Package ubic.gemma.model.expression.bioAssayData

Class CellTypeAssignment

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.analysis.Analysis

ubic.gemma.model.expression.bioAssayData.CellTypeAssignment

All Implemented Interfaces:

Describable, Identifiable, CellLevelCharacteristics

public class CellTypeAssignment
extends Analysis
implements CellLevelCharacteristics

Represents a cell type assignment where cells from a given dataset are assigned cell types.

Author:

poirigui

See Also:

SingleCellDimension

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CellTypeAssignment.Factory

Field Summary

Fields

Modifier and Type	Field	Description
static int	UNKNOWN_CELL_TYPE	A special indicator for cellTypeIndices when the cell type is unknown.

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

UNKNOWN_CHARACTERISTIC

Constructor Summary

Constructors

Constructor	Description
CellTypeAssignment()

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	getCellType(int cellIndex)	Obtain the type assignment of a given cell.
Characteristic	getCharacteristic(int cellIndex)	Use getCellType(int) instead.
List<Characteristic>	getCharacteristics()	Deprecated. Use #getCellTypes() instead.
int[]	getIndices()	Deprecated. Use #getCellTypeIndices() instead.
int	getNumberOfCharacteristics()	Deprecated. Use #getNumberOfCellTypes() instead.
int	hashCode()	Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
String	toString()

Methods inherited from class ubic.gemma.model.analysis.Analysis

getProtocol, setProtocol

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

getNumberOfAssignedCells

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

getId

Field Detail

UNKNOWN_CELL_TYPE

public static final int UNKNOWN_CELL_TYPE

A special indicator for cellTypeIndices when the cell type is unknown.

See Also:

Constant Field Values

Constructor Detail

CellTypeAssignment

public CellTypeAssignment()

Method Detail

getCellType

@Nullable
public Characteristic getCellType(int cellIndex)
                           throws IndexOutOfBoundsException

Obtain the type assignment of a given cell.

Returns:

the type assignment of a given cell, or null if the type was assigne to UNKNOWN_CELL_TYPE.

Throws:

IndexOutOfBoundsException - if the cell index is out of bounds

getCharacteristics

public List<Characteristic> getCharacteristics()

Deprecated.

Use #getCellTypes() instead.

Description copied from interface: CellLevelCharacteristics

List of characteristic.

Specified by:

getCharacteristics in interface CellLevelCharacteristics

getNumberOfCharacteristics

public int getNumberOfCharacteristics()

Deprecated.

Use #getNumberOfCellTypes() instead.

Description copied from interface: CellLevelCharacteristics

The number of characteristics in CellLevelCharacteristics.getCharacteristics().

Specified by:

getNumberOfCharacteristics in interface CellLevelCharacteristics

getIndices

public int[] getIndices()

Deprecated.

Use #getCellTypeIndices() instead.

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

getCharacteristic

@Nullable
public Characteristic getCharacteristic(int cellIndex)

Use getCellType(int) instead.

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