Package ubic.basecode.dataStructure.matrix

Class RCDoubleMatrix1D

  • All Implemented Interfaces:
    Serializable, Cloneable
    public class RCDoubleMatrix1D
extends cern.colt.matrix.DoubleMatrix1D
    A row-compressed 1D matrix. The only deviation from the contract of DoubleMatrix1D is in apply(), which only operates on the non-empty (0) elements. This implementation has a highly optimized dot product computer. If you need to compute the dot product of a RCDoubleMatrix1D with another DoubleMatrix1D, call zDotProduct on this, not on the other. This is because getQuick() and setQuick() are not very fast for this.
    Author:
    pavlidis
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected cern.colt.list.IntArrayList indexes  
      protected cern.colt.list.DoubleArrayList values  

      • Fields inherited from class cern.colt.matrix.impl.AbstractMatrix1D

        size, stride, zero

      • Fields inherited from class cern.colt.matrix.impl.AbstractMatrix

        isNoView

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      cern.colt.matrix.DoubleMatrix1D assign​(double[] v)  
      cern.colt.matrix.DoubleMatrix1D assign​(cern.colt.function.DoubleFunction function)
      WARNING this only assigns to the non-empty values, for performance reasons.
      double get​(int index)  
      double getQuick​(int index)  
      cern.colt.matrix.DoubleMatrix1D like​(int s)  
      cern.colt.matrix.DoubleMatrix2D like2D​(int rows, int columns)  
      void setQuick​(int column, double value)  
      String toString()  
      protected cern.colt.matrix.DoubleMatrix1D viewSelectionLike​(int[] offsets)  
      double zDotProduct​(cern.colt.matrix.DoubleMatrix1D y)  
      double zSum()  

      • Methods inherited from class cern.colt.matrix.DoubleMatrix1D

        aggregate, aggregate, assign, assign, assign, assign, cardinality, cardinality, copy, equals, equals, getContent, getNonZeros, getNonZeros, haveSharedCells, haveSharedCellsRaw, like, set, swap, toArray, toArray, view, viewFlip, viewPart, viewSelection, viewSelection, viewSorted, viewStrides, zDotProduct, zDotProduct, zDotProduct

      • Methods inherited from class cern.colt.matrix.impl.AbstractMatrix1D

        _offset, _rank, checkIndex, checkIndexes, checkRange, checkSize, checkSize, index, setUp, setUp, size, stride, toStringShort, vFlip, vPart, vStrides

      • Methods inherited from class cern.colt.matrix.impl.AbstractMatrix

        ensureCapacity, isView, trimToSize

      • Methods inherited from class cern.colt.PersistentObject

        clone

    • Field Detail

      • indexes

        protected cern.colt.list.IntArrayList indexes

      • values

        protected cern.colt.list.DoubleArrayList values

    • Constructor Detail

      • RCDoubleMatrix1D

        public RCDoubleMatrix1D​(double[] values)
        Parameters:
        values -

      • RCDoubleMatrix1D

        public RCDoubleMatrix1D​(int length)
        Parameters:
        length -

      • RCDoubleMatrix1D

        public RCDoubleMatrix1D​(cern.colt.list.IntArrayList indexes,
                        cern.colt.list.DoubleArrayList values)
        Parameters:
        indexes - These MUST be in sorted order.
        values - These MuST be in the same order as the indexes, meaning that indexes[0] is the column for values[0].

    • Method Detail

      • assign

        public cern.colt.matrix.DoubleMatrix1D assign​(double[] v)
        Overrides:
        assign in class cern.colt.matrix.DoubleMatrix1D

      • assign

        public cern.colt.matrix.DoubleMatrix1D assign​(cern.colt.function.DoubleFunction function)
        WARNING this only assigns to the non-empty values, for performance reasons. If you need to assign to any index, you have to use another way.
        Overrides:
        assign in class cern.colt.matrix.DoubleMatrix1D
        See Also:
        DoubleMatrix1D.assign(cern.colt.function.DoubleFunction)

      • get

        public double get​(int index)
        Overrides:
        get in class cern.colt.matrix.DoubleMatrix1D

      • getQuick

        public double getQuick​(int index)
        Specified by:
        getQuick in class cern.colt.matrix.DoubleMatrix1D

      • like

        public cern.colt.matrix.DoubleMatrix1D like​(int s)
        Specified by:
        like in class cern.colt.matrix.DoubleMatrix1D

      • like2D

        public cern.colt.matrix.DoubleMatrix2D like2D​(int rows,
                                              int columns)
        Specified by:
        like2D in class cern.colt.matrix.DoubleMatrix1D

      • setQuick

        public void setQuick​(int column,
                     double value)
        Specified by:
        setQuick in class cern.colt.matrix.DoubleMatrix1D

      • toString

        public String toString()
        Overrides:
        toString in class cern.colt.matrix.DoubleMatrix1D

      • zDotProduct

        public double zDotProduct​(cern.colt.matrix.DoubleMatrix1D y)
        Overrides:
        zDotProduct in class cern.colt.matrix.DoubleMatrix1D

      • zSum

        public double zSum()
        Overrides:
        zSum in class cern.colt.matrix.DoubleMatrix1D

      • viewSelectionLike

        protected cern.colt.matrix.DoubleMatrix1D viewSelectionLike​(int[] offsets)
        Specified by:
        viewSelectionLike in class cern.colt.matrix.DoubleMatrix1D