org.metaqtl.graph
Class ChromLayer

java.lang.Object
  extended by org.metaqtl.graph.AnchoredElement
      extended by org.metaqtl.graph.Layer
          extended by org.metaqtl.graph.ChromLayer

public class ChromLayer
extends Layer


Nested Class Summary
 class ChromLayer.CMrkTickPath
           
 class ChromLayer.CMrkTickPoint
           
 
Field Summary
static int ALIGN_FIRST_COMMON
           
static int ALIGN_FIRST_MARKER
           
static int LEFT_LABEL
           
static int NEG_COMMON
           
static int POS_COMMON
           
static int RIGHT_LABEL
           
static int SINGLE_COMMON
           
 
Fields inherited from class org.metaqtl.graph.Layer
height, width
 
Fields inherited from class org.metaqtl.graph.AnchoredElement
x, y
 
Constructor Summary
ChromLayer(double x, double y)
           
 
Method Summary
static void alignChromLayers(ChromLayer ref, ChromLayer layer, int mode)
           
 void attach(java.lang.Object object)
          Attach the given object to the layer.
 void build(java.awt.Graphics2D graph)
          Build the layer.
 void draw(java.awt.Graphics2D graph)
          Draws the layer on the given graph context.
 ChromAxe getChromAxe()
          Return the axe of the chromosome.
 double getChromWidth()
           
 ChromLayer.CMrkTickPath[] getCommonMarkerPaths(ChromLayer chromLayer)
           
 ChromLayer.CMrkTickPoint[] getCommonMarkerPoints(ChromLayer chromLayer)
           
 double getHeight()
           
 java.awt.geom.Point2D getMrkTickPoint2D(int mrkIdx, boolean reverse)
           
 double getWidth()
           
 double getYMax()
           
 double getYMin()
           
 boolean hasProba()
           
 void setLabelSide(int side)
           
 
Methods inherited from class org.metaqtl.graph.AnchoredElement
getX, getY, setX, setY
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

RIGHT_LABEL

public static final int RIGHT_LABEL
See Also:
Constant Field Values

LEFT_LABEL

public static final int LEFT_LABEL
See Also:
Constant Field Values

ALIGN_FIRST_COMMON

public static final int ALIGN_FIRST_COMMON
See Also:
Constant Field Values

ALIGN_FIRST_MARKER

public static final int ALIGN_FIRST_MARKER
See Also:
Constant Field Values

SINGLE_COMMON

public static final int SINGLE_COMMON
See Also:
Constant Field Values

POS_COMMON

public static final int POS_COMMON
See Also:
Constant Field Values

NEG_COMMON

public static final int NEG_COMMON
See Also:
Constant Field Values
Constructor Detail

ChromLayer

public ChromLayer(double x,
                  double y)
Parameters:
x -
y -
Method Detail

alignChromLayers

public static void alignChromLayers(ChromLayer ref,
                                    ChromLayer layer,
                                    int mode)
Parameters:
ref -
layer -
mode -

draw

public void draw(java.awt.Graphics2D graph)
Description copied from class: Layer
Draws the layer on the given graph context.

Specified by:
draw in class Layer

build

public void build(java.awt.Graphics2D graph)
Description copied from class: Layer
Build the layer.

Specified by:
build in class Layer

getChromAxe

public ChromAxe getChromAxe()
Return the axe of the chromosome.

Returns:

attach

public void attach(java.lang.Object object)
Description copied from class: Layer
Attach the given object to the layer.

Specified by:
attach in class Layer
Parameters:
object - the object to attach to the layer.

setLabelSide

public void setLabelSide(int side)

getHeight

public double getHeight()
Overrides:
getHeight in class Layer
Returns:
Returns the height.

getWidth

public double getWidth()
Overrides:
getWidth in class Layer
Returns:
Returns the width.

getYMin

public double getYMin()
Specified by:
getYMin in class Layer

getYMax

public double getYMax()
Specified by:
getYMax in class Layer

getCommonMarkerPoints

public ChromLayer.CMrkTickPoint[] getCommonMarkerPoints(ChromLayer chromLayer)
Parameters:
chromLayer -

getCommonMarkerPaths

public ChromLayer.CMrkTickPath[] getCommonMarkerPaths(ChromLayer chromLayer)

getChromWidth

public double getChromWidth()

getMrkTickPoint2D

public java.awt.geom.Point2D getMrkTickPoint2D(int mrkIdx,
                                               boolean reverse)

hasProba

public boolean hasProba()
Returns: