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## 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).

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