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

All Superinterfaces:

DSBioObject, DSDescribable, DSExtendable, DSHasActivation, 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
DSMutableMarkerValue	getMarkerValue(DSGeneMarker markerInfo)
DSMutableMarkerValue	getMarkerValue(int index)
DSMutableMarkerValue[]	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
java.util.Iterator<DSMutableMarkerValue>	iterator() Return an iterator over the markers
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

addDescription, getDescriptions, removeDescription

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

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSHasActivation

enable, enabled

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

DSMutableMarkerValue[] getMarkerValues()

Returns:

an array of microarray features.

getMarkerValue

DSMutableMarkerValue 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

DSMutableMarkerValue 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.

iterator

java.util.Iterator<DSMutableMarkerValue> iterator()

Return an iterator over the markers

Returns:

ArrayIterator

resize

void resize(int size)

Resize the number of features to a new value. This destroys all previous values

getRawMarkerData

float[] getRawMarkerData()