org.metaqtl.graph
Class MetaGraphPar

java.lang.Object
  extended by org.metaqtl.graph.MetaGraphPar

public final class MetaGraphPar
extends java.lang.Object


Field Summary
static java.awt.Color BACKGROUND_COLOR
          The color of the backgroud.
static int CHROM_ALIGN_MODE
           
static double CHROM_DISTANCE_SCALE
           
static double CHROM_FLANKING_CEX
          The default cex parameter for flanking regions at the top and the end of the chromosome.
static java.awt.Font CHROM_NAME_FONT
           
static double CHROM_NAME_HSPACE
           
static java.awt.Stroke CHROM_STROKE
          The stroke of the chromosome shape.
static java.awt.Color CHROM_STROKE_COLOR
          The color of the stroke of the Chromosome shape.
static java.awt.Color CHROM_TICK_COLOR
          The color of the marker ticks on the chromosome.
static java.awt.Stroke CHROM_TICK_STROKE
           
static double CHROM_TICK_WIDTH_1
          The width of the marker ticks.
static double CHROM_TICK_WIDTH_2
           
static double CHROM_TICK_WIDTH_3
           
static double CHROM_WIDTH
          The width of the chromosome.
static double COMMON_STROKE_WIDTH
           
static double DEFAULT_HEIGHT
          The default height.
static double DEFAULT_WIDTH
          The default width.
static double LAYER_HSPACE
          The horizontal space between layers.
static double LAYER_VSPACE
          The vertical space between layers.
static double LEGEND_BOX_CEX
           
static java.awt.Font LEGEND_FONT
           
static double LEGEND_GRAD_HEIGHT
           
static double LEGEND_GRAD_WIDTH
           
static double LEGEND_HSPACE
           
static double LEGEND_PART_HEIGHT
           
static double LEGEND_PART_WIDTH
           
static int LEGEND_SCALE_UNIT
           
static double MAKER_NAME_VSPACE
           
static java.awt.Font MARKER_NAME_FONT
           
static java.awt.Font MARKER_POSITION_FONT
           
static java.awt.Color NEG_COMMON_COLOR
           
static java.awt.Color POS_COMMON_COLOR
           
static int PROBA_BIN
           
static java.awt.Color PROBA_FROM_COLOR
           
static java.awt.Color[] PROBA_PALETTE
           
static java.awt.Color PROBA_TO_COLOR
           
static double QTL_CI_WIDTH
           
static double QTL_CI_WIDTH_CEX
           
static double QTL_HSPACE
          The horizontal space between Qtl shapes.
static java.awt.Color QTL_NAME_COLOR
          The color of the QTL names.
static java.awt.Font QTL_NAME_FONT
          The font used for the Qtl names.
static double QTL_NAME_SPACE
           
static double QTL_NAME_VSPACE_CEX
          The space magnification between the Qtl name and the Qtl confidence interval.
static java.awt.Color[] QTL_PALETTE
          The color palete for the QTL partition.
static double QTL_PCH_SIZE
           
static double QTL_POS_HEIGHT_CEX
           
static double QTL_POS_WIDTH_CEX
           
static double QTL_PROB_WIDTH
           
static double QTL_TICK_WIDTH_CEX
          The magnification for the tick of the QTL.
static double QTL_TREE_SCALE
           
static double QTL_TREE_SPACE
           
static double QTL_VSPACE
          The vertical space between Qtl shapes.
static java.awt.Color SINGLE_COMMON_COLOR
           
static double TREE_NODE_WIDTH
           
static boolean WITH_CHROM_NAME
           
static boolean WITH_COMMON_MARKER
           
static boolean WITH_LEGEND
           
static boolean WITH_MAP_NAME
           
static boolean WITH_MARKER_NAME
           
static boolean WITH_MARKER_POSITION
           
static boolean WITH_QTL_NAME
          Add the Qtl name.
 
Method Summary
static java.lang.String color2string(java.awt.Color color)
           
static java.lang.String font2string(java.awt.Font font)
           
static java.awt.Color getProbaColor(double d)
           
static java.awt.Color getProbaColor(double d, double thresh)
           
static void initPalettes()
           
static void initProbaPalette()
           
static void initQTLPalette()
           
static void initQTLPalette(int n)
           
static void set(java.lang.String parameter, java.lang.String value)
           
static java.awt.Color string2color(java.lang.String value)
           
static java.awt.Font string2font(java.lang.String value)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

LAYER_HSPACE

public static double LAYER_HSPACE
The horizontal space between layers.


LAYER_VSPACE

public static double LAYER_VSPACE
The vertical space between layers.


DEFAULT_WIDTH

public static double DEFAULT_WIDTH
The default width.


DEFAULT_HEIGHT

public static double DEFAULT_HEIGHT
The default height.


BACKGROUND_COLOR

public static java.awt.Color BACKGROUND_COLOR
The color of the backgroud. Default is white.


QTL_VSPACE

public static double QTL_VSPACE
The vertical space between Qtl shapes. Default is 5.0


QTL_HSPACE

public static double QTL_HSPACE
The horizontal space between Qtl shapes. Default is 5.0


QTL_TREE_SPACE

public static double QTL_TREE_SPACE

TREE_NODE_WIDTH

public static double TREE_NODE_WIDTH

WITH_QTL_NAME

public static boolean WITH_QTL_NAME
Add the Qtl name. Default is true


QTL_NAME_FONT

public static java.awt.Font QTL_NAME_FONT
The font used for the Qtl names. Default is Times with type plain and size 8.


