org.biopax.paxtools.impl.level3

Class ChemicalConstantImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.ChemicalConstantImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, ChemicalConstant, Level3Element, UtilityClass

Direct Known Subclasses:

DeltaGImpl, KPrimeImpl

@Entity
public abstract class ChemicalConstantImpl
extends L3ElementImpl
implements ChemicalConstant

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
ChemicalConstantImpl()

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
float	getIonicStrength() The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi).
Class<? extends ChemicalConstant>	getModelInterface() This method returns the actual model interface that a class implements.
float	getPh() A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.
float	getPMg()
float	getTemperature()
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setIonicStrength(float ionicStrength) The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi).
void	setPh(float ph) A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.
void	setPMg(float pMg)
void	setTemperature(float temperature)

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

getAnnotations, getRDFId, isEquivalent

Constructor Detail

ChemicalConstantImpl

public ChemicalConstantImpl()

Method Detail

getIonicStrength

public float getIonicStrength()

Description copied from interface: ChemicalConstant

The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M

Specified by:

getIonicStrength in interface ChemicalConstant

Returns:

The ionic strength

setIonicStrength

public void setIonicStrength(float ionicStrength)

Description copied from interface: ChemicalConstant

The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M

Specified by:

setIonicStrength in interface ChemicalConstant

Parameters:

ionicStrength - The ionic strength

getPh

public float getPh()

Description copied from interface: ChemicalConstant

A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.

Specified by:

getPh in interface ChemicalConstant

Returns:

A measure of acidity and alkalinity of a solution

setPh

public void setPh(float ph)

Description copied from interface: ChemicalConstant

A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.

Specified by:

setPh in interface ChemicalConstant

Parameters:

ph - A measure of acidity and alkalinity of a solution

getPMg

public float getPMg()

Specified by:

getPMg in interface ChemicalConstant

Returns:

A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺])

setPMg

public void setPMg(float pMg)

Specified by:

setPMg in interface ChemicalConstant

Parameters:

pMg - A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺])

getTemperature

public float getTemperature()

Specified by:

getTemperature in interface ChemicalConstant

Returns:

Temperature in Celsius

setTemperature

public void setTemperature(float temperature)

Specified by:

setTemperature in interface ChemicalConstant

Parameters:

temperature - Temperature in Celsius

getModelInterface

public Class<? extends ChemicalConstant> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class BioPAXElementImpl

Returns:

an integer that is same across all equivalent entities.