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edu.stanford.genetics.treeview.dendroview
Class ColorSet  

java.lang.Object
  edu.stanford.genetics.treeview.dendroview.ColorSet

All Implemented Interfaces:

edu.stanford.genetics.treeview.ConfigNodePersistent

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public class ColorSet

extends java.lang.Object

implements edu.stanford.genetics.treeview.ConfigNodePersistent

This class represents a set of colors which can be used by a color extractor to translate data values into colors. NOTE: This class has been superceded by the ConfigColorSet in the edu.stanford.genetics.treeview package, although I am not likely to actually rewrite any of this code spontaneously.

Version:

@version $Revision: 1.2 $ $Date: 2003/06/23 08:03:07 $

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Field Summary
private  java.lang.String	default_downColor
private  java.lang.String	default_emptyColor
private  java.lang.String	default_missingColor
private  java.lang.String	default_name
private  java.lang.String	default_upColor
private  java.lang.String	default_zeroColor
private  java.awt.Color	down
private  java.awt.Color	empty
private  java.awt.Color	missing
private  java.lang.String	name
private  edu.stanford.genetics.treeview.ConfigNode	root
private  java.awt.Color	up
private  java.awt.Color	zero

 

Constructor Summary

ColorSet()           Constructor for the ColorSet object, uses default values

ColorSet(java.lang.String name, java.lang.String up, java.lang.String zero, java.lang.String down, java.lang.String missing, java.lang.String empty)           Constructor for the ColorSet object

 

Method Summary
void	bindConfig(edu.stanford.genetics.treeview.ConfigNode root)           sets colors and name to reflect ConfigNode
void	copyStateFrom(ColorSet other)           copies colors and name from other color set.
static java.awt.Color	decodeColor(java.lang.String colorString)           Convert a color from a hex string to a Java Color object.
static java.lang.String	encodeColor(java.awt.Color color)           Convert a java Color object to a hex string.
java.awt.Color	getDown()           Color for negative values.
java.awt.Color	getEmpty()           Color for empty values.
java.awt.Color	getMissing()           Color for missing values.
java.lang.String	getName()           The name of this color set
java.awt.Color	getUp()           Color for positive values.
java.awt.Color	getZero()           color for zero values
private static java.lang.String	hex(int buf)
private static java.lang.String	hexChar(int i)
void	loadEisen(java.io.File file)           extract values from Eisen-formatted file
void	loadEisen(java.lang.String file)           extract values from Eisen-formatted file specified by the string argument The Eisen format is a 16 byte file.
static void	main(java.lang.String[] argv)           Simple test program, prints out default color set using toString.
private  void	packEisen(java.awt.Color out, java.io.OutputStream stream)
void	saveEisen(java.io.File file)           save values to Eisen-formatted file sp
void	saveEisen(java.lang.String file)           save values to Eisen-formatted file specified by the String
private  void	setDefaults()
void	setDown(java.awt.Color newColor)           Color for negative values.
void	setDown(java.lang.String newString)           Color for negative values.
void	setEmpty(java.awt.Color newColor)           Color for empty values.
void	setEmpty(java.lang.String newString)           Color for empty values.
void	setMissing(java.awt.Color newColor)           Color for missing values.
void	setMissing(java.lang.String newString)           Color for missing values.
void	setName(java.lang.String name)           The name of this color set
void	setUp(java.awt.Color newColor)           Color for positive values.
void	setUp(java.lang.String newString)           Color for positive values.
void	setZero(java.awt.Color newColor)           color for zero values
void	setZero(java.lang.String newString)           color for zero values
java.lang.String	toString()           Convert this Object to a human-readable String.
private  java.awt.Color	unpackEisen(java.io.InputStream stream)

 

Methods inherited from class java.lang.Object

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

 

Field Detail

default_upColor

private java.lang.String default_upColor

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default_zeroColor

private java.lang.String default_zeroColor

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default_downColor

private java.lang.String default_downColor

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default_missingColor

private java.lang.String default_missingColor

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default_emptyColor

private java.lang.String default_emptyColor

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default_name

private java.lang.String default_name

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name

private java.lang.String name

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up

private java.awt.Color up

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zero

private java.awt.Color zero

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down

private java.awt.Color down

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missing

private java.awt.Color missing

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empty

private java.awt.Color empty

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root

private edu.stanford.genetics.treeview.ConfigNode root

Constructor Detail

ColorSet

public ColorSet()

Constructor for the ColorSet object, uses default values

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ColorSet

public ColorSet(java.lang.String name,
                java.lang.String up,
                java.lang.String zero,
                java.lang.String down,
                java.lang.String missing,
                java.lang.String empty)

Constructor for the ColorSet object

Method Detail

setDefaults

private void setDefaults()

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copyStateFrom

public void copyStateFrom(ColorSet other)

copies colors and name from other color set.

