org.geworkbench.bison.datastructure.bioobjects.microarray
Interface DSMarkerValue

All Superinterfaces:

java.lang.Comparable, java.io.Serializable

All Known Subinterfaces:

DSAffyMarkerValue, DSGenepixMarkerValue, DSGenotypicMarkerValue, DSMutableMarkerValue

All Known Implementing Classes:

CSAffyMarkerValue, CSExpressionMarkerValue, CSGenepixMarkerValue, CSGenotypicMarkerValue, CSMarkerValue

public interface DSMarkerValue
extends java.lang.Comparable, java.io.Serializable

Model of the data collected for a single spot (feature) on a microarray. This is the "minimum" set of data expected, regardless of the underlying technology. Technology-specific data points can be added by extending this class.

Method Summary

DSMarkerValue	deepCopy() Make a deep copy of the measurements associated with this spot.
boolean	equals(java.lang.Object m) Tests if two markers are equal
double	getConfidence() A value indicating our confidence in the measured signal.
int	getDimensionality() This method returns the dimensionality of the marker.
double	getValue() Return the signal measurement for this spot.
boolean	isMasked() This method returns whether this marker should be temporarily ignored by analytical tools
boolean	isMissing() Check if the mesurement for this spot is classified as "missing".
boolean	isValid() This method returns whether the marker is both unmasked and not undefined.

Methods inherited from interface java.lang.Comparable

compareTo

Method Detail

getValue

double getValue()

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

Returns:

marker value

getConfidence

double getConfidence()

A value indicating our confidence in the measured signal.

Returns:

confidence

isMissing

boolean isMissing()

Check if the mesurement for this spot is classified as "missing".

Returns:

presence

isMasked

boolean isMasked()

This method returns whether this marker should be temporarily ignored by analytical tools

Returns:

isValid

boolean isValid()

This method returns whether the marker is both unmasked and not undefined. As a result, there is no corresponding setValid method. Should likely be moved to MarkerValue

Returns:

equals

boolean equals(java.lang.Object m)

Tests if two markers are equal

Overrides:

equals in class java.lang.Object

Parameters:

m - marker to be compared

Returns:

boolean equality

getDimensionality

int getDimensionality()

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

Returns:

int the dimensionality of the marker.

deepCopy

DSMarkerValue deepCopy()

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

Returns:

MarkerValue clone of this marker