info.bioinfweb.libralign.pherogram

Class PherogramPainter

java.lang.Object

info.bioinfweb.libralign.pherogram.PherogramPainter

public class PherogramPainter
extends java.lang.Object

Utility class used by GUI components that display a pherogram (e.g. PherogramTraceCurveView and PherogramArea) that implements common painting routines.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	INDEX_LABEL_INTERVAL

Constructor Summary

Constructors

Constructor and Description
PherogramPainter(PherogramComponent owner)

Method Summary

Modifier and Type	Method and Description
double	calculateTraceCurvesHeight() Returns the height that is used to paint the trace curves.
void	paintBaseCallIndices(java.awt.Graphics2D g, int firstBaseCallIndex, int lastBaseCallIndex, double startX, double startY, PherogramDistortion distortion, double compoundWidth)
void	paintBaseCallLines(java.awt.Graphics2D g, int firstBaseCallIndex, int lastBaseCallIndex, double startX, double startY, double height, PherogramDistortion distortion)
void	paintBaseCalls(java.awt.Graphics2D g, int firstBaseCallIndex, int lastBaseCallIndex, double startX, double startY, PherogramDistortion distortion)
void	paintGaps(java.awt.Graphics2D g, int firstBaseCallIndex, int lastBaseCallIndex, double startX, double startY, double height, PherogramDistortion distortion, double compoundWidth)
double	paintTraceCurves(java.awt.Graphics2D g, int firstBaseCallIndex, int lastBaseCallIndex, double x, double y, PherogramDistortion distortion, double compoundWidth)
void	paintUnscaledBackground(java.awt.Graphics2D g, java.awt.geom.Rectangle2D visibleRect, double horizontalScale)
void	paintUnscaledBaseCallIndices(int startX, int endX, java.awt.Graphics2D g, double paintX, double paintY, double horizontalScale)
void	paintUnscaledBaseCallLines(int startX, int endX, java.awt.Graphics2D g, double paintX, double paintY, double height, double horizontalScale)
void	paintUnscaledBaseCalls(int startX, int endX, java.awt.Graphics2D g, double paintStartX, double paintY, double horizontalScale) Paints the nucleotide characters of the base call sequence at the x-positions stored in the underlying pherogram model.
double	paintUnscaledTraceCurves(int startX, int endX, java.awt.Graphics2D g, double paintX, double paintY, double horizontalScale) Paints parts the four trace curves stored in the specified provider with a constant scale on x.

Methods inherited from class java.lang.Object

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

Field Detail

INDEX_LABEL_INTERVAL

public static final int INDEX_LABEL_INTERVAL

See Also:

Constant Field Values

Constructor Detail

PherogramPainter

public PherogramPainter(PherogramComponent owner)

Method Detail

paintUnscaledBackground

public void paintUnscaledBackground(java.awt.Graphics2D g,
                                    java.awt.geom.Rectangle2D visibleRect,
                                    double horizontalScale)

paintBaseCalls

public void paintBaseCalls(java.awt.Graphics2D g,
                           int firstBaseCallIndex,
                           int lastBaseCallIndex,
                           double startX,
                           double startY,
                           PherogramDistortion distortion)

paintUnscaledBaseCalls

public void paintUnscaledBaseCalls(int startX,
                                   int endX,
                                   java.awt.Graphics2D g,
                                   double paintStartX,
                                   double paintY,
                                   double horizontalScale)

Paints the nucleotide characters of the base call sequence at the x-positions stored in the underlying pherogram model.

Note that no background will be painted by this method and the font currently set in the specified graphics context will be used.

Parameters:

startX - the index in provider of the first trace value to be painted

endX - the index in provider after the last value to be painted

g - the graphics context to paint on

paintCenterX - the left most coordinate of the area where the trace curves will be painted

paintY - the top most coordinate of the area where the trace curves will be painted

horizontalScale - the factor by which the trace curves shall be scaled (zoomed) on the x-axis

calculateTraceCurvesHeight

public double calculateTraceCurvesHeight()

Returns the height that is used to paint the trace curves. Since the trace data in PherogramProvider is normalized to 1.0, the returned value is equal to the vertical scale value of the owning pherogram component (PherogramComponent.getVerticalScale()).

Returns:

the height in pixels

paintUnscaledTraceCurves

public double paintUnscaledTraceCurves(int startX,
                                       int endX,
                                       java.awt.Graphics2D g,
                                       double paintX,
                                       double paintY,
                                       double horizontalScale)

Paints parts the four trace curves stored in the specified provider with a constant scale on x.

Note that no background will be painted by this method.

Parameters:

startX - the index in provider of the first trace value to be painted

endX - the index in provider after the last value to be painted

g - the graphics context to paint on

paintX - the left most coordinate of the area where the trace curves will be painted

paintY - the top most coordinate of the area where the trace curves will be painted

horizontalScale - the factor by which the trace curves shall be scaled (zoomed) on the x-axis

Returns:

the height the curves used to be painted

paintUnscaledBaseCallLines

public void paintUnscaledBaseCallLines(int startX,
                                       int endX,
                                       java.awt.Graphics2D g,
                                       double paintX,
                                       double paintY,
                                       double height,
                                       double horizontalScale)

paintBaseCallLines

public void paintBaseCallLines(java.awt.Graphics2D g,
                               int firstBaseCallIndex,
                               int lastBaseCallIndex,
                               double startX,
                               double startY,
                               double height,
                               PherogramDistortion distortion)

paintUnscaledBaseCallIndices

public void paintUnscaledBaseCallIndices(int startX,
                                         int endX,
                                         java.awt.Graphics2D g,
                                         double paintX,
                                         double paintY,
                                         double horizontalScale)

paintBaseCallIndices

public void paintBaseCallIndices(java.awt.Graphics2D g,
                                 int firstBaseCallIndex,
                                 int lastBaseCallIndex,
                                 double startX,
                                 double startY,
                                 PherogramDistortion distortion,
                                 double compoundWidth)

paintTraceCurves

public double paintTraceCurves(java.awt.Graphics2D g,
                               int firstBaseCallIndex,
                               int lastBaseCallIndex,
                               double x,
                               double y,
                               PherogramDistortion distortion,
                               double compoundWidth)

paintGaps

public void paintGaps(java.awt.Graphics2D g,
                      int firstBaseCallIndex,
                      int lastBaseCallIndex,
                      double startX,
                      double startY,
                      double height,
                      PherogramDistortion distortion,
                      double compoundWidth)