Package bio.singa.simulation.model.concentrations

Class ConcentrationBuilder.ConcentrationBuilderImpl

java.lang.Object

bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

All Implemented Interfaces:

ConcentrationBuilder.AdditionalConditionsStep, ConcentrationBuilder.BuildStep, ConcentrationBuilder.ConcentrationStep, ConcentrationBuilder.ConcentrationUnitStep, ConcentrationBuilder.EntityStep, ConcentrationBuilder.PoolStep, ConcentrationBuilder.TimedUnitStep

Enclosing class:

ConcentrationBuilder

public static class ConcentrationBuilder.ConcentrationBuilderImpl
extends Object
implements ConcentrationBuilder.EntityStep, ConcentrationBuilder.PoolStep, ConcentrationBuilder.ConcentrationStep, ConcentrationBuilder.ConcentrationUnitStep, ConcentrationBuilder.AdditionalConditionsStep, ConcentrationBuilder.TimedUnitStep

Constructor Summary

Constructors

Constructor	Description
ConcentrationBuilderImpl()
ConcentrationBuilderImpl(Simulation simulation)

Method Summary

Modifier and Type	Method	Description
InitialConcentration	build()
ConcentrationBuilder.AdditionalConditionsStep	concentration(javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)
ConcentrationBuilder.ConcentrationUnitStep	concentrationValue(double value)
ConcentrationBuilder.PoolStep	entity(ChemicalEntity entity)
ConcentrationBuilder.BuildStep	evidence(bio.singa.features.model.Evidence evidence)
ConcentrationBuilder.AdditionalConditionsStep	fixed()
ConcentrationBuilder.AdditionalConditionsStep	inArea(bio.singa.mathematics.geometry.model.Polygon polygon)
ConcentrationBuilder.AdditionalConditionsStep	inRegionArea(CellRegion region)
ConcentrationBuilder.AdditionalConditionsStep	molecules(double numberOfMolecules)
ConcentrationBuilder.AdditionalConditionsStep	onlyNodes()
ConcentrationBuilder.AdditionalConditionsStep	onlyVesicles()
ConcentrationBuilder.AdditionalConditionsStep	region(CellRegion region)
ConcentrationBuilder.AdditionalConditionsStep	regions(CellRegion... regions)
ConcentrationBuilder.AdditionalConditionsStep	regions(List<CellRegion> regions)
ConcentrationBuilder.ConcentrationStep	subsection(CellSubsection subsection)
ConcentrationBuilder.TimedUnitStep	timed(TimedCondition.Relation realtion, double time)
ConcentrationBuilder.AdditionalConditionsStep	timed(TimedCondition.Relation realtion, tech.units.indriya.ComparableQuantity<javax.measure.quantity.Time> time)
ConcentrationBuilder.AdditionalConditionsStep	timeUnit(javax.measure.Unit<javax.measure.quantity.Time> timeUnit)
ConcentrationBuilder.ConcentrationStep	topology(CellTopology topology)
ConcentrationBuilder.AdditionalConditionsStep	unit(javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> concentrationUnit)
ConcentrationBuilder.AdditionalConditionsStep	updatableIdentifier(String identifier)
ConcentrationBuilder.AdditionalConditionsStep	updatableIdentifiers(String... identifiers)
ConcentrationBuilder.AdditionalConditionsStep	updatableIdentifiers(List<String> identifiers)

Methods inherited from class java.lang.Object

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

Methods inherited from interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep

microMolar, milliMolar, nanoMolar

Methods inherited from interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep

milliSeconds, minutes, seconds

Constructor Detail

ConcentrationBuilderImpl

public ConcentrationBuilderImpl()

ConcentrationBuilderImpl

public ConcentrationBuilderImpl(Simulation simulation)

Method Detail

entity

public ConcentrationBuilder.PoolStep entity(ChemicalEntity entity)

Specified by:

entity in interface ConcentrationBuilder.EntityStep

subsection

public ConcentrationBuilder.ConcentrationStep subsection(CellSubsection subsection)

Specified by:

subsection in interface ConcentrationBuilder.PoolStep

topology

public ConcentrationBuilder.ConcentrationStep topology(CellTopology topology)

