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

java.lang.Object
  extended by org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
      extended by org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<DSMarkerValue>, 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.
 
Method Summary
 int compareTo(DSMarkerValue 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.
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

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(DSMarkerValue o)
Specified by:
compareTo in interface java.lang.Comparable<DSMarkerValue>