org.geworkbench.bison.datastructure.bioobjects.microarray
Class CSGenepixMarkerValue

java.lang.Object
  org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
      org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, DSGenepixMarkerValue, DSMarkerValue, DSMutableMarkerValue

public class CSGenepixMarkerValue
extends CSMarkerValue
implements DSGenepixMarkerValue, java.io.Serializable

Implementation of GenepixMarkerValue.

See Also:

Serialized Form

Nested Class Summary

static class

CSGenepixMarkerValue.ComputeSignalMethod

Field Summary

Fields inherited from class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue

confidence, m_threshold, MISSING, p_threshold, value

Constructor Summary

CSGenepixMarkerValue(CSGenepixMarkerValue gmvi)

CSGenepixMarkerValue(double val)

CSGenepixMarkerValue(GenepixParseContext context)
Constructs a GenepixMarkerValue object from the contents of the GenepixParseContext argument.

CSGenepixMarkerValue(NCIParseContext context)
Constructs a GenepixMarkerValue object from the contents of the NCIParseContext argument.

Method Summary

void	adjustForHousekeepingGenes(CSGenepixMarkerValue[] csgArray)
void	adjustForHousekeepingGenes(double newRatio)
int	compareTo(java.lang.Object o)
void	computeSignal() Calculate the signal value from the channel values.
DSMarkerValue	deepCopy() Make a deep copy of the measurements associated with this spot.
double	getCh1Bg() Gets the Background Value at 635 nm wavelength
double	getCh1Fg() Gets the Signal Value at 635 nm wavelength
double	getCh2Bg() Gets the Background Value at 532 nm wavelength
double	getCh2Fg() Gets the Signal Value at 532 nm wavelength
static CSGenepixMarkerValue.ComputeSignalMethod	getComputeSignalMethod()
double	getConfidence() A value indicating our confidence in the measured signal.
int	getDimensionality() This method returns the dimensionality of the marker.
java.lang.String	getFlag() Gets the flag value
double	getValue() Return the signal measurement for this spot.
void	setCh1Bg(double ch1b) Sets the Background Value at 635 nm wavelength
void	setCh1Fg(double ch1f) Sets the Signal Value at 635 nm wavelength
void	setCh2Bg(double ch2b) Sets the Background Value at 532 nm wavelength
void	setCh2Fg(double ch2f) Sets the Signal Value at 532 nm wavelength
static void	setComputeSignalMethod(CSGenepixMarkerValue.ComputeSignalMethod computeSignalMethod)
void	setConfidence(double confidence) Set the confidence level.
void	setFlag(java.lang.String flag) Sets the flag value

Methods inherited from class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue

equals, getStatusAsChar, isAbsent, isMarginal, isMasked, isMissing, isPresent, isValid, mask, setAbsent, setMarginal, setMarginalThreshold, setMissing, setPresent, setPresentThreshold, setValue, unmask

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMutableMarkerValue

mask, setMissing, setValue, unmask

Methods inherited from interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue

equals, isMasked, isMissing, isValid

Constructor Detail

CSGenepixMarkerValue

public CSGenepixMarkerValue(double val)

CSGenepixMarkerValue

public CSGenepixMarkerValue(CSGenepixMarkerValue gmvi)

CSGenepixMarkerValue

public CSGenepixMarkerValue(GenepixParseContext context)

Constructs a GenepixMarkerValue object from the contents of the GenepixParseContext argument.

Parameters:

context - The parse context used for the initialization.

CSGenepixMarkerValue

public CSGenepixMarkerValue(NCIParseContext context)

Constructs a GenepixMarkerValue object from the contents of the NCIParseContext argument.

Parameters:

context - The parse context used for the initialization.