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bindConfig

public void bindConfig(edu.stanford.genetics.treeview.ConfigNode root)

sets colors and name to reflect ConfigNode

Specified by:

bindConfig in interface edu.stanford.genetics.treeview.ConfigNodePersistent

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main

public static final void main(java.lang.String[] argv)

Simple test program, prints out default color set using toString. if argument present, saves EisenFormat to specified file.

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toString

public java.lang.String toString()

Description copied from class: java.lang.Object

Convert this Object to a human-readable String. There are no limits placed on how long this String should be or what it should contain. We suggest you make it as intuitive as possible to be able to place it into System.out.println() 55 and such.

It is typical, but not required, to ensure that this method never completes abruptly with a java.lang.RuntimeException.

This method will be called when performing string concatenation with this object. If the result is null, string concatenation will instead use "null".

The default implementation returns getClass().getName() + "@" + Integer.toHexString(hashCode()).

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loadEisen

public void loadEisen(java.lang.String file)
               throws java.io.IOException

extract values from Eisen-formatted file specified by the string argument The Eisen format is a 16 byte file. The first four bytes are interpreted as RBGA values specifying red, green, blue and alpha values from 0-255 (00 - FF in base 16) for up-regulated genes, the next four are the values for unchanged, then down regulated, then the color for missing values.

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loadEisen

public void loadEisen(java.io.File file)
               throws java.io.IOException

extract values from Eisen-formatted file

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saveEisen

public void saveEisen(java.lang.String file)
               throws java.io.IOException

save values to Eisen-formatted file specified by the String

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saveEisen

public void saveEisen(java.io.File file)
               throws java.io.IOException

save values to Eisen-formatted file sp

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unpackEisen

private java.awt.Color unpackEisen(java.io.InputStream stream)
                            throws java.io.IOException

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packEisen

private void packEisen(java.awt.Color out,
                       java.io.OutputStream stream)
                throws java.io.IOException

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getUp

public java.awt.Color getUp()

Color for positive values.

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getZero

public java.awt.Color getZero()

color for zero values

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getDown

public java.awt.Color getDown()

Color for negative values.

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getMissing

public java.awt.Color getMissing()

Color for missing values.

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getEmpty

public java.awt.Color getEmpty()

Color for empty values.

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getName

public java.lang.String getName()

The name of this color set

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setUp

public void setUp(java.lang.String newString)

Color for positive values.

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setZero

public void setZero(java.lang.String newString)

color for zero values

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setDown

public void setDown(java.lang.String newString)

Color for negative values.

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setMissing

public void setMissing(java.lang.String newString)

Color for missing values.

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setEmpty

public void setEmpty(java.lang.String newString)

Color for empty values.

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setUp

public void setUp(java.awt.Color newColor)

Color for positive values.

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setZero

public void setZero(java.awt.Color newColor)

color for zero values

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setDown

public void setDown(java.awt.Color newColor)

Color for negative values.

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setMissing

public void setMissing(java.awt.Color newColor)

Color for missing values.

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setEmpty

public void setEmpty(java.awt.Color newColor)

Color for empty values.

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setName

public void setName(java.lang.String name)

The name of this color set

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decodeColor

public static final java.awt.Color decodeColor(java.lang.String colorString)

Convert a color from a hex string to a Java Color object.

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encodeColor

public static final java.lang.String encodeColor(java.awt.Color color)

Convert a java Color object to a hex string.

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hex

private static final java.lang.String hex(int buf)

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hexChar

private static final java.lang.String hexChar(int i)

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> edu >> stanford >> genetics >> treeview >> [ dendroview overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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