org.biojava.bio.chromatogram.graphic
Class FixedBaseWidthScaler
java.lang.Object
org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
- All Implemented Interfaces:
- ChromatogramNonlinearScaler
public class FixedBaseWidthScaler
- extends java.lang.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
Constructor Summary |
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 |
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 |
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 pixelscenterPeaks
- 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.
scale
public float scale(Chromatogram c,
int traceSampleIndex)
throws java.lang.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 ChromatogramtraceSampleIndex
- the sample index
- Returns:
- the new coordinagte
- Throws:
java.lang.IndexOutOfBoundsException