double[], double[], double[], double[], boolean[], boolean[]) DescriptiveWithMissing
Highly optimized version of the correlation computation, where as much information is precomputed as possible.
correlation(DoubleArrayList, double, DoubleArrayList, double) DescriptiveWithMissing
Returns the correlation of two data sequences.
correlation(DoubleArrayList, DoubleArrayList) DescriptiveWithMissing
Calculate the pearson correlation of two arrays.
CorrelationEffectMetaAnalysis ubic.basecode.math.metaanalysis
Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of
Research Synthesis".
CorrelationEffectMetaAnalysis() CorrelationEffectMetaAnalysis
CorrelationEffectMetaAnalysis(boolean, boolean) CorrelationEffectMetaAnalysis
correlationForPvalue(double, int) CorrelationStats
Find the approximate Pearson correlation required to meet a particular pvalue.
correlationMatrix(DoubleMatrix<R, C>) MatrixStats
Compute the correlation matrix of the rows of a matrix.
correlationMatrix(DoubleMatrix<R, C>, double) MatrixStats
correlationOfStandardized(double[], double[]) Distance
Highly optimized implementation of the Pearson correlation.
correlationOfStandardized(DoubleArrayList, DoubleArrayList) Distance
Like correlationofNormedFast, but takes DoubleArrayLists as inputs, handles missing values correctly, and does
more error checking.
CorrelationStats ubic.basecode.math
Statistical evaluation and transformation tools for correlations.
CorrelationStats() CorrelationStats
correlationTstat(double, int) CorrelationStats
Compute the t-statistic associated with a Pearson correlation.
correlFast(double[], double[], double, double, double, double) CorrelationStats
Compute Pearson correlation when there are no missing values.
count(byte[]) BitUtil
count(K) CountingMap
Returns the count associated with the specified key, or zero if the key has never been incremented.
CountingMap K > - Class in ubic.basecode.dataStructure
Convenience Map that has a count as the value for each key.
CountingMap() CountingMap
Constructs a CountingMap backed by a simple HashMap.
CountingMap(Map<K, Integer>) CountingMap
Constructs a CountingMap backed by the specified Map.
cov2cor(DoubleMatrix2D) MatrixStats
Scale a covariance matrix to the corresponding correlation matrix.
covariance(DoubleArrayList, DoubleArrayList) DescriptiveWithMissing
Returns the SAMPLE covariance of two data sequences.
createColorPalette(int, Color[]) ColorMap
Allocates colors across a range.
createDir(String) FileTools
Creates the directory if it does not exist.
createEmptyRow(int) DoubleMatrixReader
createMatrix(List<DoubleArrayList>, List<String>, List<String>) DoubleMatrixReader
createRowKeys() ColorMatrix
To be able to sort the rows by an arbitrary key.
CreateSpreadSheet ubic.basecode.io.excel
TODO Document Me
CreateSpreadSheet(String, SpreadSheetSchema) CreateSpreadSheet
csvSplit(String) StringUtil
cumulate(DoubleArrayList) Stats
Convert an array into a cumulative array.
cumulateRight(DoubleArrayList) Stats
Convert an array into a cumulative array.
CV RowLevelFilter
Use the coefficient of variation as the criterion
cv(DoubleArrayList) Stats
Compute the coefficient of variation of an array (standard deviation / mean).
cvs2tsv(String) StringUtil
Made by Nicolas
DARK_RED ColorMap
DATA_EXTENSIONS FileTools
dataFrame(ObjectMatrix<String, String, Object>) AbstractRClient
dataFrame(ObjectMatrix<String, String, Object>) RClient
Convert an object matrix into an R data frame.
dataFrameEval(String) AbstractRClient
dataFrameEval(String) RClient
Evaluate a command that returns a dataFrame
DataStatement ubic.basecode.ontology.model
DatatypeProperty ubic.basecode.ontology.model
DatatypePropertyImpl ubic.basecode.ontology.model
DatatypePropertyImpl(DatatypeProperty) DatatypePropertyImpl
DateUtil ubic.basecode.util
Date Utility Class
DateUtil() DateUtil
daxpy_j(int, double, double[], int, double[], int) Blas
This method multiplies a constant times a vector and adds the product
to another vector --- dy[ ] = da*dx[ ] + dy[ ].
dbinom(double, double, double) SpecFunc
See dbinom_raw.
dcopy_j(int, double[], int, double[], int) Blas
This method copies the vector dx[ ] to the vector dy[ ].
dcopyp_j(int, double[], double[], int) Blas
This method copies a portion of vector x[ ] to the corresponding
portion of vector y[ ].
ddot_j(int, double[], int, double[], int) Blas
This method calculates the dot product of two vectors.
DEFAULT_DATA_EXTENSION FileTools
DEFAULT_IMAGE_EXTENSION FileTools
DEFAULT_SEP MatrixWriter
DEFAULT_TOP_LEFT MatrixWriter
DEFAULT_XML_EXTENSION FileTools
deleteDir(File) FileTools
Deletes the directory and subdirectories if empty.
deleteFiles(Collection<File>) FileTools
Deletes the specified
deleteLeaf(K) DirectedGraph
deleteOldCache(String) OntologyLoader
dense(double[][]) DoubleMatrixFactory
dense(DoubleMatrix<String, String>) DoubleMatrixFactory
Creates a matrix in which the underlying data is a copy; the row and column labels are not copied.
dense(int, int) DoubleMatrixFactory
DenseDouble3dMatrix R ,C ,S > - Class in ubic.basecode.dataStructure.matrix
DenseDouble3dMatrix(double[][][]) DenseDouble3dMatrix
DenseDouble3dMatrix(double[][][], List<S>, List<R>, List<C>) DenseDouble3dMatrix
DenseDouble3dMatrix(int, int, int) DenseDouble3dMatrix
DenseDouble3dMatrix(List<S>, List<R>, List<C>) DenseDouble3dMatrix
DenseDoubleMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
A dense matrix of doubles that knows about row and column names.
DenseDoubleMatrix(double[][]) DenseDoubleMatrix
DenseDoubleMatrix(int, int) DenseDoubleMatrix
DenseDoubleMatrix1D ubic.basecode.dataStructure.matrix
Use this class when fast iteration over the matrix is of primary interest.
DenseDoubleMatrix1D(double[]) DenseDoubleMatrix1D
DenseDoubleMatrix1D(int) DenseDoubleMatrix1D
DenseDoubleMatrix1D(int, double[], int, int) DenseDoubleMatrix1D
DenseObject3DMatrix R ,C ,S > - Class in ubic.basecode.dataStructure.matrix
DenseObject3DMatrix(int, int, int) DenseObject3DMatrix
DenseObject3DMatrix(List<S>, List<R>, List<C>) DenseObject3DMatrix
DenseObject3DMatrix(Object[][][]) DenseObject3DMatrix
DenseObject3DMatrix(Object[][][], List<S>, List<R>, List<C>) DenseObject3DMatrix
density(double) DensityGenerator
density(double) UniformDensityComputer
DensityGenerator ubic.basecode.math.distribution
An interface that describes a class that can produce values from a particular probability density.
DescriptiveWithMissing ubic.basecode.math
Mathematical functions for statistics that allow missing values without scotching the calculations.
DesignMatrix ubic.basecode.math.linearmodels
Represents the A matrix in regression problems posed as Ax=b.
DesignMatrix(Object[], int, String) DesignMatrix
DesignMatrix(ObjectMatrix<String, String, ? extends Object>) DesignMatrix
DesignMatrix(ObjectMatrix<String, String, ?>, boolean) DesignMatrix
DesignMatrix(StringMatrix<String, String>) DesignMatrix
DesignMatrix(ObjectMatrix<String, String, Object>, boolean, boolean) DesignMatrix
dhyper(int, int, int, int) SpecFunc
Ported from R (Catherine Loader)
DESCRIPTION
Given a sequence of r successes and b failures, we sample n (\le b+r) items without replacement.
diagnose() QRDecomposition
diagonal(DoubleMatrix2D) MatrixUtil
Extract the diagonal from a matrix.
DirectedGraph K ,V > - Class in ubic.basecode.dataStructure.graph
A graph that contains DirectedGraphNodes.
DirectedGraph() DirectedGraph
DirectedGraphNode K ,V > - Class in ubic.basecode.dataStructure.graph
A graph node that has the concept of parents and children.
DirectedGraphNode(K, V, DirectedGraph<K, V>) DirectedGraphNode
Dirichlet ubic.basecode.math.distribution
Dirichlet(DoubleArrayList, RandomEngine) Dirichlet
disconnect() AbstractRClient
disconnect() JRIClient
disconnect() RServeClient
DiseaseOntologyService ubic.basecode.ontology.providers
Holds a copy of the Disease Ontology.
DiseaseOntologyService() DiseaseOntologyService
displayMax ColorMatrix
displayMin ColorMatrix
Min and max values to display, which might not be the actual min and max values in the matrix.
Distance ubic.basecode.math
Alternative distance and similarity metrics for vectors.
Distance() Distance
dnrm2_j(int, double[], int) Blas
This method calculates the Euclidean norm of the vector
stored in dx[ ] with storage increment incx.
dnrm2p_j(int, double[], int) Blas
This method calculates the Euclidean norm of a portion
of a vector x[ ].
dof(DoubleArrayList, IntArrayList) KruskalWallis
DOID_ONTOLOGY AnnotatorClient
DoubleAddingMap K > - Class in ubic.basecode.dataStructure
Similar to ubic.gemma.util.CountingMap.
DoubleAddingMap() DoubleAddingMap
doubleArrayDoubleArrayEval(String, String, double[]) AbstractRClient
doubleArrayDoubleArrayEval(String, String, double[]) RClient
Run a command that has a single double array parameter, and returns a double array.
doubleArrayEval(String) AbstractRClient
doubleArrayEval(String) RClient
Run a command that returns a double array with no arguments.
doubleArrayToBytes(double[]) ByteArrayConverter
doubleArrayToBytes(Double[]) ByteArrayConverter
doubleArrayToBytes(DoubleArrayList) ByteArrayConverter
doubleArrayToString(double[]) StringConverter
Convert a double array to a delimited string.
doubleArrayTwoDoubleArrayEval(String, String, double[], String, double[]) AbstractRClient
doubleArrayTwoDoubleArrayEval(String, String, double[], String, double[]) RClient
Run a command that takes two double array arguments and returns a double array.
DoubleMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
Abstract base class for 2D matrices of double values with named columns and rows.
DoubleMatrix() DoubleMatrix
DoubleMatrix3D R ,C ,S > - Class in ubic.basecode.dataStructure.matrix
TODO Document Me
DoubleMatrix3D() DoubleMatrix3D
DoubleMatrixFactory ubic.basecode.dataStructure.matrix
Use this factory to create matrices of type selected at runtime (String parameterization only)
DoubleMatrixFactory() DoubleMatrixFactory
DoubleMatrixReader ubic.basecode.io.reader
Reader for basecode.dataStructure.matrix.DoubleMatrix.
DoubleMatrixReader() DoubleMatrixReader
doubleMatrixToBytes(double[][]) ByteArrayConverter
DoublePoint ubic.basecode.dataStructure
DoublePoint(double, double) DoublePoint
doubleStandardize(DoubleMatrix<R, C>) MatrixStats
Iteratively standardize the columns and rows of the matrix.
doubleTwoDoubleArrayEval(String, String, double[], String, double[]) AbstractRClient
doubleTwoDoubleArrayEval(String, String, double[], String, double[]) RClient
Run a command that takes two double arrays as arguments and returns a double value.
dqrdc_j(double[][], int, int, double[], int[], int) Dqrsl
This method decomposes an n by p matrix X into a product, QR, of
an orthogonal n by n matrix Q and an upper triangular n by p matrix R.
Dqrsl ubic.basecode.math.linalg
This class contains the LINPACK DQRDC (QR decomposition)
and DQRSL (QR solve) routines.