Method Detail

getComputeSignalMethod

public static CSGenepixMarkerValue.ComputeSignalMethod getComputeSignalMethod()

setComputeSignalMethod

public static void setComputeSignalMethod(CSGenepixMarkerValue.ComputeSignalMethod computeSignalMethod)

setCh1Fg

public void setCh1Fg(double ch1f)

Sets the Signal Value at 635 nm wavelength

Specified by:

setCh1Fg in interface DSGenepixMarkerValue

Parameters:

ch1f - Signal

setCh1Bg

public void setCh1Bg(double ch1b)

Sets the Background Value at 635 nm wavelength

Specified by:

setCh1Bg in interface DSGenepixMarkerValue

Parameters:

ch1b - Background

setCh2Fg

public void setCh2Fg(double ch2f)

Sets the Signal Value at 532 nm wavelength

Specified by:

setCh2Fg in interface DSGenepixMarkerValue

Parameters:

ch2f - Signal

setCh2Bg

public void setCh2Bg(double ch2b)

Sets the Background Value at 532 nm wavelength

Specified by:

setCh2Bg in interface DSGenepixMarkerValue

Parameters:

ch2b - Background

getCh1Fg

public double getCh1Fg()

Gets the Signal Value at 635 nm wavelength

Specified by:

getCh1Fg in interface DSGenepixMarkerValue

Returns:

Signal Value

getCh1Bg

public double getCh1Bg()

Gets the Background Value at 635 nm wavelength

Specified by:

getCh1Bg in interface DSGenepixMarkerValue

Returns:

Background Value

getCh2Fg

public double getCh2Fg()

Gets the Signal Value at 532 nm wavelength

Specified by:

getCh2Fg in interface DSGenepixMarkerValue

Returns:

Signal Value

getCh2Bg

public double getCh2Bg()

Gets the Background Value at 532 nm wavelength

Specified by:

getCh2Bg in interface DSGenepixMarkerValue

Returns:

Background Value

getValue

public double getValue()

Description copied from interface: DSMarkerValue

Return the signal measurement for this spot. For 2-channel data, this is usually the ratio of the 2 channels.

Specified by:

getValue in interface DSMarkerValue

Overrides:

getValue in class CSMarkerValue

Returns:

marker value

getConfidence

public double getConfidence()

Description copied from interface: DSMarkerValue

A value indicating our confidence in the measured signal.

Specified by:

getConfidence in interface DSMarkerValue

Overrides:

getConfidence in class CSMarkerValue

Returns:

confidence

setConfidence

public void setConfidence(double confidence)

Description copied from interface: DSMutableMarkerValue

Set the confidence level.

Specified by:

setConfidence in interface DSMutableMarkerValue

Overrides:

setConfidence in class CSMarkerValue

Parameters:

confidence - confidence of spot's measument

getFlag

public java.lang.String getFlag()

Description copied from interface: DSGenepixMarkerValue

Gets the flag value

Specified by:

getFlag in interface DSGenepixMarkerValue

setFlag

public void setFlag(java.lang.String flag)

Description copied from interface: DSGenepixMarkerValue

Sets the flag value

Specified by:

setFlag in interface DSGenepixMarkerValue

deepCopy

public DSMarkerValue deepCopy()

Description copied from interface: DSMarkerValue

Make a deep copy of the measurements associated with this spot.

Specified by:

deepCopy in interface DSMarkerValue

Returns:

MarkerValue clone of this marker

computeSignal

public void computeSignal()

Calculate the signal value from the channel values.

Specified by:

computeSignal in interface DSGenepixMarkerValue

adjustForHousekeepingGenes

public void adjustForHousekeepingGenes(double newRatio)

adjustForHousekeepingGenes

public void adjustForHousekeepingGenes(CSGenepixMarkerValue[] csgArray)

Parameters:

csgArray - CSGenepixMarkerValue[]

getDimensionality

public int getDimensionality()

This method returns the dimensionality of the marker. E.g., Genotype markers are 2-dimensional while Allele/Haplotype markers are 1-dimensional

Specified by:

getDimensionality in interface DSMarkerValue

Returns:

int the dimensionality of the marker.

compareTo

public int compareTo(java.lang.Object o)

Specified by:

compareTo in interface java.lang.Comparable