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 final Comparator<CellTypeAssignment>	COMPARATOR
static final 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.
int[]	getCellTypeIndices()	Cell types assignment to individual cells from the cellTypes collections.
List<Characteristic>	getCellTypes()	List of cell types.
Characteristic	getCharacteristic(int cellIndex)	Use getCellType(int) instead.
List<Characteristic>	getCharacteristics()	Deprecated. Use getCellTypes() instead.
int[]	getIndices()	Deprecated. Use getCellTypeIndices() instead.
Integer	getNumberOfAssignedCells()	Obtain the number of cells assigned with a characteristic.
int	getNumberOfCellTypes()	Number of cell types.
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.
boolean	isPreferred()	Indicate if this assignment is the preferred one.
void	setCellTypeIndices(int[] cellTypeIndices)	Cell types assignment to individual cells from the cellTypes collections.
void	setCellTypes(List<Characteristic> cellTypes)	List of cell types.
void	setNumberOfAssignedCells(Integer numberOfAssignedCells)
void	setNumberOfCellTypes(int numberOfCellTypes)	Number of cell types.
void	setPreferred(boolean preferred)	Indicate if this assignment is the preferred one.
String	toString()

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

getName, getProtocol, setName, setProtocol

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

getDescription, setDescription

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

Field Details

COMPARATOR

public static final Comparator<CellTypeAssignment> COMPARATOR

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 Details

CellTypeAssignment

public CellTypeAssignment()

Method Details

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

@Deprecated
public List<Characteristic> getCharacteristics()

Deprecated.

Use getCellTypes() instead.

Description copied from interface: CellLevelCharacteristics

List of characteristic.

Specified by:

getCharacteristics in interface CellLevelCharacteristics

getNumberOfCharacteristics

@Deprecated
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

@Deprecated
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

isPreferred

public boolean isPreferred()

Indicate if this assignment is the preferred one.

There can only be one preferred cell type assignment for a given SingleCellDimension.

getCellTypeIndices

public int[] getCellTypeIndices()

Cell types assignment to individual cells from the cellTypes collections.

The value -1 is used to indicate an unknown cell type.

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

getCellTypes

public List<Characteristic> getCellTypes()

List of cell types.

getNumberOfCellTypes

public int getNumberOfCellTypes()

Number of cell types.

This must always be equal to number of elements of cellTypes.

setPreferred

public void setPreferred(boolean preferred)

Indicate if this assignment is the preferred one.

There can only be one preferred cell type assignment for a given SingleCellDimension.

setCellTypeIndices

public void setCellTypeIndices(int[] cellTypeIndices)

Cell types assignment to individual cells from the cellTypes collections.

The value -1 is used to indicate an unknown cell type.

setNumberOfAssignedCells

public void setNumberOfAssignedCells(@Nullable
 Integer numberOfAssignedCells)

setCellTypes

public void setCellTypes(List<Characteristic> cellTypes)

List of cell types.

setNumberOfCellTypes

public void setNumberOfCellTypes(int numberOfCellTypes)

Number of cell types.

This must always be equal to number of elements of cellTypes.