Dqrsl() Dqrsl
dqrsl_j(double[][], int, int, double[], double[], double[], double[], double[], double[], double[], int) Dqrsl
This method "applies the output of DQRDC to compute coordinate
transformations, projections, and least squares solutions."
drawColumnNames(Graphics, boolean) MatrixDisplay
Draws column names vertically (turned 90 degrees counter-clockwise)
drawMatrix(ColorMatrix<R, C>, Graphics, boolean, boolean) MatrixDisplay
Gets called from #paintComponent and #saveImage.
drawRowNames(Graphics, boolean) MatrixDisplay
Draws row names (horizontally)
draws(int) Dirichlet
drawScaleBar(Graphics, Dimension, double, double) MatrixDisplay
drawVerticalString(Graphics, String, Font, int, int) Util
Draws a string vertically, turned 90 degrees counter-clockwise.
dropColumn(DoubleMatrix2D, int) MatrixUtil
dropColumns(DoubleMatrix2D, Collection<Integer>) MatrixUtil
drotg_j(double[]) Blas
This method constructs a Givens plane rotation.
dscal_j(int, double, double[], int) Blas
This method scales a vector by a constant.
dscalp_j(int, double, double[], int) Blas
This method scales a portion of a vector by a constant.
dswap_j(int, double[], int, double[], int) Blas
This method interchanges two vectors.
dtm DirectedGraph
durbinWatson(DoubleArrayList) DescriptiveWithMissing
Durbin-Watson computation.
F AffymetrixProbeNameFilter
Filter probes that have the "_f_at" (family) tag.
fastrow(double[][]) DoubleMatrixFactory
fastrow(int, int) DoubleMatrixFactory
FastRowAccessDoubleMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
Dense 2D matrix implementation designed for very fast access of entire rows.
FastRowAccessDoubleMatrix(double[][]) FastRowAccessDoubleMatrix
Implementation note: The input matrix is NOT COPIED (due to the way colt DoubleArrayList(double[]) is
implemented).F
FastRowAccessDoubleMatrix(int, int) FastRowAccessDoubleMatrix
filename CreateSpreadSheet
FileTools ubic.basecode.util
FileTools() FileTools
fill(double) Histogram
Fill the histogram with x.
fill(DoubleMatrix1D) Histogram
fill(int, int) Histogram
Add the given number of counts to the given bin.
fillRange(int, int) MathUtil
Create an array filled with the integer values from a to b, inclusive.
filter(M) AffymetrixProbeNameFilter
Filter M extends Matrix2D <R ,C ,V >,R ,C ,V > - Interface in ubic.basecode.datafilter
An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented
criteria.
filter(M) Filter
Filter the data
filter(DoubleMatrix<R, C>) ItemLevelFilter
filter(M) RowAbsentFilter
The data is going to be filtered in accordance to strings in 'flags'.
filter(DoubleMatrix<R, C>) RowLevelFilter
filter(M) RowMissingFilter
filter(M) RowNameFilter
Filter according to row names.
finalize() RServeClient
findCondition(boolean) AnnotatorResponse
findIndividuals(String) AbstractOntologyService
findIndividuals(String) OntologyService
Looks for any OntologyIndividuals that match the given search string.
findLabelForIdentifier(String, String) AnnotatorClient
return the label associated with an conceptid.
findLinkedPublications(Collection<Long>, Map<Long, Collection<Long>>) OmimAnnotatorClient
Giving a set of OMIM id return for each id its list of related publication
findResources(String) AbstractOntologyService
findResources(String) OntologyService
Looks for any OntologyIndividuals or ontologyTerms that match the given search string
findRserveCommand() RServeClient
findTerm(String) AnnotatorClient
findTerm(String) AbstractOntologyService
findTerm(String) OntologyService
Looks for any ontologyTerms that match the given search string.
findUsingAlternativeId(String) AbstractOntologyService
findUsingAlternativeId(String) OntologyService
fisherCombineLogPvalues(DoubleArrayList) MetaAnalysis
Fisher's method for combining p values (Cooper and Hedges 15-8)
Use for p values that have already been log transformed.
fisherCombinePvalues(DoubleArrayList) MetaAnalysis
Fisher's method for combining p values.
fisherTransform(double) CorrelationStats
Compute the Fisher z transform of the Pearson correlation.
fisherTransform(DoubleArrayList) CorrelationStats
Fisher-transform a list of Pearson correlations.
fisherTransformedSamplingVariance(double) CorrelationEffectMetaAnalysis
Equation 18-8 from CH.
fisherTransformedSamplingVariances(DoubleArrayList) CorrelationEffectMetaAnalysis
Run equation CH 18-8 on a list of sample sizes.
fitFDist(DoubleMatrix1D, DoubleMatrix1D) ModeratedTstat
FMAOntologyService ubic.basecode.ontology.providers
Holds a copy of the FMA Ontology on disk.
FMAOntologyService() FMAOntologyService
formatter MatrixWriter
fractionDistinctValuesNonNA(DoubleArrayList, double) Stats
Compute the fraction of values which are distinct.
fromList(DoubleArrayList) MatrixUtil
Makes a copy
ftpDownloadFile(FTPClient, String, File, boolean) NetUtils
ftpDownloadFile(FTPClient, String, String, boolean) NetUtils
ftpFileSize(FTPClient, String) NetUtils
Get the size of a remote file.
G AffymetrixProbeNameFilter
Filter probes that have the "_g_at" (group) tag.
GenericAnovaResult ubic.basecode.math.linearmodels
A generic representation of an R-style ANOVA table, including interactions.
GenericAnovaResult(Collection<AnovaEffect>) GenericAnovaResult
GenericAnovaResult(REXP) GenericAnovaResult
GenericOntologyService ubic.basecode.ontology.providers
A way to create ad hoc ontology services (in memory) for testing
GenericOntologyService(String, String) GenericOntologyService
GenericOntologyService(String, String, boolean) GenericOntologyService
GenericStreamConsumer ubic.basecode.util
See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
GenericStreamConsumer(InputStream) GenericStreamConsumer
geometricMean(DoubleArrayList) DescriptiveWithMissing
Returns the geometric mean of a data sequence.
get(byte[], int) BitUtil
Check to see if the specified bit is set
get(Object) CountingMap
get() DoublePoint
get(K) AbstractGraph
Retrieve a node by key.
get(K) Graph
get(int, int) CompressedBitMatrix
get(int, int, int) CompressedBitMatrix
Checks the bit of the specified cell at the specified index.
get(int, int) CompressedSparseDoubleMatrix
get(int, int, int) DenseDouble3dMatrix
get(int, int) DenseDoubleMatrix
get(int, int, int) DenseObject3DMatrix
get(int, int) DoubleMatrix
get(int, int, int) DoubleMatrix3D
get(int, int) FastRowAccessDoubleMatrix
get(int, int) IntegerMatrix
get(int, int) ObjectMatrix
get(int, int) ObjectMatrixImpl
get(R, C) ObjectMatrixImpl
get(int) RCDoubleMatrix1D
get(int, int) SparseDoubleMatrix
get(int, int) SparseRaggedDoubleMatrix
get(int, int) StringMatrix
get(R, C) StringMatrix
get() Point
getAdjRSquared() LinearModelSummary
getAllBits(int, int) CompressedBitMatrix
Returns all of the bits for a cell
getAllChildNodes() DirectedGraphNode
Get all the children of this node, recursively.
getAllParentNodes() DirectedGraphNode
Get all the parents of this node, recursively.
getAllURIs() AbstractOntologyService
getAllURIs() OntologyService
getAlternative() HTest
getAlternativeIds() OntologyTerm
getAlternativeIds() OntologyTermImpl
getAlternativeIds() OntologyTermSimple
getAnnotations() OntologyTerm
getAnnotations() OntologyTermImpl
getAnnotations() OntologyTermSimple
getAnova() LinearModelSummary
getApproximateQuantile(int) Histogram
Find the bin below which i% of the values are contained.
getArray() Histogram
Returns the bin heights.
getAssign() DesignMatrix
getBaseline(String) DesignMatrix
getBiggestBinSize() Histogram
getBinEdges() Histogram
getBinEdgesStrings() Histogram
getBinOf(double) Histogram
getBitNum() CompressedBitMatrix
Returns the total number of bits in a matrix cell
getBoolean(String) Configuration
getBsv() CorrelationEffectMetaAnalysis
getBsv() MeanDifferenceMetaAnalysis
getByKeys(R, C) CompressedBitMatrix
getByKeys(R, C) DoubleMatrix
getByKeys(R, C) IntegerMatrix
getByKeys(R, C) Matrix2D
getByKeys(R, C) ObjectMatrixImpl
getByKeys(R, C) StringMatrix
getCardinality() OntologyCardinalityRestriction
getCardinality() OntologyCardinalityRestrictionImpl
getCardinalityType() OntologyCardinalityRestriction
getCardinalityType() OntologyCardinalityRestrictionImpl
getCause() OntologySearchJenaException
getChildCount() DirectedGraphNode
getChildGraph() DirectedGraphNode
Get the subgraph starting from this node, including this node.
getChildKeys() DirectedGraphNode
getChildNodes() DirectedGraphNode
Get the immediate children of this node.
getChildren(boolean) OntologyTerm
getChildren(boolean, boolean) OntologyTerm
getChildren(boolean) OntologyTermImpl
getChildren(boolean, boolean) OntologyTermImpl
getChildren(boolean) OntologyTermSimple
getCoefficients() LeastSquaresFit
The matrix of coefficients x for Ax = b (parameter estimates).
getCoefficients() LinearModelSummary
getCol(int, int) DenseObject3DMatrix
getColByName(C) DenseDoubleMatrix
Return a copy of a given column.
getColIndexByName(C) AbstractMatrix
getColIndexByName(Object) AbstractMatrix3D
getColIndexByName(C) Matrix2D
Get the index of a column by name.
getColIndexByName(C) Matrix3D
Get the index of a column by name.
getColName(int) AbstractMatrix
getColName(int) AbstractMatrix3D
getColName(int) Matrix2D
Gte the column name for an index.
getColName(int) Matrix3D
Get the column name for an index.
getColNameIterator() AbstractMatrix3D
getColNameIterator() Matrix3D
getColNames() AbstractMatrix
getColNames() AbstractMatrix3D
getColNames() Matrix2D
getColNames() Matrix3D
getColObj(int) CompressedSparseDoubleMatrix
getColObj(int) DenseDouble3dMatrix
getColObj(int) DenseDoubleMatrix
getColObj(int) DoubleMatrix3D
getColObj(int) FastRowAccessDoubleMatrix
getColObj(int) IntegerMatrix
getColObj(int) PrimitiveMatrix
getColObj(int) SparseDoubleMatrix
getColObj(int) SparseRaggedDoubleMatrix
getColObj(int) StringMatrix
getColor(int) ColorMap
getColor(int, int) ColorMatrix
getColor(int, int) MatrixDisplay
getColorMap() ColorMatrix
getColorMap() MatrixDisplay
getColorMatrix() MatrixDisplay
getColors() ColorMatrix
getColRange(int, int) CompressedSparseDoubleMatrix
getColRange(int, int) DenseDoubleMatrix
getColRange(int, int) DoubleMatrix
getColRange(int, int) FastRowAccessDoubleMatrix
getColRange(int, int) SparseDoubleMatrix
getColRange(int, int) SparseRaggedDoubleMatrix
getColumn(int) CompressedBitMatrix
getColumn(int) CompressedSparseDoubleMatrix
getColumn(int) DenseDouble3dMatrix
getColumn(int) DenseDoubleMatrix
getColumn(int) DoubleMatrix
getColumn(int) DoubleMatrix3D
getColumn(int) FastRowAccessDoubleMatrix
getColumn(int) IntegerMatrix
getColumn(int) ObjectMatrix
getColumn(int) ObjectMatrixImpl
getColumn(int) SparseDoubleMatrix
getColumn(int) SparseRaggedDoubleMatrix
getColumn(int) StringMatrix
getColumnByName(C) DoubleMatrix
getColumnByName(C) DoubleMatrix3D
getColumnCount() ColorMatrix
getColumnCount() MatrixDisplay
getColumnName(int) ColorMatrix
getColumnName(int) MatrixDisplay
getColumnNames() ColorMatrix
getColumnNames() MatrixDisplay
getComment() OntologyTerm
getComment() OntologyTermImpl
getComment() OntologyTermSimple
getConfigBuilder(File) ConfigUtils
getConfigBuilder(String) ConfigUtils
getConfigBuilder(URL) ConfigUtils
getContents() BinaryTreeNode
getContents() AnnotationProperty
getContents() AnnotationPropertyImpl
getContrastCoefficients() LinearModelSummary
getContrastCoefficients(String) LinearModelSummary
getContrastCoefficientStderr(String) LinearModelSummary
For the requested factor, return the standard errors associated with the contrast coefficient estimates.
