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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Class ColorMatrix<A,​B>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

colorMap

colors

displayMax

displayMin

m_matrixReader

m_rowKeys

m_totalRows

m_totalColumns

max

maxtrix

min

missingColor

Constructor Detail

ColorMatrix

ColorMatrix

Method Detail

newInstance

clone

getColor

getColorMap

getColors

getColumnCount

getColumnName

getColumnNames

getDisplayMax

getDisplayMin

getMatrix

getMax

getMaxtrix

getMin

getMissingColor

getRow

getRowByName

getRowCount

getRowIndexByName

getRowName

getRowNames

getValue

mapValuesToColors

resetRowKeys

setColor

setColorMap

setDisplayRange

setRowKeys

standardize

createRowKeys

getTrueRowIndex

setRow

Class ColorMatrix<A,B>