Package ubic.gemma.model.expression.bioAssayData

Interface CellLevelCharacteristics

All Superinterfaces:

Describable, Identifiable

All Known Implementing Classes:

CellTypeAssignment, GenericCellLevelCharacteristics

public interface CellLevelCharacteristics
extends Describable

Characteristics applicable to individual cells in a SingleCellDimension.

Author:

poirigui

See Also:

• CellTypeAssignment
• GenericCellLevelCharacteristics

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	CellLevelCharacteristics.Factory

Field Summary

Fields

Modifier and Type	Field	Description
static final Comparator<CellLevelCharacteristics>	COMPARATOR
static final int	UNKNOWN_CHARACTERISTIC	Indicator for an unknown characteristic.

Method Summary

Modifier and Type	Method	Description
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 getCharacteristics() is applicable for a given cell.
String	getName()	Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
Integer	getNumberOfAssignedCells()	Obtain the number of cells assigned with a characteristic.
int	getNumberOfCharacteristics()	The number of characteristics in getCharacteristics().

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

getDescription

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

getId

Field Details

COMPARATOR

static final Comparator<CellLevelCharacteristics> COMPARATOR

UNKNOWN_CHARACTERISTIC

static final int UNKNOWN_CHARACTERISTIC

Indicator for an unknown characteristic.

See Also:

• Constant Field Values

Method Details

getName

@Nullable
String getName()

Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.

The name is not mandatory, but if set it will appear in lieu of the category.

Specified by:

getName in interface Describable

getCharacteristics

List<Characteristic> getCharacteristics()

List of characteristic.

getNumberOfCharacteristics

int getNumberOfCharacteristics()

The number of characteristics in getCharacteristics().

getIndices

int[] getIndices()

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

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

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

getNumberOfAssignedCells

@Nullable
Integer getNumberOfAssignedCells()

Obtain the number of cells assigned with a characteristic.

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

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

getCharacteristic

@Nullable
Characteristic getCharacteristic(int cellIndex)
                          throws IndexOutOfBoundsException

Obtain the characteristic assigned to a given cell.

Returns:

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

Throws:

IndexOutOfBoundsException - if the cell index is out of bounds