Package org.lifstools.jgoslin.domain

Class FattyAcid

java.lang.Object

org.lifstools.jgoslin.domain.FunctionalGroup

org.lifstools.jgoslin.domain.FattyAcid

Direct Known Subclasses:

LipidSpeciesInfo

public class FattyAcid
extends FunctionalGroup

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 / functional groups and can report double bond positions.

Author:

Dominik Kopczynski, Nils Hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
static final Set<String>	fgExceptions
static final Set<LipidFaBondType>	LCB_STATES
protected LipidFaBondType	lipidFaBondType
protected int	numCarbon

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

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

Constructor Summary

Constructors

Constructor	Description
FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds)
FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, LipidFaBondType _lipid_FA_bond_type, int _position, KnownFunctionalGroups knownFunctionalGroups)
FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, LipidFaBondType _lipid_FA_bond_type, KnownFunctionalGroups knownFunctionalGroups)
FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, KnownFunctionalGroups knownFunctionalGroups)
FattyAcid(String _name, int _num_carbon, KnownFunctionalGroups knownFunctionalGroups)
FattyAcid(String _name, KnownFunctionalGroups knownFunctionalGroups)

Method Summary

Modifier and Type	Method	Description
void	computeElements()
FunctionalGroup	copy()
ElementTable	getFunctionalGroupElements()
LipidFaBondType	getLipidFaBondType()
int	getNDoubleBonds()
int	getNumCarbon()
String	getPrefix(LipidFaBondType lipid_FA_bond_type)
boolean	lipidFaBondTypePrefix(LipidFaBondType lipid_FA_bond_type)
void	setLipidFaBondType(LipidFaBondType lipidFaBondType)
void	setNumCarbon(int numCarbon)
void	setType(LipidFaBondType _lipid_FA_bond_type)
String	toString(LipidLevel level)

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

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

Methods inherited from class java.lang.Object

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

Field Details

fgExceptions

public static final Set<String> fgExceptions

LCB_STATES

public static final Set<LipidFaBondType> LCB_STATES

numCarbon

protected int numCarbon

lipidFaBondType

protected LipidFaBondType lipidFaBondType

Constructor Details

FattyAcid

public FattyAcid(String _name,
 KnownFunctionalGroups knownFunctionalGroups)

FattyAcid

public FattyAcid(String _name,
 int _num_carbon,
 DoubleBonds _double_bonds)

FattyAcid

public FattyAcid(String _name,
 int _num_carbon,
 DoubleBonds _double_bonds,
 KnownFunctionalGroups knownFunctionalGroups)

FattyAcid

public FattyAcid(String _name,
 int _num_carbon,
 KnownFunctionalGroups knownFunctionalGroups)

FattyAcid

public FattyAcid(String _name,
 int _num_carbon,
 DoubleBonds _double_bonds,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 KnownFunctionalGroups knownFunctionalGroups)

FattyAcid

public FattyAcid(String _name,
 int _num_carbon,
 DoubleBonds _double_bonds,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 LipidFaBondType _lipid_FA_bond_type,
 KnownFunctionalGroups knownFunctionalGroups)

FattyAcid

public FattyAcid(String _name,
 int _num_carbon,
 DoubleBonds _double_bonds,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 LipidFaBondType _lipid_FA_bond_type,
 int _position,
 KnownFunctionalGroups knownFunctionalGroups)

Method Details

copy

public FunctionalGroup copy()

Overrides:

copy in class FunctionalGroup

setType

public void setType(LipidFaBondType _lipid_FA_bond_type)

getPrefix

public String getPrefix(LipidFaBondType lipid_FA_bond_type)

getNDoubleBonds

public int getNDoubleBonds()

Overrides:

getNDoubleBonds in class FunctionalGroup

lipidFaBondTypePrefix

public boolean lipidFaBondTypePrefix(LipidFaBondType lipid_FA_bond_type)

toString

public String toString(LipidLevel level)

Overrides:

toString in class FunctionalGroup

getFunctionalGroupElements

public ElementTable getFunctionalGroupElements()

Overrides:

getFunctionalGroupElements in class FunctionalGroup

computeElements

public void computeElements()

Overrides:

computeElements in class FunctionalGroup

getNumCarbon

public int getNumCarbon()

setNumCarbon

public void setNumCarbon(int numCarbon)

getLipidFaBondType

public LipidFaBondType getLipidFaBondType()

setLipidFaBondType

public void setLipidFaBondType(LipidFaBondType lipidFaBondType)