MARKER_NAME_FONT

public static java.awt.Font MARKER_NAME_FONT

MARKER_POSITION_FONT

public static java.awt.Font MARKER_POSITION_FONT

CHROM_NAME_FONT

public static java.awt.Font CHROM_NAME_FONT

QTL_NAME_COLOR

public static java.awt.Color QTL_NAME_COLOR
The color of the QTL names. Default is black


QTL_NAME_VSPACE_CEX

public static double QTL_NAME_VSPACE_CEX
The space magnification between the Qtl name and the Qtl confidence interval.


WITH_MAP_NAME

public static boolean WITH_MAP_NAME

WITH_CHROM_NAME

public static boolean WITH_CHROM_NAME

QTL_PCH_SIZE

public static double QTL_PCH_SIZE

WITH_LEGEND

public static boolean WITH_LEGEND

QTL_TICK_WIDTH_CEX

public static double QTL_TICK_WIDTH_CEX
The magnification for the tick of the QTL.


QTL_PALETTE

public static java.awt.Color[] QTL_PALETTE
The color palete for the QTL partition. Default is null.


PROBA_PALETTE

public static java.awt.Color[] PROBA_PALETTE

PROBA_BIN

public static int PROBA_BIN

CHROM_WIDTH

public static double CHROM_WIDTH
The width of the chromosome. Default is 20.0


QTL_CI_WIDTH

public static double QTL_CI_WIDTH

CHROM_NAME_HSPACE

public static double CHROM_NAME_HSPACE

WITH_MARKER_NAME

public static boolean WITH_MARKER_NAME

CHROM_ALIGN_MODE

public static int CHROM_ALIGN_MODE

WITH_MARKER_POSITION

public static boolean WITH_MARKER_POSITION

CHROM_FLANKING_CEX

public static double CHROM_FLANKING_CEX
The default cex parameter for flanking regions at the top and the end of the chromosome.


CHROM_STROKE

public static java.awt.Stroke CHROM_STROKE
The stroke of the chromosome shape. Default is BasicStroke


CHROM_TICK_STROKE

public static java.awt.Stroke CHROM_TICK_STROKE

MAKER_NAME_VSPACE

public static double MAKER_NAME_VSPACE

CHROM_STROKE_COLOR

public static java.awt.Color CHROM_STROKE_COLOR
The color of the stroke of the Chromosome shape. Default is black.


CHROM_TICK_WIDTH_1

public static double CHROM_TICK_WIDTH_1
The width of the marker ticks.


CHROM_TICK_WIDTH_2

public static double CHROM_TICK_WIDTH_2

CHROM_TICK_WIDTH_3

public static double CHROM_TICK_WIDTH_3

QTL_POS_HEIGHT_CEX

public static double QTL_POS_HEIGHT_CEX

QTL_POS_WIDTH_CEX

public static double QTL_POS_WIDTH_CEX

CHROM_TICK_COLOR

public static java.awt.Color CHROM_TICK_COLOR
The color of the marker ticks on the chromosome. Default is black.


QTL_NAME_SPACE

public static double QTL_NAME_SPACE

CHROM_DISTANCE_SCALE

public static double CHROM_DISTANCE_SCALE

QTL_CI_WIDTH_CEX

public static double QTL_CI_WIDTH_CEX

QTL_PROB_WIDTH

public static double QTL_PROB_WIDTH

LEGEND_FONT

public static java.awt.Font LEGEND_FONT

LEGEND_PART_HEIGHT

public static double LEGEND_PART_HEIGHT

LEGEND_PART_WIDTH

public static double LEGEND_PART_WIDTH

LEGEND_HSPACE

public static double LEGEND_HSPACE

LEGEND_BOX_CEX

public static double LEGEND_BOX_CEX

LEGEND_SCALE_UNIT

public static int LEGEND_SCALE_UNIT

WITH_COMMON_MARKER

public static boolean WITH_COMMON_MARKER

PROBA_FROM_COLOR

public static java.awt.Color PROBA_FROM_COLOR

PROBA_TO_COLOR

public static java.awt.Color PROBA_TO_COLOR

SINGLE_COMMON_COLOR

public static java.awt.Color SINGLE_COMMON_COLOR

POS_COMMON_COLOR

public static java.awt.Color POS_COMMON_COLOR

NEG_COMMON_COLOR

public static java.awt.Color NEG_COMMON_COLOR

COMMON_STROKE_WIDTH

public static double COMMON_STROKE_WIDTH

LEGEND_GRAD_HEIGHT

public static double LEGEND_GRAD_HEIGHT

LEGEND_GRAD_WIDTH

public static double LEGEND_GRAD_WIDTH

QTL_TREE_SCALE

public static double QTL_TREE_SCALE
Method Detail

set

public static void set(java.lang.String parameter,
                       java.lang.String value)
                throws java.lang.IllegalArgumentException
Parameters:
parameter -
value -
Throws:
java.lang.IllegalArgumentException

string2color

public static java.awt.Color string2color(java.lang.String value)
Parameters:
value -
Returns:

color2string

public static java.lang.String color2string(java.awt.Color color)

string2font

public static java.awt.Font string2font(java.lang.String value)
Parameters:
value -
Returns:

font2string

public static java.lang.String font2string(java.awt.Font font)
Parameters:
font -
Returns:

getProbaColor

public static java.awt.Color getProbaColor(double d)
Parameters:
d -
Returns:

getProbaColor

public static java.awt.Color getProbaColor(double d,
                                           double thresh)
Parameters:
d -
Returns:

initProbaPalette

public static void initProbaPalette()

initQTLPalette

public static void initQTLPalette()

initQTLPalette

public static void initQTLPalette(int n)

initPalettes

public static void initPalettes()