Package org.lifstools.jgoslin.domain

Class FunctionalGroup

java.lang.Object

org.lifstools.jgoslin.domain.FunctionalGroup

Direct Known Subclasses:

AcylAlkylGroup, CarbonChain, Cycle, FattyAcid, HeadgroupDecorator

public class FunctionalGroup
extends Object

A functional group of a fatty acid, it can contain nested functional groups.

Author:

Dominik Kopczynski, Nils Hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	atomic
protected int	count
protected DoubleBonds	doubleBonds
protected ElementTable	elements
protected Map<String,ArrayList<FunctionalGroup>>	functionalGroups
protected KnownFunctionalGroups	knownFunctionalGroups
protected String	name
protected int	position
protected String	ringStereo
protected String	stereochemistry

Constructor Summary

Constructors

Constructor	Description
FunctionalGroup(String _name, int _position, int _count, DoubleBonds _double_bonds, boolean _is_atomic, String _stereochemistry, ElementTable _elements, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
FunctionalGroup(String _name, int _position, int _count, DoubleBonds _double_bonds, boolean _is_atomic, String _stereochemistry, ElementTable _elements, KnownFunctionalGroups knownFunctionalGroups)
FunctionalGroup(String _name, int _position, int _count, KnownFunctionalGroups knownFunctionalGroups)
FunctionalGroup(String _name, KnownFunctionalGroups knownFunctionalGroups)

Method Summary

Modifier and Type	Method	Description
void	addPosition(int pos)
ElementTable	computeAndCopyElements()
void	computeElements()
FunctionalGroup	copy()
int	getCount()
DoubleBonds	getDoubleBonds()
ElementTable	getElements()
ElementTable	getFunctionalGroupElements()
Map<String,ArrayList<FunctionalGroup>>	getFunctionalGroups()	Returns a copy of the internally used functional groups map, with the virtual [X] group for regular LCBs removed.
Map<String,ArrayList<FunctionalGroup>>	getFunctionalGroupsInternal()	Returns the internal representation of the functional groups, including the virtual [X] group for regular LCBs.
String	getName()
int	getNDoubleBonds()
int	getPosition()
String	getRingStereo()
String	getStereochemistry()
Integer	getTotalFunctionalGroupCount(String functionalGroup)	Return the total count for the given functional group name, or 0.
boolean	isAtomic()
void	setAtomic(boolean atomic)
void	setCount(int count)
void	setDoubleBonds(DoubleBonds doubleBonds)
void	setElements(ElementTable elements)
void	setFunctionalGroups(Map<String,ArrayList<FunctionalGroup>> functionalGroups)	Set the internal functional groups.
void	setName(String name)
void	setPosition(int position)
void	setRingStereo(String ringStereo)
void	setStereochemistry(String stereochemistry)
void	shiftPositions(int shift)
String	toString(LipidLevel level)

Methods inherited from class java.lang.Object

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

Field Details

name

protected String name

position

protected int position

count

protected int count

stereochemistry

protected String stereochemistry

ringStereo

protected String ringStereo

doubleBonds

protected DoubleBonds doubleBonds

atomic

protected boolean atomic

elements

protected ElementTable elements

functionalGroups

protected Map<String,ArrayList<FunctionalGroup>> functionalGroups

knownFunctionalGroups

protected KnownFunctionalGroups knownFunctionalGroups

Constructor Details

FunctionalGroup

public FunctionalGroup(String _name,
 KnownFunctionalGroups knownFunctionalGroups)

FunctionalGroup

public FunctionalGroup(String _name,
 int _position,
 int _count,
 KnownFunctionalGroups knownFunctionalGroups)

FunctionalGroup

public FunctionalGroup(String _name,
 int _position,
 int _count,
 DoubleBonds _double_bonds,
 boolean _is_atomic,
 String _stereochemistry,
 ElementTable _elements,
 KnownFunctionalGroups knownFunctionalGroups)

FunctionalGroup

public FunctionalGroup(String _name,
 int _position,
 int _count,
 DoubleBonds _double_bonds,
 boolean _is_atomic,
 String _stereochemistry,
 ElementTable _elements,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 KnownFunctionalGroups knownFunctionalGroups)

Method Details

copy

public FunctionalGroup copy()

setName

public void setName(String name)

getName

public String getName()

setPosition

public void setPosition(int position)

getPosition

public int getPosition()

setCount

public void setCount(int count)

getCount

public int getCount()

getStereochemistry

public String getStereochemistry()

setStereochemistry

public void setStereochemistry(String stereochemistry)

getRingStereo

public String getRingStereo()

setRingStereo

public void setRingStereo(String ringStereo)

getDoubleBonds

public DoubleBonds getDoubleBonds()

setDoubleBonds

public void setDoubleBonds(DoubleBonds doubleBonds)

setAtomic

public void setAtomic(boolean atomic)

isAtomic

public boolean isAtomic()

getElements

public ElementTable getElements()

setElements

public void setElements(ElementTable elements)

computeAndCopyElements

public ElementTable computeAndCopyElements()

shiftPositions

public void shiftPositions(int shift)

getTotalFunctionalGroupCount

public Integer getTotalFunctionalGroupCount(String functionalGroup)

Return the total count for the given functional group name, or 0.

Parameters:

functionalGroup - the functional group name.

Returns:

the total count

getFunctionalGroups

public Map<String,ArrayList<FunctionalGroup>> getFunctionalGroups()

Returns a copy of the internally used functional groups map, with the virtual [X] group for regular LCBs removed.

Returns:

a copy of the internal functional groups

See Also:

• to obtain the internal datastructure by reference.

getFunctionalGroupsInternal

public Map<String,ArrayList<FunctionalGroup>> getFunctionalGroupsInternal()

Returns the internal representation of the functional groups, including the virtual [X] group for regular LCBs.

Returns:

the internal datastructure by reference.

setFunctionalGroups

public void setFunctionalGroups(Map<String,ArrayList<FunctionalGroup>> functionalGroups)

Set the internal functional groups.

Parameters:

functionalGroups - the functional groups to set

getFunctionalGroupElements

public ElementTable getFunctionalGroupElements()

computeElements

public void computeElements()

toString

public String toString(LipidLevel level)

getNDoubleBonds

public int getNDoubleBonds()
                    throws ConstraintViolationException

Throws:

ConstraintViolationException

addPosition

public void addPosition(int pos)