getContrastPValues(String) LinearModelSummary
getContrastTStats(String) LinearModelSummary
getDataname() HTest
getDateTime(String, Date) DateUtil
This method generates a string representation of a date's date/time in the format you specify on input
getDegreesOfFreedom() AnovaEffect
getDf() OneWayAnovaResult
getDfPrior() LeastSquaresFit
getDiskCachePath(String) OntologyLoader
getDisplayMax() ColorMatrix
getDisplayMax() MatrixDisplay
getDisplayMin() ColorMatrix
getDisplayMin() MatrixDisplay
getDisplayRange() MatrixDisplay
getDoubleMatrix() DesignMatrix
getE() CorrelationEffectMetaAnalysis
getE() MeanDifferenceMetaAnalysis
getEffectName() AnovaEffect
getEffects() LinearModelSummary
getEntry(int, int) CompressedBitMatrix
getEntry(int, int) DoubleMatrix
getEntry(int, int) IntegerMatrix
getEntry(int, int) Matrix2D
getEntry(int, int) ObjectMatrixImpl
getEntry(int, int) StringMatrix
getEstimate() HTest
getExpandedSize() StringToStringSetMap
getExpandedValues() StringToStringSetMap
getExtension(String) FileTools
Returns the extension of a file.
getF() LinearModelSummary
getFactorAName() TwoWayAnovaResult
getFactorBName() TwoWayAnovaResult
getFactorName() OneWayAnovaResult
getFactorNames() LinearModelSummary
getFactorValueNames(String) LinearModelSummary
Return the factor names in the order they are stored here.
getFirstAttemptCause() RetryWithoutWildcardFailedException
Obtain the cause or error for the first attempt.
getFitted() LeastSquaresFit
getFormula() LinearModelSummary
getFStatistic() AnovaEffect
getFVal() OneWayAnovaResult
getGraph() DirectedGraphNode
getGraph() GraphNode
getGraph() UndirectedGraphNode
getHeaderRow() SpreadSheetSchema
getIndexFrom() AnnotatorResponse
getIndexTo() AnnotatorResponse
getIndividuals() OntologyTerm
getIndividuals(boolean) OntologyTerm
getIndividuals() OntologyTermImpl
getIndividuals(boolean) OntologyTermImpl
getIndividuals() OntologyTermSimple
getIndividuals(boolean) OntologyTermSimple
getInputStreamFromPlainOrCompressedFile(String) FileTools
Open a non-compresed, zipped, or gzipped file.
getInstanceOf() OntologyIndividual
Return the term that this is an instance of.
getInstanceOf() OntologyIndividualImpl
getInteractionDf() TwoWayAnovaResult
getInteractionEffectF() GenericAnovaResult
getInteractionEffectP() GenericAnovaResult
getInteractionEffectP(String...) GenericAnovaResult
getInteractionEffectP(String...) LinearModelSummary
getInteractionfVal() TwoWayAnovaResult
getInteractionPval() TwoWayAnovaResult
getInteractionTerms() DesignMatrix
getInterceptCoeff() LinearModelSummary
getInterceptP() LinearModelSummary
getInterceptT() LinearModelSummary
getItem() AbstractGraphNode
Get the actual contents of the node.
getItem() GraphNode
getItems() AbstractGraph
getItems() DirectedGraph
getKey() AbstractGraphNode
Get the key for the node.
getKey() GraphNode
getKey() LinearModelSummary
getKey() AnovaResult
getLabel() DatatypePropertyImpl
getLabel() ObjectPropertyImpl
getLabel() OntologyIndividualImpl
getLabel() OntologyResource
getLabel() OntologyTermImpl
getLabel() OntologyTermSimple
getLastError() JRIClient
getLastError() RClient
getLastError() RServeClient
getLeft() BinaryTreeNode
getLevelsForFactors() DesignMatrix
getLibrarySize() MeanVarianceEstimator
getLines(File) FileTools
opens a file and returns its contents as a list of lines.
getLines(String) FileTools
opens a file and returns its contents as a list of lines.
getLocalName() OntologyTerm
getLocalName() OntologyTermImpl
getLocalName() OntologyTermSimple
getLoess() MeanVarianceEstimator
getMainEffectADf() TwoWayAnovaResult
getMainEffectAfVal() TwoWayAnovaResult
getMainEffectAPval() TwoWayAnovaResult
getMainEffectBDf() TwoWayAnovaResult
getMainEffectBfVal() TwoWayAnovaResult
getMainEffectBPval() TwoWayAnovaResult
getMainEffectDof(String) GenericAnovaResult
getMainEffectF(String) GenericAnovaResult
getMainEffectFactorNames() GenericAnovaResult
getMainEffectFactorNames() LinearModelSummary
getMainEffectP(String) GenericAnovaResult
getMainEffectP(String) LinearModelSummary
getMatchType() AnnotatorResponse
getMatrix() ColorMatrix
getMatrix() MatrixDisplay
getMatrix() DesignMatrix
getMax() ColorMatrix
getMax() MatrixDisplay
getMaxColumnLength() MatrixDisplay
getMaxtrix() ColorMatrix
getMeanSq() AnovaEffect
getMeanVariance() MeanVarianceEstimator
getMethod() HTest
getMin() ColorMatrix
getMin() MatrixDisplay
getMissingColor() ColorMatrix
getMissingColor() MatrixDisplay
getModel() OntologyTerm
getModel() OntologyTermImpl
getModel() OntologyTermSimple
getN() CorrelationEffectMetaAnalysis
getN() MeanDifferenceMetaAnalysis
getName() Histogram
The name of the histogram.
getNodeContents(K) AbstractGraph
Retrieve the contents of a node by key.
getNodeContents(K) Graph
getNormalizedValue() MeanVarianceEstimator
getNullvalue() HTest
getNumeratorDof() LinearModelSummary
getObject(int, int) CompressedSparseDoubleMatrix
getObject(int, int, int) DenseDouble3dMatrix
getObject(int, int) DenseDoubleMatrix
Converts to a String that can be read by read.table in R, using default parameters
getObject(int, int, int) DenseObject3DMatrix
getObject(int, int) FastRowAccessDoubleMatrix
getObject(int, int) IntegerMatrix
getObject(int, int, int) Matrix3D
getObject(Matrix2D<R, C, V>, int, int) MatrixUtil
getObject(int, int) PrimitiveMatrix
getObject(int, int) SparseDoubleMatrix
getObject(int, int) SparseRaggedDoubleMatrix
getObject(int, int) StringMatrix
getObject() CharacteristicStatement
getObject() ClassStatement
getObject() DataStatement
getObject() InstanceStatement
getObject() IndexerSelector
getOntologyName() AbstractOntologyService
The simple getOntologyName() of the ontology.
getOntologyName() CellLineOntologyService
getOntologyName() CellTypeOntologyService
getOntologyName() ChebiOntologyService
getOntologyName() DiseaseOntologyService
getOntologyName() ExperimentalFactorOntologyService
getOntologyName() FMAOntologyService
getOntologyName() GenericOntologyService
getOntologyName() HumanDevelopmentOntologyService
getOntologyName() HumanPhenotypeOntologyService
getOntologyName() MammalianPhenotypeOntologyService
getOntologyName() MedicOntologyService
getOntologyName() MouseDevelopmentOntologyService
getOntologyName() NIFSTDOntologyService
getOntologyName() ObiService
getOntologyName() SequenceOntologyService
getOntologyName() UberonOntologyService
getOntologyName() UnitsOntologyService
getOntologyUrl() AbstractOntologyService
Defines the location of the ontology eg:
MGED
getOntologyUrl() CellLineOntologyService
getOntologyUrl() CellTypeOntologyService
getOntologyUrl() ChebiOntologyService
getOntologyUrl() DiseaseOntologyService
getOntologyUrl() ExperimentalFactorOntologyService
getOntologyUrl() FMAOntologyService
getOntologyUrl() GenericOntologyService
getOntologyUrl() HumanDevelopmentOntologyService
getOntologyUrl() HumanPhenotypeOntologyService
getOntologyUrl() MammalianPhenotypeOntologyService
getOntologyUrl() MedicOntologyService
getOntologyUrl() MouseDevelopmentOntologyService
getOntologyUrl() NIFSTDOntologyService
getOntologyUrl() ObiService
getOntologyUrl() SequenceOntologyService
getOntologyUrl() UberonOntologyService
getOntologyUrl() UnitsOntologyService
getOntologyUsed() AnnotatorResponse
getOutputMatrix(M, int, int) AbstractFilter
getP() LinearModelSummary
Overall p value for F stat of model fit (upper tail probability)
getP() CorrelationEffectMetaAnalysis
getP() MeanDifferenceMetaAnalysis
getPalette() ColorMap
getPaletteSize() ColorMap
getParameter() HTest
getParams(Class<?>, Object) ParameterGrabber
Given an instance of a class this method will extract its primitive variable names and their values using
reflection.
getParentKeys() DirectedGraphNode
getParentNodes() DirectedGraphNode
Get the immediate parents of this node.
getParents(boolean) OntologyTerm
Note that any restriction superclasses are not returned, unless they are has_proper_part
getParents(boolean, boolean) OntologyTerm
getParents(boolean) OntologyTermImpl
getParents(boolean, boolean) OntologyTermImpl
getParents(boolean) OntologyTermSimple
getPivotOrder() QRDecomposition
getPosition(String) SpreadSheetSchema
getPredicate() IndexerSelector
getPriorDof() LinearModelSummary
getProperty() AnnotationProperty
getProperty() AnnotationPropertyImpl
getProperty() CharacteristicStatement
getPval() OneWayAnovaResult
getPValue() AnovaEffect
getPvalue() HTest
getQ() QRDecomposition
Generates and returns the (economy-sized - first p columns only) orthogonal factor Q .
getQ() CorrelationEffectMetaAnalysis
getQ() MeanDifferenceMetaAnalysis
getQR() QRDecomposition
For testing.
getQraux() QRDecomposition
getQuery() OntologySearchException
getQuick(int) DenseDoubleMatrix1D
This is an optimized version of getQuick.
getQuick(int) RCDoubleMatrix1D
getR() QRDecomposition
Returns the upper triangular factor, R .
getRange() ObjectProperty
getRange() ObjectPropertyImpl
getRank() QRDecomposition
getRawMatrix() DoubleMatrix
getRawValue(int, int) MatrixDisplay
getRConnection() RConnectionFactory
Get connection; if Rserve is used, connect to localhost.
getRConnection(String) RConnectionFactory
getRelativeDate(Date, String) DateUtil
Turn a string like '-7d' into the date equivalent to "seven days ago".
getResidualDf() AnovaResult
getResidualDof() LeastSquaresFit
getResidualDof() LinearModelSummary
getResidualDofs() LeastSquaresFit
getResiduals() LeastSquaresFit
getResiduals() LinearModelSummary
getResource(String) AbstractOntologyService
getResource(String) OntologyService
Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given.
