toxTree.data

Class ListOfAtomContainers

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<org.openscience.cdk.interfaces.IAtomContainer>

toxTree.data.ListOfAtomContainers

All Implemented Interfaces:

Serializable, Cloneable, Iterable<org.openscience.cdk.interfaces.IAtomContainer>, Collection<org.openscience.cdk.interfaces.IAtomContainer>, List<org.openscience.cdk.interfaces.IAtomContainer>, RandomAccess, org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject

Direct Known Subclasses:

QueryAtomContainers

public class ListOfAtomContainers
extends ArrayList<org.openscience.cdk.interfaces.IAtomContainer>
implements org.openscience.cdk.interfaces.IAtomContainerSet

An attempt to implement org.openscience.cdk.interfaces.SetOfAtomContainers interface as a List

Author:

Nina Jeliazkova

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	id
protected static Logger	logger
protected Map	properties

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
ListOfAtomContainers()
ListOfAtomContainers(Collection arg0)
ListOfAtomContainers(int arg0)

Method Summary

Modifier and Type	Method and Description
void	add(org.openscience.cdk.interfaces.IAtomContainerSet atomContainerSet)
void	addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
void	addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer atomContainer, double multiplier)
void	addListener(org.openscience.cdk.interfaces.IChemObjectListener col)
void	addProperties(Map<Object,Object> properties)
Iterable<org.openscience.cdk.interfaces.IAtomContainer>	atomContainers()
org.openscience.cdk.interfaces.IAtomContainer	getAtomContainer(int number)
int	getAtomContainerCount()
org.openscience.cdk.interfaces.IAtomContainer[]	getAtomContainers()
org.openscience.cdk.interfaces.IChemObjectBuilder	getBuilder()
boolean	getFlag(int flag_type)
boolean[]	getFlags()
Number	getFlagValue()
String	getID()
int	getListenerCount()
Double	getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
Double	getMultiplier(int arg0)
Double[]	getMultipliers()
boolean	getNotification()
Map	getProperties()
Object	getProperty(Object description)
<T> T	getProperty(Object description, Class<T> c)
void	notifyChanged()
void	notifyChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent arg0)
void	removeAllAtomContainers()
void	removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
void	removeAtomContainer(int pos)
void	removeListener(org.openscience.cdk.interfaces.IChemObjectListener col)
void	removeProperty(Object description)
void	replaceAtomContainer(int position, org.openscience.cdk.interfaces.IAtomContainer container)
void	setFlag(int flag_type, boolean flag_value)
void	setFlags(boolean[] flagsNew)
void	setID(String identifier)
boolean	setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0, Double arg1)
void	setMultiplier(int position, Double multiplier)
boolean	setMultipliers(Double[] newMultipliers)
void	setNotification(boolean arg0)
void	setProperties(Map<Object,Object> properties)
void	setProperty(Object description, Object property)
void	sortAtomContainers(Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, forEach, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeIf, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode

Methods inherited from class java.util.AbstractCollection

containsAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainerSet

isEmpty

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

clone, toString

Methods inherited from interface java.util.List

containsAll, equals, hashCode

Methods inherited from interface java.util.Collection

parallelStream, stream

Field Detail

logger

protected static transient Logger logger

id

protected String id

properties

protected Map properties

Constructor Detail

ListOfAtomContainers

public ListOfAtomContainers()

ListOfAtomContainers

public ListOfAtomContainers(int arg0)

ListOfAtomContainers

public ListOfAtomContainers(Collection arg0)

Method Detail

addAtomContainer

public void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Specified by:

addAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Specified by:

removeAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAllAtomContainers

public void removeAllAtomContainers()

Specified by:

removeAllAtomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(int pos)

Specified by:

removeAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultiplier

public void setMultiplier(int position,
                          Double multiplier)

Specified by:

setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public Double getMultiplier(int arg0)

Specified by:

getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultipliers

public Double[] getMultipliers()

Specified by:

getMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultipliers

public boolean setMultipliers(Double[] newMultipliers)

Specified by:

setMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

addAtomContainer

public void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
                             double multiplier)

