info.bioinfweb.libralign.pherogram.distortion

Interface PherogramDistortion

All Known Implementing Classes:

ScaledPherogramDistortion, UnscaledPherogramDistortion

public interface PherogramDistortion

Classes to be used with PherogramPainter the define the distortion of the pherogram at each base call index should implement this interface.

Since:

0.2.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
GapPattern	getGapPattern(int baseCallIndex) A description of gaps in the pherogram in the area surrounding the specified base call.
double	getHorizontalScale(int baseCallIndex) Returns the scale (pixels per trace value) in the area surrounding the specified base call.
double	getPaintCenterX(int baseCallIndex) Returns the x coordinate relative to the left border of the pherogram where the base call with the specified index shall be painted.
double	getPaintStartX(int baseCallIndex) Returns the x coordinate relative to the left border of the pherogram where the first trace position of the area associated with the specified base call index shall be painted.

Method Detail

getHorizontalScale

double getHorizontalScale(int baseCallIndex)

Returns the scale (pixels per trace value) in the area surrounding the specified base call.

Parameters:

baseCallIndex - the index of the base call

Returns:

a floating point value greater than zero

getPaintStartX

double getPaintStartX(int baseCallIndex)

Returns the x coordinate relative to the left border of the pherogram where the first trace position of the area associated with the specified base call index shall be painted.

Parameters:

baseCallIndex - the index of the base call.

Returns:

a floating point value greater than or equal to zero

getPaintCenterX

double getPaintCenterX(int baseCallIndex)

Returns the x coordinate relative to the left border of the pherogram where the base call with the specified index shall be painted. (That would be the center of trace curve area belonging to this base call.)

Parameters:

baseCallIndex - the index of the base call.

Returns:

a floating point value greater than or equal to zero

getGapPattern

GapPattern getGapPattern(int baseCallIndex)

A description of gaps in the pherogram in the area surrounding the specified base call.

Parameters:

baseCallIndex - the index of the base call

Returns:

a gap pattern or null if no gaps are present in the specified area