Package org.lifstools.jgoslin.domain

Class Cycle

java.lang.Object

org.lifstools.jgoslin.domain.FunctionalGroup

org.lifstools.jgoslin.domain.Cycle

public final class Cycle
extends FunctionalGroup

A cyclic hydrocarbon chain as a functional group.

Author:

Dominik Kopczynski, Nils Hoffmann

Field Summary

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

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

Constructor Summary

Constructors

Constructor	Description
Cycle(int _cycle, int _start, int _end, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
Cycle(int _cycle, int _start, int _end, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, ArrayList<Element> _bridge_chain, KnownFunctionalGroups knownFunctionalGroups)
Cycle(int _cycle, int _start, int _end, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
Cycle(int _cycle, int _start, int _end, KnownFunctionalGroups knownFunctionalGroups)
Cycle(int _cycle, KnownFunctionalGroups knownFunctionalGroups)

Method Summary

Modifier and Type	Method	Description
void	addPosition(int pos)
void	computeElements()
FunctionalGroup	copy()
ArrayList<Element>	getBridgeChain()
int	getCycle()
int	getEnd()
int	getNDoubleBonds()
int	getStart()
void	rearrangeFunctionalGroups(FunctionalGroup parent, int shift)
void	setCycle(int cycle)
void	setEnd(int end)
void	setStart(int start)
void	shiftPositions(int shift)
String	toString(LipidLevel level)

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

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

Methods inherited from class java.lang.Object

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

Constructor Details

Cycle

public Cycle(int _cycle,
 KnownFunctionalGroups knownFunctionalGroups)

Cycle

public Cycle(int _cycle,
 int _start,
 int _end,
 KnownFunctionalGroups knownFunctionalGroups)

Cycle

public Cycle(int _cycle,
 int _start,
 int _end,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 KnownFunctionalGroups knownFunctionalGroups)

Cycle

public Cycle(int _cycle,
 int _start,
 int _end,
 DoubleBonds _double_bonds,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 KnownFunctionalGroups knownFunctionalGroups)

Cycle

public Cycle(int _cycle,
 int _start,
 int _end,
 DoubleBonds _double_bonds,
 HashMap<String,ArrayList<FunctionalGroup>> _functional_groups,
 ArrayList<Element> _bridge_chain,
 KnownFunctionalGroups knownFunctionalGroups)

Method Details

copy

public FunctionalGroup copy()

Overrides:

copy in class FunctionalGroup

getCycle

public int getCycle()

setCycle

public void setCycle(int cycle)

getStart

public int getStart()

setStart

public void setStart(int start)

getEnd

public int getEnd()

setEnd

public void setEnd(int end)

getBridgeChain

public ArrayList<Element> getBridgeChain()

getNDoubleBonds

public int getNDoubleBonds()
                    throws ConstraintViolationException

Overrides:

getNDoubleBonds in class FunctionalGroup

Throws:

ConstraintViolationException

addPosition

public void addPosition(int pos)

Overrides:

addPosition in class FunctionalGroup

rearrangeFunctionalGroups

public void rearrangeFunctionalGroups(FunctionalGroup parent,
 int shift)

shiftPositions

public void shiftPositions(int shift)

Overrides:

shiftPositions in class FunctionalGroup

computeElements

public void computeElements()

Overrides:

computeElements in class FunctionalGroup

toString

public String toString(LipidLevel level)

Overrides:

toString in class FunctionalGroup