Package de.isas.lipidomics.domain

Class FattyAcid

java.lang.Object

de.isas.lipidomics.domain.FattyAcid

Direct Known Subclasses:

LipidSpeciesInfo

public class FattyAcid
extends Object

A fatty acid with a specific type. This object defines the name, position, number of carbon atoms, hydroxyls and double bonds, as well as the bond type to the head group. A FattyAcid can carry optional modifications and can report double bond positions.

Author:

nils.hoffmann

Constructor Summary

Constructors

Constructor	Description
FattyAcid(String name, int position, int nCarbon, int nHydroxy, int nDoubleBonds, LipidFaBondType lipidFaBondType, boolean lcb, ModificationsList modifications)	Create a new structural level FattyAcid.
FattyAcid(String name, int nCarbon, int nHydroxy, int nDoubleBonds, LipidFaBondType lipidFaBondType, boolean lcb, ModificationsList modifications)	Create a new molecular level FattyAcid.
FattyAcid(String name, int position, int nCarbon, int nHydroxy, LipidFaBondType lipidFaBondType, boolean lcb, ModificationsList modifications, int nDoubleBonds, Map<Integer,String> doubleBondPositions)	Create a new isomeric level FattyAcid.

Method Summary

Modifier and Type	Method	Description
String	buildSubstructureName(LipidLevel level)	Build the name of this substructure.
ElementTable	getElements()

Methods inherited from class java.lang.Object

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

Constructor Detail

FattyAcid

public FattyAcid(String name,
                 int position,
                 int nCarbon,
                 int nHydroxy,
                 LipidFaBondType lipidFaBondType,
                 boolean lcb,
                 ModificationsList modifications,
                 int nDoubleBonds,
                 Map<Integer,String> doubleBondPositions)

Create a new isomeric level FattyAcid.

Parameters:

name - the name, e.g. FA1 for the first FA.

position - the sn position. -1 if undefined or unknown.

nCarbon - the number of carbons in this FA.

nHydroxy - the number of hydroxyls on this FA.

lipidFaBondType - the bond type, e.g. ESTER.

lcb - true if this is a long-chain base, e.g. in a Ceramide.

modifications - optional modifications for this FA.

nDoubleBonds - the number of double bonds in this FA.

doubleBondPositions - double bond positions in this FA.

See Also:

LipidFaBondType

FattyAcid

public FattyAcid(String name,
                 int position,
                 int nCarbon,
                 int nHydroxy,
                 int nDoubleBonds,
                 LipidFaBondType lipidFaBondType,
                 boolean lcb,
                 ModificationsList modifications)

Create a new structural level FattyAcid.

Parameters:

name - the name, e.g. FA1 for the first FA.

position - the sn position. -1 if undefined or unknown.

nCarbon - the number of carbons in this FA.

nHydroxy - the number of hydroxyls on this FA.

nDoubleBonds - the number of double bonds in this FA.

lipidFaBondType - the bond type, e.g. ESTER.

lcb - true if this is a long-chain base, e.g. in a Ceramide.

modifications - optional modifications for this FA.

See Also:

LipidFaBondType

FattyAcid

public FattyAcid(String name,
                 int nCarbon,
                 int nHydroxy,
                 int nDoubleBonds,
                 LipidFaBondType lipidFaBondType,
                 boolean lcb,
                 ModificationsList modifications)

Create a new molecular level FattyAcid.

Parameters:

name - the name, e.g. FA1 for the first FA.

nCarbon - the number of carbons in this FA.

nHydroxy - the number of hydroxyls on this FA.

nDoubleBonds - the number of double bonds in this FA.

lipidFaBondType - the bond type, e.g. ESTER.

lcb - true if this is a long-chain base, e.g. in a Ceramide.

modifications - optional modifications for this FA.

See Also:

LipidFaBondType

Method Detail

buildSubstructureName

public String buildSubstructureName(LipidLevel level)

Build the name of this substructure.

Parameters:

level - the structural lipid level to return this substructure's name on.

Returns:

the name of this substructure.

getElements

public ElementTable getElements()