if ( i == startRow ) {
                    C colName = this.getColName( j );
                    returnval.setColumnName( colName, j );
                }
                returnval.set( k, j, this.get( i, j ) );
            }
            k++;
        }
        return returnval;
    }

    @Override
    public boolean isMissing( int i, int j ) {
        return Double.isNaN( get( i, j ) );
    }

    @Override
    public int rows() {
        return matrix.rows();
    }

    @Override
    public void set( int row, int column, Double value ) {
        matrix.set( row, column, value );
    }

    /**
     * @return int
     * @see AbstractMatrix2D#size()
     */
    @Override
    public int size() {
        return matrix.size();
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.basecode.dataStructure.matrix.DoubleMatrix#subsetColumns(java.util.List)
     */
    @Override
    public DoubleMatrix<R, C> subsetColumns( List<C> columns ) {

        DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( this.rows(), columns.size() );
        returnval.setRowNames( this.getRowNames() );
        for ( int i = 0; i < this.rows(); i++ ) {
            int currentColumn = 0;
            for ( C c : columns ) {
                int j = this.getColIndexByName( c );

                returnval.set( i, currentColumn, this.get( i, j ) );

                if ( i == 0 ) {
                    returnval.setColumnName( c, currentColumn );
                }

                currentColumn++;

            }

        }
        return returnval;
    }

    @Override
    public DoubleMatrix<R, C> subsetRows( List<R> rowNames ) {

        DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( rowNames.size(), this.columns() );

if ( rowName != null ) returnval.addRowName( rowName );
                }
                returnval.set( j, k, this.get( j, i ) );
            }
            k++;
        }
        return returnval;
    }

    /*
     * (non-Javadoc)
     * 
     * @see basecode.dataStructure.matrix.DoubleMatrixNamed#getColumn(int)
     */
    @Override
    public double[] getColumn( int col ) {
        double[] result = new double[rows()];
        for ( int i = 0; i < rows(); i++ ) {
            result[i] = get( i, col );
        }
        return result;
    }

    /**
     * Converts to a String that can be read by read.table in R, using default parameters
     * 
     * @return java.lang.String
     */
    /*
     * public String toRReadTableString() { Format nf = new Format( "%.4g" ); StringBuffer result = new StringBuffer(
     * this.rows() * this.columns() ); if ( this.hasColNames() ) { for ( int i = 0; i < this.columns(); i++ ) {
     * result.append( "\"" + this.getColName( i ) +"\" "); System.out.println("\"" + this.getColName( i ) +"\" "); }
     * result.append( "\n" ); } for ( int i = 0; i < this.rows(); i++ ) { if ( this.hasRowNames() ) { result.append("\""
     * + this.getRowName( i ) + "\"" ); } for ( int j = 0; j < this.columns(); j++ ) { if ( Double.isNaN( this.get( i, j
     * ) ) ) { result.append( " NA" ); } else { result.append( " " + nf.format( this.get( i, j ) ) ); } } result.append(
     * "\n" ); } return result.toString(); }
     */

    @Override
    public Double getObject( int row, int col ) {
        return new Double( get( row, col ) );
    }

    /**
     * Return a reference to a specific row.
     * 
     * @param row int
     * @return double[]
     */
    @Override
    public double[] getRow( int row ) {
        return viewRow( row ).toArray();
    }

    /*
     * (non-Javadoc)
     * 
     * @see basecode.dataStructure.matrix.AbstractNamedDoubleMatrix#getRowArrayList(int)
     */
    @Override
    public DoubleArrayList getRowArrayList( int i ) {
        return new DoubleArrayList( getRow( i ) );
    }

    /**
     * Return a reference to a specific row.
     * 
     * @param s String
     * @return double[]
     */
    @Override
    public double[] getRowByName( R s ) {
        return getRow( getRowIndexByName( s ) );
    }

    @Override
    public Double[] getRowObj( int row ) {
        Double[] result = new Double[columns()];
        for ( int i = 0; i < columns(); i++ ) {
            result[i] = new Double( get( row, i ) );
        }
        return result;
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.basecode.dataStructure.matrix.Matrix2D#getRowRange(int, int)
     */
    @Override
    public DoubleMatrix<R, C> getRowRange( int startRow, int endRow ) {
        super.checkRowRange( startRow, endRow );

        DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( 1 + endRow - startRow, this.columns() );

DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( this.rows(), this.columns() );

        for ( int i = 0; i < this.rows(); i++ ) {
            returnval.setRowName( this.getRowName( i ), i );
            for ( int j = 0; j < this.columns(); j++ ) {
                if ( i == 0 ) {
                    returnval.setColumnName( this.getColName( j ), j );
                }
                returnval.set( i, j, this.get( i, j ) );
            }
        }
        return returnval;

    }

    /**
     * @param row
     * @param column
     * @return
     */
    @Override
    public double get( int row, int column ) {
        return matrix.get( row, column );
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.basecode.dataStructure.matrix.NamedPrimitiveMatrix#getColObj(int)
     */
    @Override
    public Double[] getColObj( int col ) {
        Double[] result = new Double[rows()];
        for ( int i = 0; i < rows(); i++ ) {
            result[i] = new Double( get( i, col ) );
        }
        return result;
    }

    @Override
    public DoubleMatrix<R, C> getColRange( int startCol, int endCol ) {
        super.checkColRange( startCol, endCol );

        DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( this.rows(), 1 + endCol - startCol );

DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( this.rows(), 1 + endCol - startCol );
        int k = 0;
        for ( int i = startCol; i <= endCol; i++ ) {
            C colName = this.getColName( i );
            if ( colName != null ) {
                returnval.setColumnName( colName, i );
            }
            for ( int j = 0, m = this.rows(); j < m; j++ ) {
                if ( i == startCol ) {
                    R rowName = this.getRowName( j );
                    returnval.setRowName( rowName, j );
                }
                returnval.set( j, k, this.get( j, i ) );
            }
            k++;
        }
        return returnval;
    }

    /*
     * (non-Javadoc)
     * 
     * @see basecode.dataStructure.matrix.DoubleMatrixNamed#getColumn(int)
     */
    @Override
    public double[] getColumn( int col ) {
        double[] result = new double[rows()];
        for ( int i = 0; i < rows(); i++ ) {
            result[i] = get( i, col );
        }
        return result;
    }

    @Override
    public Double getObject( int row, int col ) {
        return new Double( get( row, col ) );
    }

    /**
     * Return a reference to a specific row.
     * 
     * @param row int
     * @return double[]
     */
    @Override
    public double[] getRow( int row ) {

return matrix.size();
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.basecode.dataStructure.matrix.DoubleMatrix#subsetColumns(java.util.List)
     */
    @Override
    public DoubleMatrix<R, C> subsetColumns( List<C> columns ) {

        DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( this.rows(), columns.size() );
        returnval.setRowNames( this.getRowNames() );
        for ( int i = 0; i < this.rows(); i++ ) {
            int currentColumn = 0;
            for ( C c : columns ) {
                int j = this.getColIndexByName( c );

                returnval.set( i, currentColumn, this.get( i, j ) );

                if ( i == 0 ) {
                    returnval.setColumnName( c, currentColumn );
                }

                currentColumn++;

            }

        }
        return returnval;
    }

    @Override
    public DoubleMatrix<R, C> subsetRows( List<R> rowNames ) {

        DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( rowNames.size(), this.columns() );

return matrix.numColumns() * matrix.numRows();
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.basecode.dataStructure.matrix.DoubleMatrix#subsetColumns(java.util.List)
     */
    @Override
    public DoubleMatrix<R, C> subsetColumns( List<C> columns ) {

        DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( this.rows(), columns.size() );
        returnval.setRowNames( this.getRowNames() );
        for ( int i = 0; i < this.rows(); i++ ) {
            int currentColumn = 0;
            for ( C c : columns ) {
                int j = this.getColIndexByName( c );

                returnval.set( i, currentColumn, this.get( i, j ) );

                if ( i == 0 ) {
                    returnval.setColumnName( c, currentColumn );
                }

                currentColumn++;