getRestrictedTo() OntologyClassRestriction
getRestrictedTo() OntologyClassRestrictionImpl
getRestrictedTo() OntologyDatatypeRestriction
getRestrictedTo() OntologyDatatypeRestrictionImpl
getRestrictionOn() OntologyRestriction
getRestrictionOn() OntologyRestrictionImpl
getRestrictions() OntologyTerm
getRestrictions() OntologyTermImpl
getRestrictions() OntologyTermSimple
getRight() BinaryTreeNode
getRoot() DirectedGraph
getRoot() BinaryTree
getRow(int) CompressedBitMatrix
getRow(int) CompressedSparseDoubleMatrix
Return a reference to a specific row.
getRow(int) DenseDouble3dMatrix
getRow(int) DenseDoubleMatrix
Return a reference to a specific row.
getRow(int, int) DenseObject3DMatrix
getRow(int) DoubleMatrix
getRow(int) DoubleMatrix3D
getRow(int) FastRowAccessDoubleMatrix
getRow(int) IntegerMatrix
getRow(Matrix2D<R, C, V>, int) MatrixUtil
getRow(int) ObjectMatrix
getRow(int) ObjectMatrixImpl
getRow(int) SparseDoubleMatrix
Return a reference to a specific row.
getRow(int) SparseRaggedDoubleMatrix
getRow(int) StringMatrix
getRow(int) ColorMatrix
getRow(int) MatrixDisplay
getRowArrayList(int) CompressedSparseDoubleMatrix
getRowArrayList(int) DenseDoubleMatrix
getRowArrayList(int) DoubleMatrix
getRowArrayList(int) FastRowAccessDoubleMatrix
getRowArrayList(int) SparseDoubleMatrix
getRowArrayList(int) SparseRaggedDoubleMatrix
This gives just the list of values in the row - make sure this is what you want.
getRowBitCount(int) CompressedBitMatrix
getRowByName(R) CompressedSparseDoubleMatrix
getRowByName(R) DenseDoubleMatrix
Return a reference to a specific row.
getRowByName(R) DoubleMatrix
getRowByName(R) DoubleMatrix3D
getRowByName(R) SparseDoubleMatrix
getRowByName(A) ColorMatrix
getRowByName(R) MatrixDisplay
getRowCount() ColorMatrix
getRowCount() MatrixDisplay
getRowHeight() MatrixDisplay
getRowIndexByName(R) AbstractMatrix
getRowIndexByName(R) AbstractMatrix3D
getRowIndexByName(R) Matrix2D
Get the index of a row by name..
getRowIndexByName(R) Matrix3D
Get the index of a row by name.
getRowIndexByName(A) ColorMatrix
getRowIndexByName(R) MatrixDisplay
getRowName(int) AbstractMatrix
getRowName(int) AbstractMatrix3D
getRowName(int) Matrix2D
Get the row name for an index
getRowName(int) Matrix3D
Get the row name for an index
getRowName(int) ColorMatrix
getRowName(int) MatrixDisplay
getRowNameIterator() AbstractMatrix3D
getRowNameIterator() Matrix3D
getRowNameMapIterator() AbstractMatrix
getRowNameMapIterator() Matrix2D
getRowNames() AbstractMatrix
getRowNames() AbstractMatrix3D
getRowNames() Matrix2D
getRowNames() Matrix3D
getRowNames() ColorMatrix
getRowNames() MatrixDisplay
getRowObj(int) CompressedSparseDoubleMatrix
getRowObj(int) DenseDouble3dMatrix
getRowObj(int) DenseDoubleMatrix
getRowObj(int) DoubleMatrix3D
getRowObj(int) FastRowAccessDoubleMatrix
getRowObj(int) IntegerMatrix
getRowObj(int) PrimitiveMatrix
getRowObj(int) SparseDoubleMatrix
getRowObj(int) SparseRaggedDoubleMatrix
getRowRange(int, int) CompressedSparseDoubleMatrix
getRowRange(int, int) DenseDoubleMatrix
getRowRange(int, int) DoubleMatrix
getRowRange(int, int) FastRowAccessDoubleMatrix
getRowRange(int, int) SparseDoubleMatrix
getRowRange(int, int) SparseRaggedDoubleMatrix
getRSquared() LinearModelSummary
getS() SingularValueDecomposition
getSearchQueryUsed() AnnotatorResponse
getSeenValues() StringToStringSetMap
getSheetFromFile(String, String) ExcelUtil
getSigma() LinearModelSummary
Residual standard deviation
getSingularValues() SingularValueDecomposition
getSize(String) StringToStringSetMap
getSlice(int) DenseDouble3dMatrix
getSlice(int) DenseObject3DMatrix
getSlice(int) DoubleMatrix3D
getSliceByName(S) DoubleMatrix3D
getSliceIndexByName(S) AbstractMatrix3D
getSliceIndexByName(S) Matrix3D
Get a slice index
getSliceName(int) AbstractMatrix3D
getSliceName(int) Matrix3D
Get a slice name
getSliceNameIterator() AbstractMatrix3D
getSliceNameIterator() Matrix3D
getSliceNames() AbstractMatrix3D
getSliceNames() Matrix3D
getSliceObj(int) DenseDouble3dMatrix
getSliceObj(int) DoubleMatrix3D
getSsQ() AnovaEffect
getStandardizedEnabled() MatrixDisplay
getStatistic() HTest
getStdevUnscaled() LinearModelSummary
Unscaled standard deviations for the coefficient estimators in same order as coefficients.
getStepSize(int, int, int) ColorMap
Calculate how fast we have to change color components.
getString(String) Configuration
getStringListFromFile(File) FileTools
Used for reading output generated by Collection.toString().
getStudentizedResiduals() LeastSquaresFit
getSubject() CharacteristicStatement
getSubject() IndexerSelector
getSubjectIndex(String) OntologyIndexer
getTerm() OntologyTerm
getTerm() OntologyTermImpl
getTerm() OntologyTermSimple
getTerm(String) AbstractOntologyService
getTerm(String) OntologyService
Looks for a OntologyTerm that has the match in URI given
getTermIndividuals(String) AbstractOntologyService
getTermIndividuals(String) OntologyService
getTerms() DesignMatrix
getTodayDate(boolean) DateUtil
return today date as a String
getTolerance() QRDecomposition
getTopoSortOrder() DirectedGraphNode
getTreeModel() DirectedGraph
getTrueRowIndex(int) ColorMatrix
getTxtMatched() AnnotatorResponse
getType() DatatypeProperty
getType() DatatypePropertyImpl
getU() SingularValueDecomposition
getUri() AbstractOntologyResource
getUri() DatatypePropertyImpl
getUri() ObjectPropertyImpl
getUri() OntologyIndividualImpl
getUri() OntologyResource
getUri() OntologyTerm
getUri() OntologyTermImpl
getUri() OntologyTermSimple
getV() SingularValueDecomposition
getV() CorrelationEffectMetaAnalysis
getV() MeanDifferenceMetaAnalysis
getValue(int, int) ColorMatrix
getValue(int, int) MatrixDisplay
getValue(HSSFSheet, int, int) ExcelUtil
getValues() DirectedGraph
Get all the values in thee graph.
getValuesForFactors() DesignMatrix
getValueUri() AnnotatorResponse
getVarPost() LeastSquaresFit
getVarPrior() LeastSquaresFit
getWeight() Link
getWeights() LeastSquaresFit
getWeights() MeanVarianceEstimator
getx() DoublePoint
getx() Point
gety() DoublePoint
gety() Point
getZ() CorrelationEffectMetaAnalysis
getZ() MeanDifferenceMetaAnalysis
GIF_EXTENSION FileTools
grabColumnValues(HSSFSheet, int, boolean, boolean) ExcelUtil
grabColumnValues(HSSFSheet, int, boolean, boolean, SpreadSheetFilter) ExcelUtil
Gets all the strings from a column, possibly excluding header and possibly trimming and lowercasing
grabColumnValuesList(HSSFSheet, int, boolean, boolean) ExcelUtil
grabColumnValuesList(HSSFSheet, int, boolean, boolean, SpreadSheetFilter) ExcelUtil
gradient JGradientBar
Graph R extends GraphNode <K ,V >,K ,V > - Interface in ubic.basecode.dataStructure.graph
GraphNode K ,V > - Interface in ubic.basecode.dataStructure.graph
GREENRED_COLORMAP ColorMap
IMAGE_EXTENSIONS FileTools
in HistogramReader
increment(K) CountingMap
Increments the count associated with the specified key and returns the incremented count.
incrementAll(Collection<K>) CountingMap
Increments the count associated with the specified keys.
incrementalUpdate(DoubleArrayList, int, int, double[]) DescriptiveWithMissing
Incrementally maintains and updates minimum, maximum, sum and sum of squares of a data sequence.
incrementalUpdateSumsOfPowers(DoubleArrayList, int, int, int, int, double[]) DescriptiveWithMissing
Not supported.
incrementalWeightedUpdate(DoubleArrayList, DoubleArrayList, int, int, double[]) DescriptiveWithMissing
Not supported.
inDegree() DirectedGraphNode
index(boolean) AbstractOntologyService
index(boolean) OntologyService
Index the ontology for performing full-text searches.
IndexerSelector ubic.basecode.ontology.search
Used to limit which parts of ontologies get indexed for searching.
IndexerSelector() IndexerSelector
indexes RCDoubleMatrix1D
indexOntology(String, OntModel) OntologyIndexer
indexOntology(String, OntModel, boolean) OntologyIndexer
Loads or creates an index from an existing OntModel.
init(ColorMatrix<R, C>) MatrixDisplay
init() CreateSpreadSheet
init(long) RandomChooser
Initialized the random number generator with a given seed.
initialize(boolean, boolean) AbstractOntologyService
initialize(boolean, boolean) OntologyService
Initialize this ontology service.
initSize() MatrixDisplay
Sets the display size
insertLeft(BinaryTreeNode<T>, T) BinaryTree
insertLeft(T) BinaryTreeNode
insertRight(BinaryTreeNode<T>, T) BinaryTree
insertRight(T) BinaryTreeNode
InstanceStatement ubic.basecode.ontology.model
intArrayEval(String) AbstractRClient
intArrayEval(String) RClient
intArrayToBytes(int[]) ByteArrayConverter
IntegerMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
IntegerMatrix(int, int) IntegerMatrix
INTERCEPT_COEFFICIENT_NAME LinearModelSummary
interpolate(double[], double[], double[]) Smooth
Linearlly interpolate values from a given data set
Similar implementation of R's stats.approxfun(..., rule = 2) where values outside the interval ['min(x)',
'max(x)'] get the value at the closest data extreme.
isamax_j(int, double[], int) Blas
This method finds the index of the element of a vector
that has the maximum absolute value.
isBaseline(String) LinearModelSummary
isConnected() JRIClient
isConnected() RClient
isConnected() RServeClient
isDiseaseUsed() AnnotatorResponse
isEmpty() CountingMap
isEmpty() BinaryTree
isEnabled() AbstractOntologyService
isEnabled() OntologyService
isExactMatch() AnnotatorResponse
isExactSynonym() AnnotatorResponse
isFunctional() OntologyProperty
isFunctional OntologyPropertyImpl
isFunctional() OntologyPropertyImpl
isGZipped(String) FileTools
isHasBeenShrunken() LeastSquaresFit
isHasInteractionEstimate() TwoWayAnovaResult
isHasIntercept() DesignMatrix
isHasMissing() LeastSquaresFit
isHpUsed() AnnotatorResponse
isInitializationThreadAlive() AbstractOntologyService
isInitializationThreadAlive() OntologyService
isInitializationThreadCancelled() AbstractOntologyService
isInitializationThreadCancelled() OntologyService
isInteraction() AnovaEffect
isLatinLetter(char) StringUtil
isLeaf() DirectedGraphNode
isLeaf() BinaryTreeNode
isMissing(int, int, int) AbstractMatrix3D
isMissing(int, int) CompressedBitMatrix
isMissing(int, int) CompressedSparseDoubleMatrix
isMissing(int, int, int) DenseDouble3dMatrix
isMissing(int, int) DenseDoubleMatrix
isMissing(int, int, int) DenseObject3DMatrix
isMissing(int, int, int) DoubleMatrix3D
isMissing(int, int) FastRowAccessDoubleMatrix
isMissing(int, int) IntegerMatrix
isMissing(int, int) Matrix2D
Check if the value at a given index is missing.
