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

All Superinterfaces:
DSBioObject, DSDescribable, DSExtendable, DSIdentifiable, DSNamed, DSSequential, java.io.Serializable
All Known Implementing Classes:
CSMicroarray

public interface DSMicroarray
extends DSBioObject

The microarray abstraction. Every microarray contains values for each one of its associated set of markers. Every microarray belongs to a microarray set, along with other microarrays. In the context of its host microarray set, a microarray has an index position (or "serial") that distinguishes it from the other microarrays in the set.


Method Summary
 DSMicroarray deepCopy()
           
 int getMarkerNo()
          Returns the number of features in the chip
 DSMarkerValue getMarkerValue(DSGeneMarker markerInfo)
           
 DSMarkerValue getMarkerValue(int index)
           
 DSMarkerValue[] getMarkerValues()
           
 float[] getRawMarkerData()
           
 boolean isMarkerUndefined(int i)
          Convenience method to access the undefined status of the i-th feature directly
 boolean isMarkerValid(int i)
          Convenience method to access the valid status of the i-th feature directly
 void resize(int size)
          Resize the number of features to a new value.
 void setMarkerValue(int index, DSMarkerValue markerValue)
          Add the designated marker value at the specified index
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSExtendable
addNameValuePair, allowMultipleValues, clearName, forceUniqueValue, getValuesForName, isUniqueValue
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable
getDescription, setDescription
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSIdentifiable
getID, setID
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSSequential
getSerial, setSerial
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSNamed
getLabel, setLabel
 

Method Detail

getMarkerNo

int getMarkerNo()
Returns the number of features in the chip

Returns:
int

isMarkerValid

boolean isMarkerValid(int i)
Convenience method to access the valid status of the i-th feature directly

Parameters:
i - int
Returns:
boolean

isMarkerUndefined

boolean isMarkerUndefined(int i)
Convenience method to access the undefined status of the i-th feature directly

Parameters:
i - int
Returns:
boolean

setMarkerValue

void setMarkerValue(int index,
                    DSMarkerValue markerValue)
Add the designated marker value at the specified index

Parameters:
index - int at which marker vale is to be added
markerValue - MarkerValue to be added

getMarkerValues

DSMarkerValue[] getMarkerValues()
Returns:
an array of microarray features.

getMarkerValue

DSMarkerValue getMarkerValue(DSGeneMarker markerInfo)
Parameters:
markerInfo - A marker whose value is requested.
Returns:
The MarkerValue for the designated marker within this microarray, if the marker exists in the microarray. Null, otherwise.

getMarkerValue

DSMarkerValue getMarkerValue(int index)
Parameters:
index - The relative position (index) of a marker within the microarray.
Returns:
The marker value for the desiganted index position, if index is non-negative and no larger than the microarray size. null, otherwise.

deepCopy

DSMicroarray deepCopy()
Returns:
A deep copy of the microarray.

resize

void resize(int size)
Resize the number of features to a new value. This destroys all previous values


getRawMarkerData

float[] getRawMarkerData()