Specified by:

topology in interface ConcentrationBuilder.PoolStep

concentration

public ConcentrationBuilder.AdditionalConditionsStep concentration(javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)

Specified by:

concentration in interface ConcentrationBuilder.ConcentrationStep

molecules

public ConcentrationBuilder.AdditionalConditionsStep molecules(double numberOfMolecules)

Specified by:

molecules in interface ConcentrationBuilder.ConcentrationStep

concentrationValue

public ConcentrationBuilder.ConcentrationUnitStep concentrationValue(double value)

Specified by:

concentrationValue in interface ConcentrationBuilder.ConcentrationStep

unit

public ConcentrationBuilder.AdditionalConditionsStep unit(javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> concentrationUnit)

Specified by:

unit in interface ConcentrationBuilder.ConcentrationUnitStep

updatableIdentifiers

public ConcentrationBuilder.AdditionalConditionsStep updatableIdentifiers(List<String> identifiers)

Specified by:

updatableIdentifiers in interface ConcentrationBuilder.AdditionalConditionsStep

updatableIdentifiers

public ConcentrationBuilder.AdditionalConditionsStep updatableIdentifiers(String... identifiers)

Specified by:

updatableIdentifiers in interface ConcentrationBuilder.AdditionalConditionsStep

updatableIdentifier

public ConcentrationBuilder.AdditionalConditionsStep updatableIdentifier(String identifier)

Specified by:

updatableIdentifier in interface ConcentrationBuilder.AdditionalConditionsStep

regions

public ConcentrationBuilder.AdditionalConditionsStep regions(List<CellRegion> regions)

Specified by:

regions in interface ConcentrationBuilder.AdditionalConditionsStep

regions

public ConcentrationBuilder.AdditionalConditionsStep regions(CellRegion... regions)

Specified by:

regions in interface ConcentrationBuilder.AdditionalConditionsStep

region

public ConcentrationBuilder.AdditionalConditionsStep region(CellRegion region)

Specified by:

region in interface ConcentrationBuilder.AdditionalConditionsStep

inArea

public ConcentrationBuilder.AdditionalConditionsStep inArea(bio.singa.mathematics.geometry.model.Polygon polygon)

Specified by:

inArea in interface ConcentrationBuilder.AdditionalConditionsStep

inRegionArea

public ConcentrationBuilder.AdditionalConditionsStep inRegionArea(CellRegion region)

Specified by:

inRegionArea in interface ConcentrationBuilder.AdditionalConditionsStep

timed

public ConcentrationBuilder.AdditionalConditionsStep timed(TimedCondition.Relation realtion,
                                                           tech.units.indriya.ComparableQuantity<javax.measure.quantity.Time> time)

Specified by:

timed in interface ConcentrationBuilder.AdditionalConditionsStep

fixed

public ConcentrationBuilder.AdditionalConditionsStep fixed()

Specified by:

fixed in interface ConcentrationBuilder.AdditionalConditionsStep

onlyNodes

public ConcentrationBuilder.AdditionalConditionsStep onlyNodes()

Specified by:

onlyNodes in interface ConcentrationBuilder.AdditionalConditionsStep

onlyVesicles

public ConcentrationBuilder.AdditionalConditionsStep onlyVesicles()

Specified by:

onlyVesicles in interface ConcentrationBuilder.AdditionalConditionsStep

timed

public ConcentrationBuilder.TimedUnitStep timed(TimedCondition.Relation realtion,
                                                double time)

Specified by:

timed in interface ConcentrationBuilder.AdditionalConditionsStep

timeUnit

public ConcentrationBuilder.AdditionalConditionsStep timeUnit(javax.measure.Unit<javax.measure.quantity.Time> timeUnit)

Specified by:

timeUnit in interface ConcentrationBuilder.TimedUnitStep

evidence

public ConcentrationBuilder.BuildStep evidence(bio.singa.features.model.Evidence evidence)

Specified by:

evidence in interface ConcentrationBuilder.BuildStep

build

public InitialConcentration build()

Specified by:

build in interface ConcentrationBuilder.BuildStep