info.bioinfweb.libralign.pherogram.distortion

Class UnscaledPherogramDistortion

java.lang.Object

info.bioinfweb.libralign.pherogram.distortion.UnscaledPherogramDistortion

All Implemented Interfaces:

PherogramDistortion

public class UnscaledPherogramDistortion
extends java.lang.Object
implements PherogramDistortion

Implementation that does not scale the pherogram or insert any gaps. (Used e.g. with PherogramTraceCurveView).

Since:

0.2.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
UnscaledPherogramDistortion(double horizontalScale, PherogramProvider provider)

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.

Methods inherited from class java.lang.Object

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

Constructor Detail

UnscaledPherogramDistortion

public UnscaledPherogramDistortion(double horizontalScale,
                                   PherogramProvider provider)

Method Detail

getHorizontalScale

public double getHorizontalScale(int baseCallIndex)

Description copied from interface: PherogramDistortion

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

Specified by:

getHorizontalScale in interface PherogramDistortion

Parameters:

baseCallIndex - the index of the base call

Returns:

a floating point value greater than zero

getPaintStartX

public double getPaintStartX(int baseCallIndex)

Description copied from interface: PherogramDistortion

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.

Specified by:

getPaintStartX in interface PherogramDistortion

Parameters:

baseCallIndex - the index of the base call.

Returns:

a floating point value greater than or equal to zero

getPaintCenterX

public double getPaintCenterX(int baseCallIndex)

Description copied from interface: PherogramDistortion

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.)

Specified by:

getPaintCenterX in interface PherogramDistortion

Parameters:

baseCallIndex - the index of the base call.

Returns:

a floating point value greater than or equal to zero

getGapPattern

public GapPattern getGapPattern(int baseCallIndex)

Description copied from interface: PherogramDistortion

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

Specified by:

getGapPattern in interface PherogramDistortion

Parameters:

baseCallIndex - the index of the base call

Returns:

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