isMissing(int, int, int) Matrix3D
Check if the value at a given index is missing.
isMissing(int, int) ObjectMatrixImpl
isMissing(int, int) SparseDoubleMatrix
isMissing(int, int) SparseRaggedDoubleMatrix
(non-Javadoc) Note that in a sparse matrix, zero values are considered "missing"!
isMissing(int, int) StringMatrix
Strings are considered missing if they are whitespace, null or empty.
isOntologyLoaded() AbstractOntologyService
isOntologyLoaded() OntologyService
Used for determining if the Ontology has finished loading into memory.
isPivoting() QRDecomposition
isRoot() BinaryTreeNode
isRoot() OntologyTerm
isRoot() OntologyTermImpl
isRoot() OntologyTermSimple
isShrunken() LinearModelSummary
Whether this is the result of emprical bayes shrinkage of variance estimates
isSimple() IndexerSelector
isTermObsolete() OntologyTerm
check to see if the term is obsolete, if it is it should not be used
isTermObsolete() OntologyTermImpl
isTermObsolete() OntologyTermSimple
isValidFraction(double) Stats
Test whether a value is a valid fractional or probability value.
isValidPearsonCorrelation(double) 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() AbstractGraphNode
isVisited() Visitable
isZipped(String) FileTools
item AbstractGraphNode
ItemLevelFilter R ,C > - Class in ubic.basecode.datafilter
Filter that removes individual values that are outside of a range.
ItemLevelFilter() ItemLevelFilter
items DirectedGraph
iterator() BatchIterator
lag1(DoubleArrayList, double) DescriptiveWithMissing
Not supported.
LeastSquaresFit ubic.basecode.math.linearmodels
For performing "bulk" linear model fits, but also offers simple methods for simple univariate and multivariate
regression for a single vector of dependent variables (data).
LeastSquaresFit(DesignMatrix, DoubleMatrix<String, String>) LeastSquaresFit
Preferred interface if you want control over how the design is set up.
LeastSquaresFit(DesignMatrix, DoubleMatrix<String, String>, DoubleMatrix2D) LeastSquaresFit
Weighted least squares fit between two matrices
LeastSquaresFit(DesignMatrix, DoubleMatrix2D, DoubleMatrix2D) LeastSquaresFit
Preferred interface for weighted least squares fit between two matrices
LeastSquaresFit(DoubleMatrix1D, DoubleMatrix1D) LeastSquaresFit
Least squares fit between two vectors.
LeastSquaresFit(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) LeastSquaresFit
Stripped-down interface for simple use.
LeastSquaresFit(DoubleMatrix2D, DoubleMatrix2D) LeastSquaresFit
ANOVA not possible (use the other constructors)
LeastSquaresFit(DoubleMatrix2D, DoubleMatrix2D, DoubleMatrix2D) LeastSquaresFit
Weighted least squares fit between two matrices
LeastSquaresFit(ObjectMatrix<String, String, Object>, DenseDoubleMatrix2D) LeastSquaresFit
LeastSquaresFit(ObjectMatrix<String, String, Object>, DenseDoubleMatrix2D, boolean) LeastSquaresFit
LeastSquaresFit(ObjectMatrix<String, String, Object>, DoubleMatrix<String, String>) LeastSquaresFit
NamedMatrix allows easier handling of the results.
LeastSquaresFit(ObjectMatrix<String, String, Object>, DoubleMatrix<String, String>, boolean) LeastSquaresFit
NamedMatrix allows easier handling of the results.
like(int) RCDoubleMatrix1D
like2D(int, int) RCDoubleMatrix1D
linearModel(double[], Map<String, List<?>>) AbstractRClient
linearModel(double[], ObjectMatrix<String, String, Object>) AbstractRClient
linearModel(double[], Map<String, List<?>>) RClient
Lower level access to linear model.
linearModel(double[], ObjectMatrix<String, String, Object>) RClient
LinearModelSummary ubic.basecode.math.linearmodels
Represents the results of a linear model analysis from R.
LinearModelSummary(REXP, REXP, String[]) LinearModelSummary
Construct from the result of evaluation of an R call. should be deprecated because we're not using R integration
LinearModelSummary(String) LinearModelSummary
Construct an empty summary.
LinearModelSummary(String, Double[], Double[], List<String>, DoubleMatrix<String, String>, Double[], Double[], double, double, double, Integer, Integer, GenericAnovaResult, double, boolean) LinearModelSummary
LinearModelSummary() LinearModelSummary
Construct an empty summary.
Link ubic.basecode.dataStructure
Implements comparable, which sorts by the 'x' coordinate and then secondarily by the 'y' coordinate.
Link(int, int, double) Link
listDirectoryFiles(File) FileTools
Given a File object representing a directory, return a collection of File objects representing the files
contained in that directory.
listEval(Class<?>, String) AbstractRClient
FIXME only partly implemented, possibly not going to stay.
listEval(Class<?>, String) RClient
listSubDirectories(File) FileTools
Given a File object representing a directory, return a collection of File objects representing the directories
contained in that directory.
loadClasspathConfig(String) ConfigUtils
loadConfig(File) ConfigUtils
loadConfig(String) ConfigUtils
loadConfig(URL) ConfigUtils
loadLibrary(String) AbstractRClient
loadLibrary(String) RClient
loadMedicOntologyFromFile() MedicOntologyService
Warning, this uses a method intended only for tests.
loadMemoryModel(InputStream, String) OntologyLoader
Load an ontology into memory.
loadMemoryModel(String) OntologyLoader
Load an ontology into memory.
loadMemoryModel(String, String) OntologyLoader
Load an ontology into memory.
loadModel() AbstractOntologyMemoryBackedService
loadModel() AbstractOntologyService
Delegates the call as to load the model into memory or leave it on disk.
loadModel() GenericOntologyService
loadScript(InputStream) AbstractRClient
There is a pretty annoying limitation of this.
loadTermsInNameSpace(InputStream, boolean) AbstractOntologyService
loadTermsInNameSpace(InputStream, boolean) OntologyService
For testing!
locate(String) ConfigUtils
loessFit(DoubleMatrix2D) Smooth
loessFit(DoubleMatrix2D, double) Smooth
Computes a loess regression line to fit the data
log AbstractFilter
log AbstractMatrixReader
log AbstractOntologyResource
log AbstractOntologyService
log AbstractRClient
logTransform(DoubleMatrix<R, C>) MatrixStats
Log-transform the values in a matrix (log base 2).
longArrayToBytes(long[]) ByteArrayConverter
lowCut AbstractLevelFilter
M_1_PI Constants
M_1_SQRT_2 Constants
M_1_SQRT_2PI Constants
m_cellSize MatrixDisplay
m_colorPalette ColorMap
m_columnLabelHeight MatrixDisplay
m_currentColorMap ColorMap
m_customColorMap ColorMap
m_defaultResolution MatrixDisplay
m_defaultSuggestedNumberOfColors ColorMap
m_fontGutter MatrixDisplay
m_fontSize MatrixDisplay
m_isShowLabels MatrixDisplay
m_isShowScale MatrixDisplay
m_labelFont MatrixDisplay
m_labelGutter MatrixDisplay
M_LN_2 Constants
M_LN_SQRT_2PI Constants
M_LN_SQRT_PI Constants
M_LN_SQRT_PId2 Constants
M_LOG10_2 Constants
m_matrixReader ColorMatrix
m_max JGradientBar
m_maxColor ColorMap
last color in the current color map
m_maxColumnLength MatrixDisplay
m_maxFontSize MatrixDisplay
m_min JGradientBar
m_minColor ColorMap
first color in the current color map
M_PI_2 Constants
M_PI_4 Constants
M_PI_half Constants
m_ratioWidth MatrixDisplay
m_resolution MatrixDisplay
m_rowKeys ColorMatrix
to be able to sort the rows by an arbitrary key
m_rowLabelWidth MatrixDisplay
M_SQRT_2 Constants
M_SQRT_2dPI Constants
M_SQRT_PI Constants
m_textSize MatrixDisplay
m_totalColumns ColorMatrix
m_totalRows ColorMatrix
mad(DoubleArrayList) DescriptiveWithMissing
main(String[]) ExcelUtil
makeContrasts() DesignMatrix
In limma, the contrasts are built by referring to the coefficients by name, which isn't what we want.
makeValidForR(String) StringUtil
Mimics the make.names method in R (character.c) to make valid variables names; we use this for column headers in
some output files.
MammalianPhenotypeOntologyService ubic.basecode.ontology.providers
MammalianPhenotypeOntologyService() MammalianPhenotypeOntologyService
manhattanDistance(DoubleArrayList, DoubleArrayList) Distance
Calculate the Manhattan distance between two vectors.
MapReader ubic.basecode.io.reader
Reads a tab-delimited file with keys in first column, values in second.
MapReader() MapReader
mapValuesToColors() ColorMatrix
mark() AbstractGraphNode
mark() Visitable
maskMissing(DoubleMatrix2D, DoubleMatrix2D) MatrixUtil
matchClasses(OntModel, SearchIndex, String) OntologySearch
Find classes that match the query string.
matchIndividuals(OntModel, SearchIndex, String) OntologySearch
Find individuals that match the query string
matchingCriteria(DoubleMatrix1D, DoubleFunction<Boolean>) MatrixUtil
matchResources(OntModel, SearchIndex, String) OntologySearch
Find OntologyIndividuals and OntologyTerms that match the query string.
MathUtil ubic.basecode.math
MathUtil() MathUtil
matmat_j(double[][], double[][], double[][], int, int, int) Blas
This method multiplies an n x p matrix by a p x r matrix.
Matrix2D R ,C ,V > - Interface in ubic.basecode.dataStructure.matrix
Represents a matrix with index columns and rows.
Matrix3D R ,C ,S ,V > - Interface in ubic.basecode.dataStructure.matrix
MatrixDisplay R ,C > - Class in ubic.basecode.graphics
A visual component for displaying a color matrix
MatrixDisplay(ColorMatrix<R, C>) MatrixDisplay
MatrixDisplay(DoubleMatrix<R, C>) MatrixDisplay
MatrixNormalizer R ,C > - Class in ubic.basecode.math
MatrixNormalizer() MatrixNormalizer
MatrixRowStats ubic.basecode.math
Convenience functions for getting row statistics from matrices.
MatrixStats ubic.basecode.math
MatrixStats() MatrixStats
MatrixUtil ubic.basecode.dataStructure.matrix
MatrixUtil() MatrixUtil
MatrixWriter R ,C > - Class in ubic.basecode.io.writer
Class for writing matrices to disk
MatrixWriter(OutputStream) MatrixWriter
MatrixWriter(OutputStream, Format) MatrixWriter
MatrixWriter(OutputStream, Format, String) MatrixWriter
MatrixWriter(String, Format) MatrixWriter
MatrixWriter(String, Format, String) MatrixWriter
MatrixWriter(Writer) MatrixWriter
MatrixWriter(Writer, Format) MatrixWriter
MatrixWriter(Writer, Format, String) MatrixWriter
MatrixWriter(Writer, String) MatrixWriter
mattran_j(double[][], double[][], int, int) Blas
This method obtains the transpose of an n x p matrix.
matvec_j(double[][], double[], double[], int, int) Blas
This method multiplies an n x p matrix by a p x 1 vector.
MAX RowLevelFilter
Use the maximum of the row as the criterion.
max() CountingMap
max ColorMatrix
max(DoubleArrayList) DescriptiveWithMissing
max() Histogram
max(double[]) MathUtil
max(DoubleMatrix<R, C>) MatrixStats
Compute the maximum value in the matrix.
