org.biojava.bio.chromatogram.graphic

Class FixedBaseWidthScaler

java.lang.Object

org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler

All Implemented Interfaces:

ChromatogramNonlinearScaler

public class FixedBaseWidthScaler
extends Object
implements ChromatogramNonlinearScaler

A ChromatogramNonlinearScaler that scales all the base calls in a chromatogram to the same width in pixels, optionally biasing the peak of the call to the center.

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler

ChromatogramNonlinearScaler.Identity

Constructor Summary

Constructors

Constructor and Description
FixedBaseWidthScaler(float width) Creates a new scaler that will scale bases to the specified width without attempting to center their peaks.
FixedBaseWidthScaler(float width, boolean centerPeaks) Creates a new scaler that will scale bases to the specified width and may or may not bias the peaks to the center.

Method Summary

Methods

Modifier and Type	Method and Description
float	scale(Chromatogram c, int traceSampleIndex) Returns the remapped coordinate for the provided trace sample index of the given chromatogram.

Methods inherited from class java.lang.Object

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

Constructor Detail

FixedBaseWidthScaler

public FixedBaseWidthScaler(float width)

Creates a new scaler that will scale bases to the specified width without attempting to center their peaks.

Parameters:

width - the desired call width in pixels

FixedBaseWidthScaler

public FixedBaseWidthScaler(float width,
                    boolean centerPeaks)

Creates a new scaler that will scale bases to the specified width and may or may not bias the peaks to the center.

Parameters:

width - the desired call width in pixels

centerPeaks - if true, the scaler will try to put the peak of in the center of the scaled call. Otherwise, the whole call will be scaled using the same factor.

Method Detail

scale

public float scale(Chromatogram c,
          int traceSampleIndex)
            throws IndexOutOfBoundsException

Description copied from interface: ChromatogramNonlinearScaler

Returns the remapped coordinate for the provided trace sample index of the given chromatogram.

Specified by:

scale in interface ChromatogramNonlinearScaler

Parameters:

c - the Chromatogram

traceSampleIndex - the sample index

Returns:

the new coordinagte

Throws:

IndexOutOfBoundsException