info.bioinfweb.libralign.pherogram.distortion

Class ScaledPherogramDistortion

java.lang.Object

info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion

All Implemented Interfaces:

PherogramDistortion

public class ScaledPherogramDistortion
extends java.lang.Object
implements PherogramDistortion

Stores scale and gap pattern for each base call index of a pherogram. (Used with PherogramArea).

Since:

0.2.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
ScaledPherogramDistortion(int size) Creates a new instance of this class.

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.
void	setGapPattern(int baseCallIndex, GapPattern pattern)
void	setHorizontalScale(int baseCallIndex, double scale)
void	setPaintCenterX(int baseCallIndex, double paintX)
void	setPaintStartX(int baseCallIndex, double paintX)

Methods inherited from class java.lang.Object

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

Constructor Detail

ScaledPherogramDistortion

public ScaledPherogramDistortion(int size)

Creates a new instance of this class.

Parameters:

size - the number of values to be stored (should be equal to the length of the associated pherogram)

Method Detail

setHorizontalScale

public void setHorizontalScale(int baseCallIndex,
                               double scale)

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

setPaintStartX

public void setPaintStartX(int baseCallIndex,
                           double paintX)

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

setPaintCenterX

public void setPaintCenterX(int baseCallIndex,
                            double paintX)

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

setGapPattern

public void setGapPattern(int baseCallIndex,
                          GapPattern pattern)

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