trans.qc
Class CelFileStats

java.lang.Object
  trans.qc.CelFileStats

public class CelFileStats

extends java.lang.Object

Container for cel file and it's associated statistics.

Constructor Summary

CelFileStats(java.io.File serializedCelFile, java.lang.String groupName)
Loads virtualCel float[][] and calculates a rawMedian.

Method Summary

void	appendNotes(java.lang.String comment)
void	calculateControlStats(int[][][] controls, double noSynthMultiplier, double dimMultiplierHigh, double dimMultiplierLow, double brightMultiplier) Calculates the median value for each of the different classes of controls.
void	calculateStats() Reloads intensites and calculates mean, coef var, percentiles.
double	getCoefficientOfVariation()
java.lang.String	getGroupName()
float[]	getIntensities()
double	getMean()
double	getMedianBrightControls()
double	getMedianDimControls()
double	getMedianNoSynthControls()
double	getMedianScalar()
java.lang.StringBuffer	getNotes()
int	getNumBrightOutliers()
int	getNumDimOutliers()
int	getNumNoSynthOutliers()
double[]	getQuartiles()
double	getRawMedian()
java.io.File	getSerializedCelFile()
float[][]	getVirtualCel()
boolean	isOk()
void	loadFloatArrays(boolean makeCollapsedFloatArray) Loads the serialized virtualCel (float[][]) from disk and then collapses it to generate the intensities (float[]).
void	nullIntensityArrays() Nulls the virtualCel and collapsed intensities array.
void	setMedianScalar(double medianScalar)
void	setNotes(java.lang.StringBuffer notes)
void	setNumBrightOutliers(int numBrightOutliers)
void	setNumDimOutliers(int numDimOutliers)
void	setNumNoSynthOutliers(int numNoSynthOutliers)
void	setOk(boolean ok)
void	setRawMedian(double rawMedian)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

CelFileStats

public CelFileStats(java.io.File serializedCelFile,
                    java.lang.String groupName)

Loads virtualCel float[][] and calculates a rawMedian.

Method Detail

calculateStats

public void calculateStats()

Reloads intensites and calculates mean, coef var, percentiles.

calculateControlStats

public void calculateControlStats(int[][][] controls,
                                  double noSynthMultiplier,
                                  double dimMultiplierHigh,
                                  double dimMultiplierLow,
                                  double brightMultiplier)

Calculates the median value for each of the different classes of controls. NoSynt, Dim, Bright, using the virtualCel and the supplied xy coordinates. Also counts the number of feature outliers based on the number of standard deviations

nullIntensityArrays

public void nullIntensityArrays()

Nulls the virtualCel and collapsed intensities array.

loadFloatArrays

public void loadFloatArrays(boolean makeCollapsedFloatArray)

Loads the serialized virtualCel (float[][]) from disk and then collapses it to generate the intensities (float[]).

toString

public java.lang.String toString()

getCoefficientOfVariation

public double getCoefficientOfVariation()

getIntensities

public float[] getIntensities()

getMean

public double getMean()

getQuartiles

public double[] getQuartiles()

getGroupName

public java.lang.String getGroupName()

getSerializedCelFile

public java.io.File getSerializedCelFile()

isOk

public boolean isOk()

setOk

public void setOk(boolean ok)

getNotes

public java.lang.StringBuffer getNotes()

setNotes

public void setNotes(java.lang.StringBuffer notes)

appendNotes

public void appendNotes(java.lang.String comment)

getVirtualCel

public float[][] getVirtualCel()

getMedianBrightControls

public double getMedianBrightControls()

getMedianDimControls

public double getMedianDimControls()

getMedianNoSynthControls

public double getMedianNoSynthControls()

getNumBrightOutliers

public int getNumBrightOutliers()

setNumBrightOutliers

public void setNumBrightOutliers(int numBrightOutliers)

getNumDimOutliers

public int getNumDimOutliers()

setNumDimOutliers

public void setNumDimOutliers(int numDimOutliers)

getNumNoSynthOutliers

public int getNumNoSynthOutliers()

setNumNoSynthOutliers

public void setNumNoSynthOutliers(int numNoSynthOutliers)

getMedianScalar

public double getMedianScalar()

setMedianScalar

public void setMedianScalar(double medianScalar)

getRawMedian

public double getRawMedian()

setRawMedian

public void setRawMedian(double rawMedian)