MAX_ROWS_TO_PRINT AbstractMatrix
MAX_ROWS_TO_PRINT DoubleMatrix3D
MAX_SLICES_TO_PRINT DoubleMatrix3D
maxStringPixelWidth(String[], FontMetrics) Util
maxtrix ColorMatrix
MEAN RowLevelFilter
Use the mean as the criterion.
mean(double[], int) DescriptiveWithMissing
Special mean calculation where we use the effective size as an input.
mean(DoubleArrayList) DescriptiveWithMissing
mean(DoubleArrayList, int) DescriptiveWithMissing
Special mean calculation where we use the effective size as an input.
meanAboveQuantile(double, DoubleArrayList) DescriptiveWithMissing
Calculate the mean of the values above to a particular quantile of an array.
meanAboveQuantile(int, double[], int) Stats
calculate the mean of the values above (NOT greater or equal to) a particular index rank of an array.
MeanDifferenceMetaAnalysis ubic.basecode.math.metaanalysis
Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
These methods use the standardized mean difference statistic d:
d_i = ( X_i ˆ t - X_i ˆ c ) / s_i
where X i t is the mean of the treatment group in the ith study, X i ct
is the mean of the control group in the treatment group in the ith study, and s i is the pooled
standard deviation of the two groups.
MeanDifferenceMetaAnalysis(boolean) MeanDifferenceMetaAnalysis
means(DoubleMatrix<R, C>) MatrixRowStats
Calculates the means of a matrix's rows.
means(DoubleMatrix2D) MatrixRowStats
Calculate the means of a matrix's rows
MeanVarianceEstimator ubic.basecode.math.linearmodels
Estimate mean-variance relationship and use this to compute weights for least squares fitting.
MeanVarianceEstimator(DesignMatrix, DoubleMatrix<String, String>, DoubleMatrix1D) MeanVarianceEstimator
Preferred interface if you want control over how the design is set up.
MeanVarianceEstimator(DesignMatrix, DoubleMatrix2D, DoubleMatrix1D) MeanVarianceEstimator
Executes voom() to calculate weights.
MeanVarianceEstimator(DoubleMatrix2D) MeanVarianceEstimator
Generic method for calculating mean and variance, as a data diagnostic.
MEDIAN RowLevelFilter
Use the median as the criterion.
median(DoubleArrayList) DescriptiveWithMissing
Returns the median.
MedicOntologyService ubic.basecode.ontology.providers
MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a
normal mesh term doesnt have
MEDIC comes from the CTD folks.
MedicOntologyService() MedicOntologyService
Warning, this constructor initializes the ontology no matter what
MetaAnalysis ubic.basecode.math.metaanalysis
Statistics for meta-analysis.
MetaAnalysis() MetaAnalysis
metaFEWeights(DoubleArrayList) MetaAnalysis
Weights under a fixed effects model.
metaRESampleVariance(DoubleArrayList) MetaAnalysis
CH sample variance under random effects model, equation 18-20
metaREVariance(DoubleArrayList, DoubleArrayList, DoubleArrayList) MetaAnalysis
CH equation 18-23.
metaREWeights(DoubleArrayList, double) MetaAnalysis
Under a random effects model, CH eqn. 18-24, we replace the conditional variance with the sum of the
between-sample variance and the conditional variance.
metaVariance(DoubleArrayList) MetaAnalysis
CH 18-3.
metaVariance(DoubleArrayList, DoubleArrayList) MetaAnalysis
CH 18-3 version 2 for quality weighted. ( page 266 ) in Fixed effects model.
metaZscore(double, double) MetaAnalysis
Test statistic for H0: effectSize == 0.
MIN RowLevelFilter
Use the minimum of the row as the criterion.
min ColorMatrix
min(DoubleArrayList) DescriptiveWithMissing
min() Histogram
min(DoubleMatrix<R, C>) MatrixStats
Find the minimum of the entire matrix.
missingColor ColorMatrix
ModeratedTstat ubic.basecode.math.linearmodels
Implements methods described in
Smyth, G.
ModeratedTstat() ModeratedTstat
moment(DoubleArrayList, int, double) DescriptiveWithMissing
Returns the moment of k -th order with constant c of a data sequence, which is
Sum( (data[i]-c)k ) /
data.size() .
MouseDevelopmentOntologyService ubic.basecode.ontology.providers
MouseDevelopmentOntologyService() MouseDevelopmentOntologyService
movingAverage(DoubleMatrix1D, int) Smooth
Simple moving average that sums the points "backwards".
MultipleTestCorrection ubic.basecode.math
Methods for p-value correction of sets of hypothesis tests.
MultipleTestCorrection() MultipleTestCorrection
multWithMissing(DoubleMatrix1D, DoubleMatrix2D) MatrixUtil
multWithMissing(DoubleMatrix2D, DoubleMatrix1D) MatrixUtil
multWithMissing(DoubleMatrix2D, DoubleMatrix2D) MatrixUtil
Multiple two matrices, tolerate missing values.
paintComponent(Graphics) MatrixDisplay
ParameterGrabber ubic.basecode.dataStructure.params
Generates a parameter map from a class using reflection, usefull for storing experimental parameters
ParameterGrabber() ParameterGrabber
ParamKeeper ubic.basecode.dataStructure.params
Keeps track of results in the form of several key/value maps (each one can represent an experiment run), can output
to spreadsheet or csv file
ParamKeeper() ParamKeeper
ParamSpreadSheet ubic.basecode.dataStructure.params
A class to convert parametergrabber information/instances into excel speadsheet lines
ParamSpreadSheet(String, SpreadSheetSchema) ParamSpreadSheet
paramsToLine(Map<String, String>) ParameterGrabber
paramsToLine(Map<String, String>, boolean) ParameterGrabber
parents DirectedGraphNode
phyper(int, int, int, int, boolean) SpecFunc
Ported from R phyper.c
Sample of n balls from NR red and NB black ones; x are red
plot() Histogram
Provide graph for JFreePlot; counts expressed as a fraction.
Point ubic.basecode.dataStructure
Point(int, int) Point
populate(List<Map<String, String>>) ParamSpreadSheet
positions SpreadSheetSchema
PrecisionRecall ubic.basecode.math
Compute area under precision recall
PrecisionRecall() PrecisionRecall
prefixWeightedHammingDistance(String, String, double) StringDistance
Compute the Hamming distance between two strings of equal length (if they are of unequal length the longer one is
trimmed), giving higher weight to characters at the start of the strings, so strings that are similar at the
starts are given higher scores (shorter distances) than strings that are similar at the ends.
prettyPrint(byte[]) BitUtil
PrettyPrinter ubic.basecode.util
Very simple class to produce String versions of beans and other objects.
PrimitiveMatrix R ,C ,V > - Interface in ubic.basecode.dataStructure.matrix
Matrix that holds primitives, with an available object representation of the values.
print(Collection<String>, Collection<Object>) PrettyPrinter
Print out a collection of beans in a relatively pleasing format.
print(Collection<String>, Object) PrettyPrinter
Pretty-print a single bean.
print(Collection<String>, Object[]) PrettyPrinter
Print out a collection of objects in a relatively pleasing format.
probability(double) NormalProbabilityComputer
probability(double, boolean) NormalProbabilityComputer
probability(double) ProbabilityComputer
Return the probability associated with a certain value.The upper tail of the associated distribution is returned.
probability(double, boolean) ProbabilityComputer
Return the probability associated with a certain value, with choice of tail.
probability(double) UniformProbabilityComputer
probability(double, boolean) UniformProbabilityComputer
ProbabilityComputer ubic.basecode.math.distribution
An interface that describes objects that can produce probabilities according to some distribution.
product(DoubleArrayList) DescriptiveWithMissing
Returns the product of a data sequence, which is Prod( data[i] ) .
PropertyFactory ubic.basecode.ontology.model
PropertyFactory() PropertyFactory
prune() DirectedGraph
Remove edges to nodes that aren't in the graph.
prune() DirectedGraphNode
Remove connections that are to nodes not contained in this graph
put(K, Integer) CountingMap
put(String, String) StringToStringSetMap
putAll(Map<? extends K, ? extends Integer>) CountingMap
pvalue(double, int) CorrelationStats
Compute pvalue for the pearson correlation, using the t distribution method.
pvalueAsByte(double, int) CorrelationStats
Convert a p value into a value between 0 and 255 inclusive.
RandomChooser ubic.basecode.math
Fill arrays with random values
RANGE RowLevelFilter
Use the range as the criterion
range(DoubleArrayList) Stats
Compute the range of an array.
rank() SingularValueDecomposition
Rank ubic.basecode.math
Calculate rank statistics for arrays.
Rank() Rank
rankInterpolated(DoubleArrayList, double) DescriptiveWithMissing
Returns the linearly interpolated number of elements in a list less or equal to a given element.
rankSum(List<Double>) Rank
rankTransform(DoubleArrayList) Rank
Rank transform an array.
rankTransform(DoubleArrayList, boolean) Rank
Rank transform an array.
rankTransform(Map<K, ? extends Comparable<?>>) Rank
Rank transform a map, where the values are Comparable values we wish to rank.
rankTransform(Map<K, ? extends Comparable<?>>, boolean) Rank
Ties are broken as for the other methods.
rbfNormalize(DoubleMatrix<R, C>, double) MatrixStats
Normalize a matrix in place to be a transition matrix.
RCDoubleMatrix1D ubic.basecode.dataStructure.matrix
A row-compressed 1D matrix.
RCDoubleMatrix1D(double[]) RCDoubleMatrix1D
RCDoubleMatrix1D(int) RCDoubleMatrix1D
RCDoubleMatrix1D(IntArrayList, DoubleArrayList) RCDoubleMatrix1D
RClient ubic.basecode.util.r
Abstraction of a connection to R
RConnectionFactory ubic.basecode.util.r
Get a connection to R, somehow (if possible).
RConnectionFactory() RConnectionFactory
read(InputStream) AbstractMatrixReader
read(String) AbstractMatrixReader
read(String, int) AbstractMatrixReader
read(InputStream) DoubleMatrixReader
read(InputStream, Collection<String>) DoubleMatrixReader
read(InputStream, Collection<String>, boolean, int, int) DoubleMatrixReader
read(InputStream, Collection<String>, int) DoubleMatrixReader
read(String) DoubleMatrixReader
read(String, Collection<String>) DoubleMatrixReader
Read a matrix from a file, subject to filtering criteria.
read(String, Collection<String>, int) DoubleMatrixReader
read(String, int) DoubleMatrixReader
read(InputStream) MapReader
read(InputStream, boolean) MapReader
read(String) MapReader
read(String, boolean) MapReader
read(InputStream) SparseDoubleMatrixReader
Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
item1 item2 weight
item1 item5 weight
By definition the resulting matrix is square and symmetric.
read(InputStream, Collection<String>) SparseDoubleMatrixReader
read(InputStream, Collection<String>, boolean, int, int) SparseDoubleMatrixReader
read(InputStream, int) SparseRaggedMatrixReader
Read an entire sparse matrix from a stream (JW format).
read(InputStream) StringMatrixReader
read(InputStream, int, int) StringMatrixReader
read(String) StringMatrixReader
read(String, int) StringMatrixReader
read(String, int, int) StringMatrixReader
read1D() HistogramReader
readFromAdjList(InputStream) SparseRaggedMatrixReader
readFromAdjList(String) SparseRaggedMatrixReader
Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
item1 item2 weight
item1 item5 weight
IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not
explicitly listed.
readHeader(BufferedReader, int) AbstractMatrixReader
readJW(InputStream) SparseDoubleMatrixReader
Read a sparse matrix in "JW" (Jason Weston) format.
readOneRow(BufferedReader, int) SparseRaggedMatrixReader
Use this to read one row from a matrix (JW format).
readTestResult(File) RegressionTesting
readTestResult(InputStream) RegressionTesting
readTestResult(String) RegressionTesting
readTestResultFromFile(String) RegressionTesting
ready() JRIClient
rebuild() DesignMatrix
Refresh the design matrix, for example after releveling.
