Package de.isas.lipidomics.domain

Class LipidAdduct

java.lang.Object

de.isas.lipidomics.domain.LipidAdduct

public class LipidAdduct
extends Object

Base class for lipid names parsed using the different grammars. This can contain a lipid, an adduct, a sum formula and a fragment.

Author:

nils.hoffmann

See Also:

LipidSpecies, Adduct, Fragment

Constructor Summary

Constructors

Constructor	Description
LipidAdduct()

Method Summary

Modifier and Type	Method	Description
String	getClassName()	Returns the class name for this lipid adduct.
ElementTable	getElements()	Returns the elemental composition table.
String	getLipidFragmentString(LipidLevel level)	Returns the non-normalized lipid adduct name (original head group) with fragment, if available, for the given level.
String	getLipidString()	Returns the non-normalized (original head group) lipid name for the native level of this lipid.
String	getLipidString(LipidLevel level)	Returns the non-normalized (original head group) lipid name for the given level.
Double	getMass()	Calculates the mass based on the elements of this lipid adduct.
String	getNormalizedLipidFragmentString(LipidLevel level)	Returns the normalized lipid adduct name (class name as head group) with fragment for the given level.
String	getNormalizedLipidString()	Returns the normalized (class name as head group) lipid name for the native level of this lipid.
String	getNormalizedLipidString(LipidLevel level)	Returns the normalized (class name as head group) lipid name for the given level.
String	getSumFormula()	Returns the sum formula.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

LipidAdduct

public LipidAdduct()

Method Detail

getMass

public Double getMass()

Calculates the mass based on the elements of this lipid adduct.

Returns:

the mass (in Dalton).

getElements

public ElementTable getElements()

Returns the elemental composition table.

Returns:

the elemental composition table.

getSumFormula

public String getSumFormula()

Returns the sum formula.

Returns:

the sum formula.

getLipidString

public String getLipidString()

Returns the non-normalized (original head group) lipid name for the native level of this lipid.

Returns:

the non-normalized lipid name with adduct.

getLipidString

public String getLipidString(LipidLevel level)

Returns the non-normalized (original head group) lipid name for the given level.

Parameters:

level - the lipid level to generate the name on.

Returns:

the non-normalized lipid name with adduct.

getNormalizedLipidString

public String getNormalizedLipidString()

Returns the normalized (class name as head group) lipid name for the native level of this lipid.

Returns:

the normalized lipid name with adduct.

getNormalizedLipidString

public String getNormalizedLipidString(LipidLevel level)

Returns the normalized (class name as head group) lipid name for the given level.

Parameters:

level - the lipid level to generate the name on.

Returns:

the normalized lipid name with adduct.

getClassName

public String getClassName()

Returns the class name for this lipid adduct.

Returns:

the class name.

getLipidFragmentString

public String getLipidFragmentString(LipidLevel level)

Returns the non-normalized lipid adduct name (original head group) with fragment, if available, for the given level.

Parameters:

level - the lipid level to generate the name on.

Returns:

the non-normalized lipid name with adduct and fragment.

getNormalizedLipidFragmentString

public String getNormalizedLipidFragmentString(LipidLevel level)

Returns the normalized lipid adduct name (class name as head group) with fragment for the given level.

Parameters:

level - the lipid level to generate the name on.

Returns:

the normalized lipid name with adduct and fragment.

toString

public String toString()

Overrides:

toString in class Object