Package org.lifstools.jgoslin.domain

Class LipidSpeciesInfo

java.lang.Object

org.lifstools.jgoslin.domain.FunctionalGroup

org.lifstools.jgoslin.domain.FattyAcid

org.lifstools.jgoslin.domain.LipidSpeciesInfo

public final 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. ETHER PLASMANYL / PLASMENYL, if any of a lipid's FA chains has such a bond type, or ESTER, AMINE, LCB or UNDEFINED for other cases.

Author:

Dominik Kopczynski, Nils Hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
static final String[]	ETHER_PREFIX
LipidFaBondType	extendedClass
int	lipidClass
int	numEthers
int	numSpecifiedFa
int	totalFa

Fields inherited from class org.lifstools.jgoslin.domain.FattyAcid

lipidFaBondType, numCarbon

Fields inherited from class org.lifstools.jgoslin.domain.FunctionalGroup

atomic, count, doubleBonds, elements, functionalGroups, knownFunctionalGroups, name, position, ringStereo, stereochemistry

Constructor Summary

Constructors

Constructor	Description
LipidSpeciesInfo(int _lipid_class, KnownFunctionalGroups knownFunctionalGroups)

Method Summary

Modifier and Type	Method	Description
void	add(FattyAcid _fa)
LipidSpeciesInfo	copy()
ElementTable	getElements()
LipidFaBondType	getExtendedClass()
LipidLevel	getLevel()
int	getLipidClass()
int	getNumEthers()
int	getNumSpecifiedFa()
int	getTotalFa()
void	setExtendedClass(LipidFaBondType extendedClass)
void	setLevel(LipidLevel level)
void	setLipidClass(int lipidClass)
void	setNumEthers(int numEthers)
void	setNumSpecifiedFa(int numSpecifiedFa)
void	setTotalFa(int totalFa)
String	toString()

Methods inherited from class org.lifstools.jgoslin.domain.FattyAcid

computeElements, getFunctionalGroupElements, getLipidFaBondType, getNDoubleBonds, getNumCarbon, getPrefix, lipidFaBondTypePrefix, setLipidFaBondType, setNumCarbon, setType, toString

Methods inherited from class org.lifstools.jgoslin.domain.FunctionalGroup

addPosition, computeAndCopyElements, getCount, getDoubleBonds, getFunctionalGroups, getFunctionalGroupsInternal, getName, getPosition, getRingStereo, getStereochemistry, getTotalFunctionalGroupCount, isAtomic, setAtomic, setCount, setDoubleBonds, setElements, setFunctionalGroups, setName, setPosition, setRingStereo, setStereochemistry, shiftPositions

Methods inherited from class java.lang.Object

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

Field Details

numEthers

public int numEthers

numSpecifiedFa

public int numSpecifiedFa

totalFa

public int totalFa

extendedClass

public LipidFaBondType extendedClass

ETHER_PREFIX

public static final String[] ETHER_PREFIX

lipidClass

public int lipidClass

Constructor Details

LipidSpeciesInfo

public LipidSpeciesInfo(int _lipid_class,
 KnownFunctionalGroups knownFunctionalGroups)

Method Details

copy

public LipidSpeciesInfo copy()

Overrides:

copy in class FattyAcid

getElements

public ElementTable getElements()

Overrides:

getElements in class FunctionalGroup

add

public void add(FattyAcid _fa)

toString

public String toString()

Overrides:

toString in class Object

getLevel

public LipidLevel getLevel()

setLevel

public void setLevel(LipidLevel level)

getNumEthers

public int getNumEthers()

setNumEthers

public void setNumEthers(int numEthers)

getNumSpecifiedFa

public int getNumSpecifiedFa()

setNumSpecifiedFa

public void setNumSpecifiedFa(int numSpecifiedFa)

getTotalFa

public int getTotalFa()

setTotalFa

public void setTotalFa(int totalFa)

getExtendedClass

public LipidFaBondType getExtendedClass()

setExtendedClass

public void setExtendedClass(LipidFaBondType extendedClass)

getLipidClass

public int getLipidClass()

setLipidClass

public void setLipidClass(int lipidClass)