jigcell.compare.cellcycle
Class GenericPhenotype

java.lang.Object
  jigcell.compare.data.type.TypeChecker
      jigcell.compare.data.type.ListTypeChecker
          jigcell.compare.data.type.StructuredTypeChecker
              jigcell.compare.cellcycle.GenericPhenotype

All Implemented Interfaces:

IStructuredTypeChecker, ITypeChecker

public class GenericPhenotype
extends StructuredTypeChecker

Type for the generic cell cycle phenotype.

This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

Field Summary

protected static java.lang.String	TYPE_NAME Name of this type
protected static ITypeChecker	TYPE_SINGLETON Instance of this type

Fields inherited from class jigcell.compare.data.type.TypeChecker

COMPARATOR_NAME

Fields inherited from interface jigcell.compare.ITypeChecker

ATTRIBUTE_TYPE, METHOD_GENERATE, OPTION_TYPECHECKER

Constructor Summary

protected

GenericPhenotype() Creates a new type checker.

Method Summary

static IDataElement	createInviablePhenotype(double averageSubCycles, long errorCode, long cycles) A phenotype which describes an inviable mutant.
static IDataElement	createViablePhenotype(double stableG1Length, double stableDivisionMass, double averageSubCycles) A phenotype which describes a viable mutant.
static IDataElement	createViablePhenotype(double stableG1Length, double stableDivisionMass, double averageSubCycles, long cycles) A phenotype which describes a viable mutant.
static ITypeChecker	getInstance() A type checker.
java.lang.String	getName() A name for this type.
java.lang.String	getName(long pos) A name for the element at this position. Implementations that do not want to provide a name should return null.
IDataElement	getPrototype() A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.
ITypeChecker	getTypeChecker(long pos) A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
boolean	isCompatible(ITypeChecker type) Whether a data type can be converted to this type.
boolean	validate(IDataElement data) Whether a data element is an instance of this type.

Methods inherited from class jigcell.compare.data.type.StructuredTypeChecker

getDescription

Methods inherited from class jigcell.compare.data.type.ListTypeChecker

getType

Methods inherited from class jigcell.compare.data.type.TypeChecker

compareByName, getDescription, getTypeCheckerForGenerator, isCompatible, toString, validate

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface jigcell.compare.ITypeChecker

getDescription, getType

Field Detail

TYPE_NAME

protected static final java.lang.String TYPE_NAME

Name of this type

See Also:

Constant Field Values

TYPE_SINGLETON

protected static final ITypeChecker TYPE_SINGLETON

Instance of this type

Constructor Detail

GenericPhenotype

protected GenericPhenotype()

Creates a new type checker.

Method Detail

createInviablePhenotype

public static IDataElement createInviablePhenotype(double averageSubCycles,
                                                   long errorCode,
                                                   long cycles)

A phenotype which describes an inviable mutant.

Parameters:

averageSubCycles - Average number of cycles of a species per cell cycle

errorCode - Reason the mutant died

cycles - Number of cycles completed before death

createViablePhenotype

public static IDataElement createViablePhenotype(double stableG1Length,
                                                 double stableDivisionMass,
                                                 double averageSubCycles)

A phenotype which describes a viable mutant.

Parameters:

stableG1Length - Length of G1 when in steady state

stableDivisionMass - Division size when in steady state

averageSubCycles - Average number of cycles of a species per cell cycle

createViablePhenotype

public static IDataElement createViablePhenotype(double stableG1Length,
                                                 double stableDivisionMass,
                                                 double averageSubCycles,
                                                 long cycles)

A phenotype which describes a viable mutant.

Parameters:

stableG1Length - Length of G1 when in steady state

stableDivisionMass - Division size when in steady state

averageSubCycles - Average number of cycles of a species per cell cycle

cycles - Number of cycles needed to reach steady state

getInstance

public static ITypeChecker getInstance()

A type checker.

getName

public java.lang.String getName()

A name for this type.

Specified by:

getName in interface ITypeChecker

Overrides:

getName in class ListTypeChecker

getName

public java.lang.String getName(long pos)

A name for the element at this position. Implementations that do not want to provide a name should return null.

Specified by:

getName in interface IStructuredTypeChecker

Overrides:

getName in class StructuredTypeChecker

getPrototype

public IDataElement getPrototype()

A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.

Specified by:

getPrototype in interface IStructuredTypeChecker

Overrides:

getPrototype in class StructuredTypeChecker

getTypeChecker

public ITypeChecker getTypeChecker(long pos)

A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.

Specified by:

getTypeChecker in interface IStructuredTypeChecker

Overrides:

getTypeChecker in class StructuredTypeChecker

isCompatible

public boolean isCompatible(ITypeChecker type)

Whether a data type can be converted to this type.

Specified by:

isCompatible in interface ITypeChecker

Overrides:

isCompatible in class TypeChecker

Parameters:

type - Type to convert from

validate

public boolean validate(IDataElement data)

Whether a data element is an instance of this type.

Specified by:

validate in interface ITypeChecker

Overrides:

validate in class TypeChecker

Parameters:

data - Data element