Package ubic.basecode.dataStructure.matrix

Class DenseDoubleMatrix<R,C>

java.lang.Object
ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,Double>
ubic.basecode.dataStructure.matrix.DoubleMatrix<R,C>
ubic.basecode.dataStructure.matrix.DenseDoubleMatrix<R,C>
All Implemented Interfaces:
Serializable, Matrix2D<R,C,Double>, PrimitiveMatrix<R,C,Double>
public class DenseDoubleMatrix<R,C> extends DoubleMatrix<R,C>
A dense matrix of doubles that knows about row and column names.
Author:
Paul Pavlidis
See Also:

  • Constructor Details

    • DenseDoubleMatrix

      public DenseDoubleMatrix(double[][] T)
      Parameters:
      T - double[][]

    • DenseDoubleMatrix

      public DenseDoubleMatrix(int rows, int cols)
      Parameters:
      rows - int
      cols - int

  • Method Details

    • asArray

      public double[][] asArray()
      Specified by:
      asArray in class DoubleMatrix<R,C>
      Returns:
      double[][]

    • columns

      public int columns()
      Description copied from interface: Matrix2D
      Get the number of columns the matrix has.
      Returns:
      int

    • copy

      public DoubleMatrix<R,C> copy()
      Description copied from class: DoubleMatrix
      Create a deep copy of this
      Specified by:
      copy in class DoubleMatrix<R,C>
      Returns:
      basecode.dataStructure.DenseDoubleMatrix2DNamed

    • get

      public double get(int row, int column)
      Specified by:
      get in class DoubleMatrix<R,C>
      Parameters:
      row - int
      column - int
      Returns:
      See Also:

    • getColByName

      public double[] getColByName(C s)
      Return a copy of a given column.
      Parameters:
      col - int
      Returns:
      double[]

    • getColObj

      public Double[] getColObj(int col)
      Parameters:
      col -
      Returns:

    • getColRange

      public DoubleMatrix<R,C> getColRange(int startCol, int endCol)
      Specified by:
      getColRange in class DoubleMatrix<R,C>
      Parameters:
      startCol - inclusive, numbered from zero
      endCol - inclusive, numbered from zero
      Returns:
      new matrix with just the requested range of columns from this

    • getColumn

      public double[] getColumn(int col)
      Specified by:
      getColumn in class DoubleMatrix<R,C>

    • getObject

      public Double getObject(int row, int col)
      Converts to a String that can be read by read.table in R, using default parameters
      Parameters:
      row -
      col -
      Returns:
      java.lang.String

    • getRow

      public double[] getRow(int row)
      Return a reference to a specific row.
      Specified by:
      getRow in class DoubleMatrix<R,C>
      Parameters:
      row - int
      Returns:
      double[]

    • getRowArrayList

      public DoubleArrayList getRowArrayList(int i)
      Specified by:
      getRowArrayList in class DoubleMatrix<R,C>

    • getRowByName

      public double[] getRowByName(R s)
      Return a reference to a specific row.
      Overrides:
      getRowByName in class DoubleMatrix<R,C>
      Parameters:
      s - String
      Returns:
      double[]

    • getRowObj

      public Double[] getRowObj(int row)
      Parameters:
      row -
      Returns:

    • getRowRange

      public DoubleMatrix<R,C> getRowRange(int startRow, int endRow)
      Specified by:
      getRowRange in class DoubleMatrix<R,C>
      Parameters:
      startRow - inclusive, numbered from zero
      endRow - inclusive
      Returns:

    • isMissing

      public boolean isMissing(int i, int j)
      Description copied from interface: Matrix2D
      Check if the value at a given index is missing.
      Parameters:
      i - row
      j - column
      Returns:
      true if the value is missing, false otherwise.

    • rows

      public int rows()
      Description copied from interface: Matrix2D
      Get the number of rows the matrix has
      Returns:
      int

    • set

      public void set(int row, int column, Double value)
      Parameters:
      row -
      column -
      value -

    • size

      public int size()
      Specified by:
      size in class AbstractMatrix<R,C,Double>
      Returns:
      int
      See Also:

    • subsetColumns

      public DoubleMatrix<R,C> subsetColumns(List<C> columns)
      Description copied from class: DoubleMatrix
      Create a copy of this matrix with only the selected columns, in the selected order.
      Specified by:
      subsetColumns in class DoubleMatrix<R,C>
      Parameters:
      columns -
      Returns:

    • subsetRows

      public DoubleMatrix<R,C> subsetRows(List<R> rowNames)
      Description copied from class: DoubleMatrix
      Create a copy of this matrix with only the selected rows, in the selected order.
      Specified by:
      subsetRows in class DoubleMatrix<R,C>
      Parameters:
      rowNames -
      Returns:

    • transpose

      public DoubleMatrix<C,R> transpose()
      Specified by:
      transpose in class DoubleMatrix<R,C>

    • viewColumn

      public DoubleMatrix1D viewColumn(int column)
      Specified by:
      viewColumn in class DoubleMatrix<R,C>
      Parameters:
      column - int
      Returns:
      cern.colt.matrix.DoubleMatrix1D

    • viewRow

      public DoubleMatrix1D viewRow(int row)
      Specified by:
      viewRow in class DoubleMatrix<R,C>
      Parameters:
      row - int
      Returns:
      DoubleMatrix1D
      See Also: