Package ubic.gemma.core.util.matrix
package ubic.gemma.core.util.matrix
Labelled-axis matrix types ported in-tree from baseCode's
ubic.basecode.dataStructure.matrix subsystem as part of the Phase 3
baseCode retirement (see BASECODE_MATRIX_RECCE.md and
BASECODE_DEP_AUDIT.md).
The 14 reachable classes (and the PrimitiveMatrix interface they
depend on) are pulled in verbatim with only their package declaration
rewritten and the Constants import rewired to
Constants. The 3D variants,
CompressedBitMatrix, RCDoubleMatrix1D, and
SparseRaggedDoubleMatrix were dropped — no Gemma consumers.
These classes are a generic, named-axis veneer over cern.colt
(with one MTJ-backed variant). Colt and MTJ stay as direct Gemma deps;
Gemma already uses both directly outside this package.
- Author:
- pavlidis
-
ClassDescriptionAbstractMatrix<R,
C, V> Abstract class representing an object that can read in aMatrix2Dfrom a file.Supports sparse matrices (where sparse means most values are zero, not that they are missing).DenseDoubleMatrix<R,C> A dense matrix of doubles that knows about row and column names.Use this class when fast iteration over the matrix is of primary interest.DoubleMatrix<R,C> Abstract base class for 2D matrices of double values with named columns and rows.Use this factory to create matrices of type selected at runtime (String parameterization only)Reader forDoubleMatrix.Dense 2D matrix implementation designed for very fast access of entire rows.IntegerMatrix<R,C> Matrix2D<R,C, V> Represents a matrix with index columns and rows.MatrixWriter<R,C> Class for writing matrices to diskObjectMatrix<R,C, V> ObjectMatrixImpl<R,C, V> Matrix that can hold any type of objectPrimitiveMatrix<R,C, V> Matrix that holds primitives, with an available object representation of the values.SparseDoubleMatrix<R,C> A sparse matrix that knows about row and column names.StringMatrix<R,C> A NamedMatrix containing String objects.Reader forStringMatrix.