Package de.isas.lipidomics.domain

Class LipidSpeciesInfo

java.lang.Object

de.isas.lipidomics.domain.FattyAcid

de.isas.lipidomics.domain.LipidSpeciesInfo

public class LipidSpeciesInfo
extends FattyAcid

This class summarizes the FA parts of a lipid, independent of its head group. Thus, it accounts the total number of carbon atoms, double bonds, the number of hydroxylations, the overall FA-headgroup bond type, e.g. PLASMANYL / PLASMENYL, if any of a lipid's FA chains has such a bond type, or ESTER or UNDEFINED for other cases.

Author:

nils.hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
static LipidSpeciesInfo	NONE	Use this class to indicate that no lipid species info is available.

Constructor Summary

Constructors

Constructor	Description
LipidSpeciesInfo(LipidLevel level, int nCarbon, int nHydroxy, int nDoubleBonds, LipidFaBondType lipidFaBondType)	Create a new LipidSpeciesInfo on the provided level.The name is inferred from the level.
LipidSpeciesInfo(LipidLevel level, String name, int position, int nCarbon, int nHydroxy, int nDoubleBonds, LipidFaBondType lipidFaBondType, boolean lcb, ModificationsList modifications)	Create a new LipidSpeciesInfo on the provided level.
LipidSpeciesInfo(LipidLevel level, String name, int position, int nCarbon, int nHydroxy, LipidFaBondType lipidFaBondType, boolean lcb, ModificationsList modifications, int nDoubleBonds, Map<Integer,String> doubleBondPositions)	Create a new LipidSpeciesInfo on the provided level.

Method Summary

Modifier and Type	Method	Description
String	buildSubstructureName(LipidLevel level)	Build the name of this substructure.
ElementTable	getElements(int numFa)	Returns the element table for this species info adjusted for oxygen and hydrogen.

Methods inherited from class de.isas.lipidomics.domain.FattyAcid

getElements

Methods inherited from class java.lang.Object

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

Field Detail

NONE

public static final LipidSpeciesInfo NONE

Use this class to indicate that no lipid species info is available.

Constructor Detail

LipidSpeciesInfo

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

Create a new LipidSpeciesInfo on the provided level.

Parameters:

level - the level of the species info.

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

LipidSpeciesInfo

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

Create a new LipidSpeciesInfo on the provided level.

Parameters:

level - the level of the species info.

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

LipidSpeciesInfo

public LipidSpeciesInfo(LipidLevel level,
                        int nCarbon,
                        int nHydroxy,
                        int nDoubleBonds,
                        LipidFaBondType lipidFaBondType)

Create a new LipidSpeciesInfo on the provided level.The name is inferred from the level.

Parameters:

level - the level of the species info.

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.

Method Detail

buildSubstructureName

public String buildSubstructureName(LipidLevel level)

Description copied from class: FattyAcid

Build the name of this substructure.

Overrides:

buildSubstructureName in class FattyAcid

Parameters:

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

Returns:

the name of this substructure.

getElements

public ElementTable getElements(int numFa)

Returns the element table for this species info adjusted for oxygen and hydrogen.

Parameters:

numFa - the number of fatty acyls to account for.

Returns:

the element table.