Uses of Interface
baseCode.dataStructure.matrix.NamedMatrix

Packages that use NamedMatrix

baseCode.dataFilter
baseCode.dataStructure.matrix
baseCode.io.reader

Uses of NamedMatrix in baseCode.dataFilter

Methods in baseCode.dataFilter that return NamedMatrix

protected NamedMatrix	AbstractFilter.getOutputMatrix(NamedMatrix data, int numRows, int numCols)
NamedMatrix	AffymetrixProbeNameFilter.filter(NamedMatrix data)
NamedMatrix	Filter.filter(NamedMatrix data) Filter the data
NamedMatrix	RowNameFilter.filter(NamedMatrix data) Filter according to row names.
NamedMatrix	ItemLevelFilter.filter(NamedMatrix data)
NamedMatrix	RowAbsentFilter.filter(NamedMatrix data) The data is going to be filtered in accordance to strings in 'flags'.
NamedMatrix	RowAffyNameFilter.filter(NamedMatrix data)
NamedMatrix	RowLevelFilter.filter(NamedMatrix data)
NamedMatrix	RowMissingFilter.filter(NamedMatrix data)

Methods in baseCode.dataFilter with parameters of type NamedMatrix

protected NamedMatrix	AbstractFilter.getOutputMatrix(NamedMatrix data, int numRows, int numCols)
NamedMatrix	AffymetrixProbeNameFilter.filter(NamedMatrix data)
NamedMatrix	Filter.filter(NamedMatrix data) Filter the data
NamedMatrix	RowNameFilter.filter(NamedMatrix data) Filter according to row names.
NamedMatrix	ItemLevelFilter.filter(NamedMatrix data)
NamedMatrix	RowAbsentFilter.filter(NamedMatrix data) The data is going to be filtered in accordance to strings in 'flags'.
NamedMatrix	RowAffyNameFilter.filter(NamedMatrix data)
NamedMatrix	RowLevelFilter.filter(NamedMatrix data)
NamedMatrix	RowMissingFilter.filter(NamedMatrix data)

Uses of NamedMatrix in baseCode.dataStructure.matrix

Classes in baseCode.dataStructure.matrix that implement NamedMatrix

class	AbstractNamedDoubleMatrix
class	AbstractNamedMatrix Copyright (c) 2004 Columbia University
class	DenseDoubleMatrix2DNamed A matrix of doubles that knows about row and column names.
class	SparseDoubleMatrix2DNamed Title: SparseDoubleMatrix2DNamed
class	SparseRaggedDoubleMatrix2DNamed A sparse matrix class where the rows are ragged and compressed.
class	StringMatrix2DNamed A NamedMatrix containing String objects.

Uses of NamedMatrix in baseCode.io.reader

Methods in baseCode.io.reader that return NamedMatrix

abstract NamedMatrix	AbstractNamedMatrixReader.read(java.lang.String filename)
abstract NamedMatrix	AbstractNamedMatrixReader.read(java.io.InputStream stream)
abstract NamedMatrix	AbstractNamedMatrixReader.readOneRow(java.io.BufferedReader dis)
NamedMatrix	DoubleMatrixReader.read(java.lang.String filename)
NamedMatrix	DoubleMatrixReader.read(java.io.InputStream stream)
NamedMatrix	DoubleMatrixReader.read(java.io.InputStream stream, java.util.Set wantedRowNames)
NamedMatrix	DoubleMatrixReader.read(java.io.InputStream stream, java.util.Set wantedRowNames, boolean createEmptyRows)
NamedMatrix	DoubleMatrixReader.readOneRow(java.io.BufferedReader dis)
NamedMatrix	DoubleMatrixReader.read(java.lang.String filename, java.util.Set wantedRowNames) Read a matrix from a file, subject to filtering criteria.
NamedMatrix	StringMatrixReader.read(java.lang.String filename)
NamedMatrix	StringMatrixReader.read(java.io.InputStream stream) Missing values are entered as an empty string.
NamedMatrix	StringMatrixReader.readOneRow(java.io.BufferedReader dis)
NamedMatrix	SparseDoubleMatrixReader.read(java.lang.String filename)
NamedMatrix	SparseDoubleMatrixReader.read(java.io.InputStream stream)
NamedMatrix	SparseDoubleMatrixReader.read(java.lang.String filename, java.util.Set wantedRowNames) Read a matrix from a file, subject to filtering criteria.
NamedMatrix	SparseDoubleMatrixReader.readJW(java.io.InputStream stream) Read a sparse matrix in "JW" (Jason Weston) format.
NamedMatrix	SparseDoubleMatrixReader.read(java.io.InputStream stream, java.util.Set wantedRowNames) Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
NamedMatrix	SparseDoubleMatrixReader.readOneRow(java.io.BufferedReader dis)
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.readFromAdjList(java.lang.String fileName) Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.readFromAdjList(java.io.InputStream stream)
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.read(java.lang.String fileName)
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.readOneRow(java.io.BufferedReader dis)
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.readOneRow(java.io.BufferedReader dis, int offset) Use this to read one row from a matrix (JW format).
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.read(java.io.InputStream stream) Read an entire sparse matrix from a stream (JW format).
NamedMatrix	SparseRaggedDouble2DNamedMatrixReader.read(java.io.InputStream stream, int offset) Read an entire sparse matrix from a stream (JW format).