REDGREEN_COLORMAP ColorMap
RegressionTesting ubic.basecode.util
Tools to help make regression testing easier, but also useful for other purposes.
remove(Object) CountingMap
remove() BatchIterator
remove(String) AbstractRClient
remove(String) RClient
Remove a variable from the R namespace
removeMissing(DoubleMatrix1D) MatrixUtil
removeMissing(DoubleArrayList) DescriptiveWithMissing
Makes a copy of the list that doesn't have the missing values.
removeMissingOrInfinite(DoubleMatrix1D) MatrixUtil
removeMissingOrInfinite(DoubleMatrix1D, DoubleMatrix1D) MatrixUtil
Remove values from data corresponding to missing values in reference.
removeSpecialCharacters(String) AnnotatorClient
replaceValues(DoubleMatrix1D, BooleanArrayList, DoubleMatrix1D) MatrixUtil
Perform the awkward operation of substituting certain values in a vector from values in another vector.
reset(int, int) CompressedBitMatrix
resetRowKeys() ColorMatrix
resetRowKeys() MatrixDisplay
residualDf AnovaResult
resourceToPath(String) FileTools
RestrictionFactory ubic.basecode.ontology.model
RestrictionFactory() RestrictionFactory
restrictionOn OntologyRestrictionImpl
retrieveMatrix(String) JRIClient
retrieveMatrix(String) RClient
Get a matrix back out of the R context.
retrieveMatrix(String) RServeClient
RetryWithoutWildcardFailedException ubic.basecode.ontology.search
Exception raised when retrying a search without a wildcard still fails.
RetryWithoutWildcardFailedException(String, String, JenaException, JenaException) RetryWithoutWildcardFailedException
ROC ubic.basecode.math
Functions for calculating Receiver operator characteristics.
ROC() ROC
rocpval(int, List<Double>) ROC
For an AROC value, calculates a p value.
RowAbsentFilter M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Filter a data matrix according to flags given in a separate matrix.
RowAbsentFilter() RowAbsentFilter
rowApplyLinearModel(String, String, String[]) AbstractRClient
rowApplyLinearModel(String, String, String[]) RClient
Run lm with anova on all the rows of a matrix
RowLevelFilter R ,C > - Class in ubic.basecode.datafilter
Remove rows from a matrix based on some row-based statistic.
RowLevelFilter() RowLevelFilter
rowMap AbstractMatrix3D
RowMissingFilter M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Remove rows from a matrix that are missing too many points.
RowMissingFilter() RowMissingFilter
RowNameFilter M extends Matrix2D <R ,C ,V >,R ,C ,V > - Class in ubic.basecode.datafilter
Remove or retain rows that are on a list.
RowNameFilter() RowNameFilter
RowNameFilter(Set<R>) RowNameFilter
RowNameFilter(Set<R>, boolean) RowNameFilter
rowNameMap MatrixWriter
rowNames AbstractMatrix3D
rows() AbstractMatrix3D
rows() CompressedBitMatrix
rows() CompressedSparseDoubleMatrix
rows() DenseDouble3dMatrix
rows() DenseDoubleMatrix
rows() DenseObject3DMatrix
rows() DoubleMatrix3D
rows() FastRowAccessDoubleMatrix
rows() IntegerMatrix
rows() Matrix2D
Get the number of rows the matrix has
rows() Matrix3D
Get the number of rows the matrix has
rows() ObjectMatrixImpl
rows() SparseDoubleMatrix
rows() SparseRaggedDoubleMatrix
rows() StringMatrix
RServeClient ubic.basecode.util.r
RServeClient() RServeClient
Gets connection on default host (localhost) and port (6311)
RServeClient(String) RServeClient
run(DoubleArrayList, DoubleArrayList) CorrelationEffectMetaAnalysis
Following CH section 2.2.
run(DoubleArrayList, DoubleArrayList) MeanDifferenceMetaAnalysis
run(DoubleArrayList, DoubleArrayList, DoubleArrayList) MeanDifferenceMetaAnalysis
run() GenericStreamConsumer
sameArray(int[], int[]) RegressionTesting
Test whether two double arrays contain the same items in the same order
sampleKurtosis(DoubleArrayList, double, double) DescriptiveWithMissing
Returns the sample kurtosis (aka excess) of a data sequence.
sampleSkew(DoubleArrayList, double, double) DescriptiveWithMissing
Returns the sample skew of a data sequence.
sampleStandardDeviation(int, double) DescriptiveWithMissing
Returns the sample standard deviation.
sampleStandardDeviations(DoubleMatrix<R, C>) MatrixRowStats
Calculates the sample standard deviation of each row of a matrix
sampleVariance(DoubleArrayList, double) DescriptiveWithMissing
Returns the sample variance of a data sequence.
samplingVariance(double, double) CorrelationEffectMetaAnalysis
Equation 18-10 from CH.
samplingVariance(double, double, double) MeanDifferenceMetaAnalysis
CH eqn 18-7
samplingVariances(DoubleArrayList, DoubleArrayList) CorrelationEffectMetaAnalysis
Run equation CH 18-10 on a list of sample sizes and effects.
samplingVariances(DoubleArrayList, DoubleArrayList, DoubleArrayList) MeanDifferenceMetaAnalysis
Run eqn 18-7 on a set of effect sizes.
save() CreateSpreadSheet
saveImage(ColorMatrix<R, C>, String, boolean, boolean, boolean) MatrixDisplay
saveImage(String) MatrixDisplay
Saves the image to a png file.
saveImage(String, boolean, boolean) MatrixDisplay
saveImageToPng(ColorMatrix<R, C>, OutputStream, boolean, boolean, boolean) MatrixDisplay
schema CreateSpreadSheet
search(String) SearchIndex
SearchIndex ubic.basecode.ontology.search
Customization to deal with MultiReader and 'open' while indexing is going on ...?
SearchIndex(IndexReader) SearchIndex
SearchIndex(MultiReader, Analyzer) SearchIndex
seen(K) CountingMap
Returns true if the specified key has ever been incremented, false otherwise.
select(DoubleMatrix1D, Collection<Integer>) MatrixUtil
selectColumns(DoubleMatrix2D, Collection<Integer>) MatrixUtil
selectColumnsAndRows(DoubleMatrix2D, Collection<Integer>) MatrixUtil
selectRows(DoubleMatrix2D, Collection<Integer>) MatrixUtil
selfSquaredMatrix(double[][]) MatrixStats
sep MatrixWriter
SequenceOntologyService ubic.basecode.ontology.providers
Support for the Sequence Ontology
SequenceOntologyService() SequenceOntologyService
set(byte[], int) BitUtil
Set the bit at the specified position
set(double, double) DoublePoint
set(int, int, double[]) CompressedBitMatrix
Set the matrix cell to the specified bit vector
set(int, int, int) CompressedBitMatrix
Sets the bit of the specified cell at the specified index to 1.
set(int, int, Double) CompressedSparseDoubleMatrix
set(int, int, int, double) DenseDouble3dMatrix
set(int, int, Double) DenseDoubleMatrix
set(int, int, int, Object) DenseObject3DMatrix
set(int, int, int, double) DoubleMatrix3D
set(int, int, Double) FastRowAccessDoubleMatrix
set(int, int, Integer) IntegerMatrix
set(int, int, V) Matrix2D
set(int, int, V) ObjectMatrixImpl
set(int, int, Double) SparseDoubleMatrix
set(int, int, Double) SparseRaggedDoubleMatrix
set(int, int, String) StringMatrix
set(int, int) Point
setAnova(GenericAnovaResult) LinearModelSummary
setBaseline(String, String) DesignMatrix
setByKeys(R, C, double[]) CompressedBitMatrix
setByKeys(R, C, Double) DoubleMatrix
setByKeys(R, C, Integer) IntegerMatrix
setByKeys(R, C, V) Matrix2D
setByKeys(R, C, V) ObjectMatrixImpl
setByKeys(R, C, String) StringMatrix
setCellSize(Dimension) MatrixDisplay
setColNameMap(Map<C, String>) MatrixWriter
Use to customize the labels instead of relying on the toString method of the column object
setColor(int, int, Color) ColorMatrix
setColorMap(Color[]) ColorMatrix
setColorMap(Color[]) JGradientBar
setColorMap(Color[]) MatrixDisplay
setColumnName(C, int) AbstractMatrix
setColumnName(C, int) Matrix2D
Add a column name associated with an index.
setColumnNames(List<C>) AbstractMatrix
setColumnNames(List<C>) AbstractMatrix3D
setColumnNames(List<C>) Matrix2D
setColumnNames(List<C>) Matrix3D
setContents(T) BinaryTreeNode
setDelimiter(String) StringConverter
setDisplayRange(double, double) ColorMatrix
Standardized display range
setDisplayRange(double, double) MatrixDisplay
setExactMatch(boolean) AnnotatorResponse
setExactSynonym(boolean) AnnotatorResponse
setFilterNames(Set<R>, boolean) RowNameFilter
setFixed(boolean) CorrelationEffectMetaAnalysis
setFlagMatrix(StringMatrix<R, C>) RowAbsentFilter
setFormula(HSSFSheet, int, int, String) ExcelUtil
setGraph(DirectedGraph<K, V>) DirectedGraphNode
setHighCut(double) AbstractLevelFilter
Set the high threshold for removal.
setHighCut(double, boolean) AbstractLevelFilter
setIndexFrom(Integer) AnnotatorResponse
setIndexTo(Integer) AnnotatorResponse
setItem(V) AbstractGraphNode
setItem(V) GraphNode
Set the contents of the node.
setKeepMarginal(boolean) RowAbsentFilter
setKey(String) LinearModelSummary
setKey(Object) AnovaResult
setLabels(double, double) JGradientBar
setLabelsVisible(boolean) MatrixDisplay
If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
setLeft(BinaryTreeNode<T>) BinaryTreeNode
setLowCut(double) AbstractLevelFilter
Set the low threshold for removal.
setLowCut(double, boolean) AbstractLevelFilter
setMapToMatrix(StringToStringSetMap) StringToStringSetMap
setMatchType(String) AnnotatorResponse
setMatrix(ColorMatrix<R, C>) MatrixDisplay
setMaxColumnLength(int) MatrixDisplay
setMaxFractionRemoved(double) RowMissingFilter
Set the maximum fraction of rows which will be removed from the data set.
setMethod(int) RowLevelFilter
Choose the method that will be used for filtering.
setMinPresentCount(int) RowAbsentFilter
setMinPresentCount(int) RowMissingFilter
Set the minimum number of values that must be present in each row.
setMinPresentFraction(double) RowAbsentFilter
setMinPresentFraction(double) RowMissingFilter
setObj(int, int, Integer) IntegerMatrix
setObject(ChainedStatementObject) ChainedStatement
setOntologyUsed(String) AnnotatorResponse
setPriorDof(Double) LinearModelSummary
setQuick(int, int, int, double) DenseDouble3dMatrix
setQuick(int, int, int, double) DoubleMatrix3D
setQuick(int, double) RCDoubleMatrix1D
setRemoveAllNegative(boolean) RowLevelFilter
Set the filter to remove all rows that have only negative values.
setRight(BinaryTreeNode<T>) BinaryTreeNode
setRow(int, double[]) ColorMatrix
Changes values in a row, clipping if there are more values than columns.
setRowHeight(int) MatrixDisplay
setRowKeys(int[]) ColorMatrix
setRowKeys(int[]) MatrixDisplay
setRowName(R, int) AbstractMatrix
setRowName(R, int) Matrix2D
Add a row name associated with a row index.
