Package ubic.gemma.model.expression.bioAssayData

Class GenericCellLevelCharacteristics

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics

All Implemented Interfaces:

Describable, Identifiable, CellLevelCharacteristics

public class GenericCellLevelCharacteristics
extends AbstractDescribable
implements CellLevelCharacteristics

Generic cell-level characteristics.

For cell types, use CellTypeAssignment instead.

This is not meant to be used directly, prefer CellLevelCharacteristics.Factory.newInstance(java.lang.String, java.lang.String, java.util.List<ubic.gemma.model.common.description.Characteristic>, int[]) for creating cell-level characteristics or CellTypeAssignment for cell types.

Author:

poirigui

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics

CellLevelCharacteristics.Factory

Field Summary

Fields inherited from interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics

COMPARATOR, UNKNOWN_CHARACTERISTIC

Constructor Summary

Constructors

Constructor	Description
GenericCellLevelCharacteristics()

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Important note: Two objects with the same class and non-null ID must be considered equal.
Characteristic	getCharacteristic(int cellIndex)	Obtain the characteristic assigned to a given cell.
List<Characteristic>	getCharacteristics()	List of characteristic.
int[]	getIndices()	Each entry indicate which characteristic from CellLevelCharacteristics.getCharacteristics() is applicable for a given cell.
Integer	getNumberOfAssignedCells()	Obtain the number of cells assigned with a characteristic.
int	getNumberOfCharacteristics()	The number of characteristics in CellLevelCharacteristics.getCharacteristics().
int	hashCode()	Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
void	setCharacteristics(List<Characteristic> characteristics)
void	setIndices(int[] indices)
void	setNumberOfAssignedCells(Integer numberOfAssignedCells)
void	setNumberOfCharacteristics(int numberOfCharacteristics)
String	toString()

Methods inherited from class ubic.gemma.model.common.AbstractDescribable

getDescription, getName, setDescription, setName

Methods inherited from class ubic.gemma.model.common.AbstractIdentifiable

getId, setId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics

getName

Methods inherited from interface ubic.gemma.model.common.Describable

getDescription

Methods inherited from interface ubic.gemma.model.common.Identifiable

getId

Constructor Details

GenericCellLevelCharacteristics

public GenericCellLevelCharacteristics()

Method Details

getCharacteristic

@Nullable
public Characteristic getCharacteristic(int cellIndex)

Description copied from interface: CellLevelCharacteristics

Obtain the characteristic assigned to a given cell.

Specified by:

getCharacteristic in interface CellLevelCharacteristics

Returns:

the characteristic or null if the cell is assigned to CellLevelCharacteristics.UNKNOWN_CHARACTERISTIC.

hashCode

public int hashCode()

Description copied from class: AbstractIdentifiable

Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.

Overrides:

hashCode in class AbstractDescribable

equals

public boolean equals(Object object)

Description copied from class: AbstractIdentifiable

Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.

Specified by:

equals in class AbstractIdentifiable

toString

public String toString()

Overrides:

toString in class AbstractDescribable

getCharacteristics

public List<Characteristic> getCharacteristics()

Description copied from interface: CellLevelCharacteristics

List of characteristic.

Specified by:

getCharacteristics in interface CellLevelCharacteristics

getNumberOfCharacteristics

public int getNumberOfCharacteristics()

Description copied from interface: CellLevelCharacteristics

The number of characteristics in CellLevelCharacteristics.getCharacteristics().

Specified by:

getNumberOfCharacteristics in interface CellLevelCharacteristics

getIndices

public int[] getIndices()

Description copied from interface: CellLevelCharacteristics

Each entry indicate which characteristic from CellLevelCharacteristics.getCharacteristics() is applicable for a given cell.

CellLevelCharacteristics.UNKNOWN_CHARACTERISTIC is used to indicate a missing value for a cell. In this case, CellLevelCharacteristics.getCharacteristic(int) returns null.

The size of this array is the number of cells, typically in a SingleCellDimension.

Specified by:

getIndices in interface CellLevelCharacteristics

getNumberOfAssignedCells

@Nullable
public Integer getNumberOfAssignedCells()

Description copied from interface: CellLevelCharacteristics

Obtain the number of cells assigned with a characteristic.

This is equal to the number of entries in CellLevelCharacteristics.getIndices() that are not CellLevelCharacteristics.UNKNOWN_CHARACTERISTIC.

TOOD: switch to a regular int once existing CLCs have all been back-filled.

Specified by:

getNumberOfAssignedCells in interface CellLevelCharacteristics

setCharacteristics

public void setCharacteristics(List<Characteristic> characteristics)

setNumberOfCharacteristics

public void setNumberOfCharacteristics(int numberOfCharacteristics)

setIndices

public void setIndices(int[] indices)

setNumberOfAssignedCells

public void setNumberOfAssignedCells(@Nullable
 Integer numberOfAssignedCells)