org.helm.notation2.calculation

Class ExtinctionCoefficient

java.lang.Object

org.helm.notation2.calculation.ExtinctionCoefficient

public final class ExtinctionCoefficient
extends Object

ExtinctionCoefficient class to calculate the extinction coefficient

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static int	PEPTIDE_UNIT_TYPE
static int	RNA_UNIT_TYPE

Method Summary

Methods

Modifier and Type	Method and Description
float	calculate(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to calculate the extinction coefficient for the whole HELM molecule
float	calculate(org.helm.notation2.parser.notation.HELM2Notation helm2notation, int unitType) method to calculate the extinction coefficient for the whole HELM molecule
String	getDefaultUnit()
int	getDefaultUnitType()
static ExtinctionCoefficient	getInstance()
String	getPeptideUnit()
String	getRnaUnit()
String	getUnit(int unitType)

Methods inherited from class java.lang.Object

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

Field Detail

RNA_UNIT_TYPE

public static final int RNA_UNIT_TYPE

See Also:

Constant Field Values

PEPTIDE_UNIT_TYPE

public static final int PEPTIDE_UNIT_TYPE

See Also:

Constant Field Values

Method Detail

getInstance

public static ExtinctionCoefficient getInstance()
                                         throws ExtinctionCoefficientException

Throws:

ExtinctionCoefficientException

getUnit

public String getUnit(int unitType)

getRnaUnit

public String getRnaUnit()

getPeptideUnit

public String getPeptideUnit()

getDefaultUnit

public String getDefaultUnit()

getDefaultUnitType

public int getDefaultUnitType()

calculate

public float calculate(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                throws ExtinctionCoefficientException,
                       ChemistryException

method to calculate the extinction coefficient for the whole HELM molecule

Parameters:

helm2notation - input HELM2Notation

Returns:

extinction coefficient

Throws:

ExtinctionCoefficientException - if the HELM contains HELM2 features

ChemistryException - if the Chemistry Engine can not be initialized

calculate

public float calculate(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
              int unitType)
                throws ExtinctionCoefficientException,
                       ChemistryException

method to calculate the extinction coefficient for the whole HELM molecule

Parameters:

helm2notation - input HELM2Notation

unitType - Unit of the extinction coefficient

Returns:

extinction coefficient

Throws:

ExtinctionCoefficientException - if the HELM contains HELM2 features

ChemistryException - if the Chemistry Engine can not be initialized