setRowNameMap(Map<R, String>) MatrixWriter
Use to customize the labels instead of relying on the toString method of the row object
setRowNames(List<R>) AbstractMatrix
setRowNames(List<R>) AbstractMatrix3D
setRowNames(List<R>) Matrix2D
setRowNames(List<R>) Matrix3D
setScaleBarVisible(boolean) MatrixDisplay
setSearchQueryUsed(String) AnnotatorResponse
setSep(String) MatrixWriter
setSliceNameMap(Map<?, String>) MatrixWriter
setSliceNames(List<S>) AbstractMatrix3D
setSliceNames(List<S>) Matrix3D
setStandardizedEnabled(boolean) MatrixDisplay
setString(String, Object) Configuration
setTopLeft(String) MatrixWriter
setTopoSortOrder(int) DirectedGraphNode
setTransform(boolean) CorrelationEffectMetaAnalysis
setTxtMatched(String) AnnotatorResponse
setUseAsFraction(boolean) 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) AbstractLevelFilter
setUseLowCutAsFraction(boolean) AbstractLevelFilter
setValue(K, V) AbstractGraphNode
setValue(K, V) GraphNode
Set the key and value associated with this node.
setValue(HSSFSheet, int, int, double) ExcelUtil
setValue(HSSFSheet, int, int, int) ExcelUtil
setValue(HSSFSheet, int, int, String) ExcelUtil
setValueUri(String) AnnotatorResponse
showError(String) StatusDebugLogger
showError(String, Throwable) StatusDebugLogger
showError(Throwable) StatusDebugLogger
showError(String) StatusStderr
showError(String, Throwable) StatusStderr
showError(Throwable) StatusStderr
showError(String) StatusViewer
Print an error status messge.
showError(String, Throwable) StatusViewer
showError(Throwable) StatusViewer
showProgress(String) StatusDebugLogger
showProgress(String) StatusStderr
showProgress(String) StatusViewer
showStatus(String) StatusDebugLogger
showStatus(String, boolean) StatusDebugLogger
showStatus(String) StatusStderr
showStatus(String, boolean) StatusStderr
showStatus(String) StatusViewer
Print the status to the location appropriate for this application.
showStatus(String, boolean) StatusViewer
showWarning(String) StatusDebugLogger
showWarning(String) StatusStderr
showWarning(String) StatusViewer
sign_j(double, double) Blas
This method implements the FORTRAN sign (not sin) function.
SingularValueDecomposition R ,C > - Class in ubic.basecode.math.linalg
SVD for DoubleMatrix.
SingularValueDecomposition(DoubleMatrix<R, C>) SingularValueDecomposition
size() CountingMap
size() AbstractMatrix
size() CompressedBitMatrix
size() CompressedSparseDoubleMatrix
size() DenseDoubleMatrix
size() FastRowAccessDoubleMatrix
size() IntegerMatrix
size() ObjectMatrixImpl
size() SparseDoubleMatrix
size() SparseRaggedDoubleMatrix
size() StringMatrix
sizeWithoutMissingValues(DoubleMatrix1D) MatrixUtil
sizeWithoutMissingValues(DoubleArrayList) DescriptiveWithMissing
Return the size of the list, ignoring missing values.
skew(DoubleArrayList, double, double) DescriptiveWithMissing
Returns the skew of a data sequence, which is moment(data,3,mean) /
standardDeviation3 .
sliceMap AbstractMatrix3D
sliceNameMap MatrixWriter
sliceNames AbstractMatrix3D
slices() AbstractMatrix3D
slices() DenseDouble3dMatrix
slices() DenseObject3DMatrix
slices() DoubleMatrix3D
slices() Matrix3D
SMALL Constants
SMALLISH Constants
Smooth ubic.basecode.math
Methods for moving averages, loess
Smooth() Smooth
solve(DoubleMatrix2D) QRDecomposition
Least squares solution of A*X = y ; returns X using the stored QR decomposition of A.
sortByColumnAbsoluteValues(int, boolean) DoubleMatrix
sortedKeyList() CountingMap
Returns a list of the keys in this map, sorted by ascending count.
sortedKeyList(boolean) CountingMap
Returns a list of the keys in this map, sorted as specified.
sparse(double[][]) DoubleMatrixFactory
sparse(int, int) DoubleMatrixFactory
SparseDoubleMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
A sparse matrix that knows about row and column names.
SparseDoubleMatrix(double[][]) SparseDoubleMatrix
SparseDoubleMatrix(int, int) SparseDoubleMatrix
SparseDoubleMatrix(int, int, int, double, double) SparseDoubleMatrix
SparseDoubleMatrixReader ubic.basecode.io.reader
SparseDoubleMatrixReader() SparseDoubleMatrixReader
SparseRaggedDoubleMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
A sparse matrix class where the rows are ragged and compressed.
SparseRaggedDoubleMatrix() SparseRaggedDoubleMatrix
SparseRaggedMatrixReader ubic.basecode.io.reader
Best data structure for reading really big, really sparse matrices when a matrix represetation is needed.
SparseRaggedMatrixReader() SparseRaggedMatrixReader
spearmanPvalue(double, int) CorrelationStats
spearmanRankCorrelation(DoubleArrayList) Distance
Convenience function to compute the rank correlation when we just want to know if the values are "in order".
spearmanRankCorrelation(DoubleArrayList, DoubleArrayList) Distance
Spearman Rank Correlation.
SpecFunc ubic.basecode.math
Assorted special functions, primarily concerning probability distributions.
SpecFunc() SpecFunc
spreadsheet CreateSpreadSheet
SpreadSheetFilter ubic.basecode.io.excel
Processing spreadsheet values.
SpreadSheetSchema ubic.basecode.io.excel
This class is to determine what information is put in the spreadsheet and its column position
SpreadSheetSchema() SpreadSheetSchema
SpreadSheetSchema(Map<String, Integer>) SpreadSheetSchema
SQLUtils ubic.basecode.util
SQLUtils() SQLUtils
squeezeVar(DoubleMatrix1D, DoubleMatrix1D, LeastSquaresFit) ModeratedTstat
Ignoring robust and covariate for now
squeezeVariances(DoubleMatrix1D, DoubleMatrix1D, double[]) ModeratedTstat
ST AffymetrixProbeNameFilter
Filter probes that contain the '_st' (sense strand) tag
standardize() 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) DescriptiveWithMissing
Standardize.
standardize(DoubleArrayList, double, double) DescriptiveWithMissing
Modifies a data sequence to be standardized.
standardize(DoubleMatrix<R, C>) MatrixStats
Scale the rows of the matrix; returns a new matrix.
startInitializationThread(boolean, boolean) AbstractOntologyService
startInitializationThread(boolean, boolean) OntologyService
Start the initialization thread.
Stats ubic.basecode.math
Miscellaneous functions used for statistical analysis.
StatusDebugLogger ubic.basecode.util
StatusDebugLogger() StatusDebugLogger
StatusStderr ubic.basecode.util
Prints status info to stderr
StatusStderr() StatusStderr
StatusViewer ubic.basecode.util
Intended use is to display 'status' information or other messages to users in a non-disruptive fashion (though the
actual use is up to the implementer).
stepSize() Histogram
stringArrayToBytes(Object[]) ByteArrayConverter
Note that this method cannot differentiate between empty strings and null strings.
stringArrayToDoubles(String[]) StringConverter
StringConverter ubic.basecode.io
StringConverter() StringConverter
StringDistance ubic.basecode.math
StringDistance() StringDistance
stringEval(String) AbstractRClient
stringEval(String) RClient
Evaluate any command and return a string
stringListEval(String) AbstractRClient
stringListEval(String) RClient
StringMatrix R ,C > - Class in ubic.basecode.dataStructure.matrix
A NamedMatrix containing String objects.
StringMatrix(int, int) StringMatrix
StringMatrixReader ubic.basecode.io.reader
Reader for basecode.dataStructure.matrix.StringMatrix
StringMatrixReader() StringMatrixReader
stringPixelWidth(String, FontMetrics) Util
stringsToFile(Collection<String>, File) FileTools
Outputs a many strings to a file, one line at a time.
stringsToFile(Collection<String>, File, boolean) FileTools
Outputs many strings to a file, one line at a time.
stringsToFile(Collection<String>, String) FileTools
Outputs a many strings to a file, one line at a time.
stringToDoubles(String) StringConverter
stringToFile(String, File) FileTools
Outputs a string to a file.
stringToFile(String, File, boolean) FileTools
Outputs a string to a file, one line at a time.
StringToStringSetMap ubic.basecode.dataStructure
Implemented to store string based many to many relationships.
StringToStringSetMap() StringToStringSetMap
StringToStringSetMap(Map<String, Set<String>>) StringToStringSetMap
StringUtil ubic.basecode.util
StringUtil() StringUtil
stripByCriterion(DoubleMatrix1D, DoubleFunction<Boolean>) MatrixUtil
stripInvalidCharacters(String) OntologySearch
Will remove characters that jena is unable to parse.
stripNegative(DoubleMatrix1D) MatrixUtil
stripNonOK(DoubleMatrix1D, BooleanArrayList) MatrixUtil
subset(int, int, int, int) CompressedBitMatrix
subset(int, int, int, int) ObjectMatrix
subset(int, int, int, int) ObjectMatrixImpl
subset(int, int, int, int) StringMatrix
subsetColumns(List<C>) CompressedBitMatrix
subsetColumns(List<C>) CompressedSparseDoubleMatrix
subsetColumns(List<C>) DenseDoubleMatrix
subsetColumns(List<C>) DoubleMatrix
Create a copy of this matrix with only the selected columns, in the selected order.
subsetColumns(List<C>) FastRowAccessDoubleMatrix
subsetColumns(List<C>) ObjectMatrix
subsetColumns(List<C>) ObjectMatrixImpl
subsetColumns(List<C>) SparseDoubleMatrix
subsetColumns(List<C>) SparseRaggedDoubleMatrix
subsetColumns(List<C>) StringMatrix
subsetRows(List<R>) CompressedSparseDoubleMatrix
subsetRows(List<R>) DenseDoubleMatrix
subsetRows(List<R>) DoubleMatrix
Create a copy of this matrix with only the selected rows, in the selected order.
subsetRows(List<R>) FastRowAccessDoubleMatrix
subsetRows(List<R>) SparseDoubleMatrix
subsetRows(List<R>) SparseRaggedDoubleMatrix
suffixWeightedHammingDistance(String, String, double) StringDistance
sum(DoubleArrayList) DescriptiveWithMissing
Returns the sum of a data sequence.
sumArray(int[]) MathUtil
summarize() LeastSquaresFit
summarize(boolean) LeastSquaresFit
summarize(int) LeastSquaresFit
Compute and organize the various summary statistics for a fit.
summarizeByKeys(boolean) LeastSquaresFit
sumOfInversions(DoubleArrayList, int, int) DescriptiveWithMissing
Returns the sum of inversions of a data sequence, which is Sum( 1.0 /
data[i]) .
sumOfLogarithms(DoubleArrayList, int, int) DescriptiveWithMissing
Returns the sum of logarithms of a data sequence, which is Sum(
Log(data[i]) .
sumOfPowerDeviations(DoubleArrayList, int, double) DescriptiveWithMissing
Returns Sum( (data[i]-c)k ) ; optimized for common parameters like c == 0.0 and/or
k == -2 .. 4 .
sumOfPowerDeviations(DoubleArrayList, int, double, int, int) DescriptiveWithMissing
Returns Sum( (data[i]-c)k ) for all i = from ..
sumOfPowers(DoubleArrayList, int) DescriptiveWithMissing
Returns the sum of powers of a data sequence, which is Sum (
data[i]k ) .
sumOfSquaredDeviations(DoubleArrayList) DescriptiveWithMissing
Compute the sum of the squared deviations from the mean of a data sequence.
sumOfSquares(DoubleArrayList) DescriptiveWithMissing
Returns the sum of squares of a data sequence.
sumOfSquares(DoubleMatrix<R, C>) MatrixRowStats
Calculates the sum of squares for each row of a matrix
sums(DoubleMatrix<R, C>) MatrixRowStats
Calculate the sums of a matrix's rows.