            }

        }
        return returnval;
    }

    @Override
    public DoubleMatrix<R, C> subsetRows( List<R> rowNames ) {
        DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( rowNames.size(), this.columns() );

return Objects.compare( this, other, comparator );
    }

    @Override
    public boolean equals( Object obj ) {
        if ( this == obj ) return true;
        if ( obj == null ) return false;
        if ( getClass() != obj.getClass() ) return false;
        final OntologyResource other = ( OntologyResource ) obj;
        if ( getLabel() == null ) {
            if ( other.getLabel() != null ) return false;
        } else if ( !getLabel().equals( other.getLabel() ) ) return false;
        if ( getUri() == null ) {
            if ( other.getUri() != null ) return false;
        } else if ( !getUri().equals( other.getUri() ) ) return false;
        return true;
    }

    @Override
    public int hashCode() {
        return Objects.hash( getLabel(), getUri() );
    }

DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( this.rows(), this.columns() );

        for ( int i = 0; i < this.rows(); i++ ) {
            returnval.setRowName( this.getRowName( i ), i );
            for ( int j = 0; j < this.columns(); j++ ) {
                if ( i == 0 ) {
                    returnval.setColumnName( this.getColName( j ), j );
                }
                returnval.set( i, j, this.get( i, j ) );
            }
        }
        return returnval;

    }

    /**
     * @param row
     * @param column
     * @return
     */
    @Override
    public double get( int row, int column ) {

if ( rowName != null ) returnval.addRowName( rowName );
                }
                returnval.set( j, k, this.get( j, i ) );
            }
            k++;
        }
        return returnval;
    }

    /*
     * (non-Javadoc)
     * 
     * @see basecode.dataStructure.matrix.DoubleMatrixNamed#getColumn(int)
     */
    @Override
    public double[] getColumn( int col ) {
        double[] result = new double[rows()];
        for ( int i = 0; i < rows(); i++ ) {
            result[i] = get( i, col );
        }
        return result;
    }

    /**
     * Converts to a String that can be read by read.table in R, using default parameters
     * 
     * @return java.lang.String
     */
    /*
     * public String toRReadTableString() { Format nf = new Format( "%.4g" ); StringBuffer result = new StringBuffer(
     * this.rows() * this.columns() ); if ( this.hasColNames() ) { for ( int i = 0; i < this.columns(); i++ ) {
     * result.append( "\"" + this.getColName( i ) +"\" "); System.out.println("\"" + this.getColName( i ) +"\" "); }
     * result.append( "\n" ); } for ( int i = 0; i < this.rows(); i++ ) { if ( this.hasRowNames() ) { result.append("\""
     * + this.getRowName( i ) + "\"" ); } for ( int j = 0; j < this.columns(); j++ ) { if ( Double.isNaN( this.get( i, j
     * ) ) ) { result.append( " NA" ); } else { result.append( " " + nf.format( this.get( i, j ) ) ); } } result.append(
     * "\n" ); } return result.toString(); }
     */

    @Override
    public Double getObject( int row, int col ) {
        return new Double( get( row, col ) );
    }

    /**
     * Return a reference to a specific row.
     * 
     * @param row int
     * @return double[]
     */
    @Override
    public double[] getRow( int row ) {

DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( this.rows(), columns.size() );
        returnval.setRowNames( this.getRowNames() );
        for ( int i = 0; i < this.rows(); i++ ) {
            int currentColumn = 0;
            for ( C c : columns ) {
                int j = this.getColIndexByName( c );

                returnval.set( i, currentColumn, this.get( i, j ) );

                if ( i == 0 ) {
                    returnval.setColumnName( c, currentColumn );
                }

                currentColumn++;

            }

        }
        return returnval;
    }

assert this.assign.isEmpty() || this.assign.size() == this.coefficients.rows() : assign.size()
                + " != # coefficients " + this.coefficients.rows();

        assert this.coefficients.rows() == A.columns();

        // It is somewhat wasteful to hold on to this.
        this.fitted = solver.transpose(MatrixUtil.multWithMissing(A, coefficients));

        if (this.hasMissing) {
            MatrixUtil.maskMissing(b, fitted);
        }

        this.residuals = b.copy().assign(fitted, Functions.minus);
    }