baseCode.gui
Class ColorMatrix

java.lang.Object
  baseCode.gui.ColorMatrix

All Implemented Interfaces:

java.lang.Cloneable

public class ColorMatrix

extends java.lang.Object

implements java.lang.Cloneable

Title: ColorMatrix

Description: Creates a color matrix from a matrix of doubles

Copyright (c) 2004

Institution:: Columbia University

Version:

$Id: ColorMatrix.java,v 1.42 2004/09/20 22:19:02 pavlidis Exp $

Author:

Will Braynen

Field Summary

protected java.awt.Color[]	m_colorMap
protected java.awt.Color[][]	m_colors
protected double	m_displayMax
protected double	m_displayMin Min and max values to display, which might not be the actual min and max values in the matrix.
protected AbstractNamedDoubleMatrix	m_matrix
protected DoubleMatrixReader	m_matrixReader
protected double	m_max
protected double	m_min
protected java.awt.Color	m_missingColor
protected int[]	m_rowKeys to be able to sort the rows by an arbitrary key
protected int	m_totalColumns
protected int	m_totalRows

Constructor Summary

ColorMatrix(AbstractNamedDoubleMatrix matrix, java.awt.Color[] colorMap, java.awt.Color missingColor)

ColorMatrix(DenseDoubleMatrix2DNamed matrix)

ColorMatrix(java.lang.String filename)

ColorMatrix(java.lang.String filename, java.awt.Color[] colorMap, java.awt.Color missingColor)

Method Summary

java.lang.Object	clone()
protected int[]	createRowKeys() To be able to sort the rows by an arbitrary key.
java.awt.Color	getColor(int row, int column)
int	getColumnCount()
java.lang.String	getColumnName(int column)
java.lang.String[]	getColumnNames()
double	getDisplayMax()
double	getDisplayMin()
AbstractNamedDoubleMatrix	getMatrix()
double[]	getRow(int row)
double[]	getRowByName(java.lang.String rowName)
int	getRowCount()
int	getRowIndexByName(java.lang.String rowName)
java.lang.String	getRowName(int row)
java.lang.String[]	getRowNames()
protected int	getTrueRowIndex(int row)
double	getValue(int row, int column)
void	init(AbstractNamedDoubleMatrix matrix)
void	loadMatrixFromFile(java.lang.String filename) A convenience method for loading data files
void	mapValuesToColors()
void	resetRowKeys()
void	setColor(int row, int column, java.awt.Color newColor)
void	setColorMap(java.awt.Color[] colorMap)
void	setDisplayRange(double min, double max)
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

m_displayMin

protected double m_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_displayMax

protected double m_displayMax

m_min

protected double m_min

m_max

protected double m_max

m_colors

protected java.awt.Color[][] m_colors

m_missingColor

protected java.awt.Color m_missingColor

m_colorMap

protected java.awt.Color[] m_colorMap

m_matrix

protected AbstractNamedDoubleMatrix m_matrix

m_matrixReader

protected DoubleMatrixReader m_matrixReader

m_totalRows

protected int m_totalRows

m_totalColumns

protected int m_totalColumns

m_rowKeys

protected int[] m_rowKeys

to be able to sort the rows by an arbitrary key

Constructor Detail

ColorMatrix

public ColorMatrix(java.lang.String filename)
            throws java.io.IOException

Parameters:

filename - either an absolute path, or if providing a relative path (e.g. data.txt), then keep in mind that it will be relative to the java interpreter, not the class (not my fault -- that's how java treats relative paths)

Throws:

java.io.IOException

ColorMatrix

public ColorMatrix(DenseDoubleMatrix2DNamed matrix)

ColorMatrix

public ColorMatrix(java.lang.String filename,
                   java.awt.Color[] colorMap,
                   java.awt.Color missingColor)
            throws java.io.IOException

Parameters:

filename - data filename

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

Throws:

java.io.IOException

ColorMatrix

public ColorMatrix(AbstractNamedDoubleMatrix matrix,
                   java.awt.Color[] colorMap,
                   java.awt.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

getRowCount

public int getRowCount()

getColumnCount

public int getColumnCount()

getTrueRowIndex

protected int getTrueRowIndex(int row)

getValue

public double getValue(int row,
                       int column)
                throws java.lang.ArrayIndexOutOfBoundsException

Throws:

java.lang.ArrayIndexOutOfBoundsException

getRow

public double[] getRow(int row)
                throws java.lang.ArrayIndexOutOfBoundsException

Throws:

java.lang.ArrayIndexOutOfBoundsException

getRowByName

public double[] getRowByName(java.lang.String rowName)

getColor

public java.awt.Color getColor(int row,
                               int column)
                        throws java.lang.ArrayIndexOutOfBoundsException

Throws:

java.lang.ArrayIndexOutOfBoundsException

setColor

public void setColor(int row,
                     int column,
                     java.awt.Color newColor)
              throws java.lang.ArrayIndexOutOfBoundsException

Throws:

java.lang.ArrayIndexOutOfBoundsException

getRowName

public java.lang.String getRowName(int row)
                            throws java.lang.ArrayIndexOutOfBoundsException

Throws:

java.lang.ArrayIndexOutOfBoundsException

getColumnName

public java.lang.String getColumnName(int column)
                               throws java.lang.ArrayIndexOutOfBoundsException

Throws:

java.lang.ArrayIndexOutOfBoundsException

getRowNames

public java.lang.String[] getRowNames()

getColumnNames

public java.lang.String[] getColumnNames()

getRowIndexByName

public int getRowIndexByName(java.lang.String rowName)

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

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[]

setRowKeys

public void setRowKeys(int[] rowKeys)

resetRowKeys

public void resetRowKeys()

init

public void init(AbstractNamedDoubleMatrix matrix)

loadMatrixFromFile

public void loadMatrixFromFile(java.lang.String filename)
                        throws java.io.IOException

A convenience method for loading data files

Parameters:

filename - the name of the data file

Throws:

java.io.IOException

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.

getMatrix

public AbstractNamedDoubleMatrix getMatrix()

Returns:

a DenseDoubleMatrix2DNamed object

setDisplayRange

public void setDisplayRange(double min,
                            double max)

getDisplayMin

public double getDisplayMin()

getDisplayMax

public double getDisplayMax()

setColorMap

public void setColorMap(java.awt.Color[] colorMap)
                 throws java.lang.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:

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

mapValuesToColors

public void mapValuesToColors()

clone

public java.lang.Object clone()