ubic.basecode.graphics

Class ColorMatrix<A,B>

java.lang.Object

ubic.basecode.graphics.ColorMatrix<A,B>

All Implemented Interfaces:

Cloneable

public class ColorMatrix<A,B>
extends Object
implements Cloneable

Creates a color matrix from a matrix of doubles

Author:

Will Braynen

Field Summary

Fields

Modifier and Type	Field and Description
protected Color[]	colorMap
protected Color[][]	colors
protected double	displayMax
protected double	displayMin Min and max values to display, which might not be the actual min and max values in the matrix.
protected DoubleMatrixReader	m_matrixReader
protected int[]	m_rowKeys to be able to sort the rows by an arbitrary key
protected int	m_totalColumns
protected int	m_totalRows
protected double	max
protected DoubleMatrix<A,B>	maxtrix
protected double	min
protected Color	missingColor

Constructor Summary

Constructors

Constructor and Description
ColorMatrix(DoubleMatrix<A,B> matrix)
ColorMatrix(DoubleMatrix<A,B> matrix, Color[] colorMap, Color missingColor)

Method Summary

Modifier and Type	Method and Description
ColorMatrix<A,B>	clone()
protected int[]	createRowKeys() To be able to sort the rows by an arbitrary key.
Color	getColor(int row, int column)
Color[]	getColorMap()
Color[][]	getColors()
int	getColumnCount()
B	getColumnName(int column)
String[]	getColumnNames()
double	getDisplayMax()
double	getDisplayMin()
DoubleMatrix<A,B>	getMatrix()
double	getMax()
DoubleMatrix<A,B>	getMaxtrix()
double	getMin()
Color	getMissingColor()
double[]	getRow(int row)
double[]	getRowByName(A rowName)
int	getRowCount()
int	getRowIndexByName(A rowName)
Object	getRowName(int row)
String[]	getRowNames()
protected int	getTrueRowIndex(int row)
double	getValue(int row, int column)
void	mapValuesToColors()
static <R,C> ColorMatrix<R,C>	newInstance(DoubleMatrix<R,C> matrix)
void	resetRowKeys()
void	setColor(int row, int column, Color newColor)
void	setColorMap(Color[] colorMap)
void	setDisplayRange(double min, double max) Standardized display range
protected void	setRow(int row, double[] values) Changes values in a row, clipping if there are more values than columns.
void	setRowKeys(int[] rowKeys)
void	standardize() Normalizes the elements of a matrix to variance one and mean zero, ignoring missing values todo move this to matrixstats or something.

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

colorMap

protected Color[] colorMap

colors

protected Color[][] colors

displayMax

protected double displayMax

displayMin

protected double displayMin

Min and max values to display, which might not be the actual min and max values in the matrix. For instance, we might want to clip values, or show a bigger color range for equal comparison with other rows or matrices.

m_matrixReader

protected DoubleMatrixReader m_matrixReader

m_rowKeys

protected int[] m_rowKeys

to be able to sort the rows by an arbitrary key

m_totalRows

protected int m_totalRows

m_totalColumns

protected int m_totalColumns

max

protected double max

maxtrix

protected DoubleMatrix<A,B> maxtrix

min

protected double min

missingColor

protected Color missingColor

Constructor Detail

ColorMatrix

public ColorMatrix(DoubleMatrix<A,B> matrix)

ColorMatrix

public ColorMatrix(DoubleMatrix<A,B> matrix,
                   Color[] colorMap,
                   Color missingColor)

Parameters:

matrix - the matrix

colorMap - the simplest color map is one with just two colors: { minColor, maxColor }

missingColor - values missing from the matrix or non-numeric entries will be displayed using this color

Method Detail

newInstance

public static <R,C> ColorMatrix<R,C> newInstance(DoubleMatrix<R,C> matrix)

clone

public ColorMatrix<A,B> clone()

Overrides:

clone in class Object

getColor

public Color getColor(int row,
                      int column)
               throws ArrayIndexOutOfBoundsException

Throws:

ArrayIndexOutOfBoundsException

getColorMap

public Color[] getColorMap()

getColors

public Color[][] getColors()

getColumnCount

public int getColumnCount()

getColumnName

public B getColumnName(int column)
                throws ArrayIndexOutOfBoundsException

Throws:

ArrayIndexOutOfBoundsException

getColumnNames

public String[] getColumnNames()

getDisplayMax

public double getDisplayMax()

getDisplayMin

public double getDisplayMin()

getMatrix

public DoubleMatrix<A,B> getMatrix()

Returns:

a DenseDoubleMatrix2DNamed object

getMax

public double getMax()

getMaxtrix

public DoubleMatrix<A,B> getMaxtrix()

getMin

public double getMin()

getMissingColor

public Color getMissingColor()

getRow

public double[] getRow(int row)
                throws ArrayIndexOutOfBoundsException

Throws:

ArrayIndexOutOfBoundsException

getRowByName

public double[] getRowByName(A rowName)

getRowCount

public int getRowCount()

getRowIndexByName

public int getRowIndexByName(A rowName)

getRowName

public Object getRowName(int row)
                  throws ArrayIndexOutOfBoundsException

Throws:

ArrayIndexOutOfBoundsException

getRowNames

public String[] getRowNames()

getValue

public double getValue(int row,
                       int column)
                throws ArrayIndexOutOfBoundsException

Throws:

ArrayIndexOutOfBoundsException

mapValuesToColors

public void mapValuesToColors()

resetRowKeys

public void resetRowKeys()

setColor

public void setColor(int row,
                     int column,
                     Color newColor)
              throws ArrayIndexOutOfBoundsException

Parameters:

row -

column -

newColor -

Throws:

ArrayIndexOutOfBoundsException

setColorMap

public void setColorMap(Color[] colorMap)
                 throws IllegalArgumentException

Parameters:

colorMap - an array of colors which define the midpoints in the color map; this can be one of the constants defined in the ColorMap class, like ColorMap.REDGREEN_COLORMAP and ColorMap.BLACKBODY_COLORMAP

Throws:

IllegalArgumentException - if the colorMap array argument contains less than two colors.

setDisplayRange

public void setDisplayRange(double min,
                            double max)

Standardized display range

setRowKeys

public void setRowKeys(int[] rowKeys)

Parameters:

rowKeys -

standardize

public void standardize()

Normalizes the elements of a matrix to variance one and mean zero, ignoring missing values todo move this to matrixstats or something.

createRowKeys

protected int[] createRowKeys()

To be able to sort the rows by an arbitrary key. Creates m_rowKeys array and initializes it in ascending order from 0 to m_totalRows -1, so that by default it matches the physical order of the columns: [0,1,2,...,m_totalRows-1]

Returns:

int[]

getTrueRowIndex

protected int getTrueRowIndex(int row)

setRow

protected void setRow(int row,
                      double[] values)

Changes values in a row, clipping if there are more values than columns.

Parameters:

row - row whose values we want to change

values - new row values