Package 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
public abstract class ChemicalConstantImpl extends L3ElementImpl implements ChemicalConstant
See Also:

  • Field Summary

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

    UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

  • Constructor Summary

    Constructors
    Constructor
    Description
    ChemicalConstantImpl()
     

  • Method Summary

    Modifier and Type
    Method
    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, removeComment, setComment

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

    equals, getAnnotations, getUri, 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.BioPAXElement

    getAnnotations, getUri, isEquivalent

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

    addComment, getComment, removeComment

  • Constructor Details

    • ChemicalConstantImpl

      public ChemicalConstantImpl()

  • Method Details

    • 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.