Specified by:

addAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

add

public void add(org.openscience.cdk.interfaces.IAtomContainerSet atomContainerSet)

Specified by:

add in interface org.openscience.cdk.interfaces.IAtomContainerSet

getAtomContainers

public org.openscience.cdk.interfaces.IAtomContainer[] getAtomContainers()

getAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(int number)

Specified by:

getAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public Double getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)

Specified by:

getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultiplier

public boolean setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0,
                             Double arg1)

Specified by:

setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getAtomContainerCount

public int getAtomContainerCount()

Specified by:

getAtomContainerCount in interface org.openscience.cdk.interfaces.IAtomContainerSet

addListener

public void addListener(org.openscience.cdk.interfaces.IChemObjectListener col)

Specified by:

addListener in interface org.openscience.cdk.interfaces.IChemObject

getListenerCount

public int getListenerCount()

Specified by:

getListenerCount in interface org.openscience.cdk.interfaces.IChemObject

removeListener

public void removeListener(org.openscience.cdk.interfaces.IChemObjectListener col)

Specified by:

removeListener in interface org.openscience.cdk.interfaces.IChemObject

notifyChanged

public void notifyChanged()

Specified by:

notifyChanged in interface org.openscience.cdk.interfaces.IChemObject

setProperty

public void setProperty(Object description,
                        Object property)

Specified by:

setProperty in interface org.openscience.cdk.interfaces.IChemObject

removeProperty

public void removeProperty(Object description)

Specified by:

removeProperty in interface org.openscience.cdk.interfaces.IChemObject

getProperty

public Object getProperty(Object description)

Specified by:

getProperty in interface org.openscience.cdk.interfaces.IChemObject

getProperties

public Map getProperties()

Specified by:

getProperties in interface org.openscience.cdk.interfaces.IChemObject

getID

public String getID()

Specified by:

getID in interface org.openscience.cdk.interfaces.IChemObject

setID

public void setID(String identifier)

Specified by:

setID in interface org.openscience.cdk.interfaces.IChemObject

setFlag

public void setFlag(int flag_type,
                    boolean flag_value)

Specified by:

setFlag in interface org.openscience.cdk.interfaces.IChemObject

getFlag

public boolean getFlag(int flag_type)

Specified by:

getFlag in interface org.openscience.cdk.interfaces.IChemObject

setProperties

public void setProperties(Map<Object,Object> properties)

Specified by:

setProperties in interface org.openscience.cdk.interfaces.IChemObject

setFlags

public void setFlags(boolean[] flagsNew)

Specified by:

setFlags in interface org.openscience.cdk.interfaces.IChemObject

getFlags

public boolean[] getFlags()

Specified by:

getFlags in interface org.openscience.cdk.interfaces.IChemObject

getBuilder

public org.openscience.cdk.interfaces.IChemObjectBuilder getBuilder()

Specified by:

getBuilder in interface org.openscience.cdk.interfaces.ICDKObject

setNotification

public void setNotification(boolean arg0)

Specified by:

setNotification in interface org.openscience.cdk.interfaces.IChemObject

getNotification

public boolean getNotification()

Specified by:

getNotification in interface org.openscience.cdk.interfaces.IChemObject

notifyChanged

public void notifyChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent arg0)

Specified by:

notifyChanged in interface org.openscience.cdk.interfaces.IChemObject

atomContainers

public Iterable<org.openscience.cdk.interfaces.IAtomContainer> atomContainers()

Specified by:

atomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

sortAtomContainers

public void sortAtomContainers(Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)

Specified by:

sortAtomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

replaceAtomContainer

public void replaceAtomContainer(int position,
                                 org.openscience.cdk.interfaces.IAtomContainer container)

Specified by:

replaceAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

addProperties

public void addProperties(Map<Object,Object> properties)

Specified by:

addProperties in interface org.openscience.cdk.interfaces.IChemObject

getFlagValue

public Number getFlagValue()

Specified by:

getFlagValue in interface org.openscience.cdk.interfaces.IChemObject

getProperty

public <T> T getProperty(Object description,
                         Class<T> c)

Specified by:

getProperty in interface org.openscience.cdk.interfaces.IChemObject