toxTree.data
Class ListOfAtomContainers

java.lang.Object
  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.ArrayList<org.openscience.cdk.interfaces.IAtomContainer>
              extended by toxTree.data.ListOfAtomContainers
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<org.openscience.cdk.interfaces.IAtomContainer>, java.util.Collection<org.openscience.cdk.interfaces.IAtomContainer>, java.util.List<org.openscience.cdk.interfaces.IAtomContainer>, java.util.RandomAccess, org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject
Direct Known Subclasses:
QueryAtomContainers

public class ListOfAtomContainers
extends java.util.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
protected  java.lang.String id
           
protected  TTLogger logger
           
protected  java.util.Map properties
           
 
Fields inherited from class java.util.AbstractList
modCount
 
Constructor Summary
ListOfAtomContainers()
           
ListOfAtomContainers(java.util.Collection arg0)
           
ListOfAtomContainers(int arg0)
           
 
Method Summary
 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)
           
 java.lang.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()
           
 java.lang.String getID()
           
 int getListenerCount()
           
 java.lang.Double getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
           
 java.lang.Double getMultiplier(int arg0)
           
 java.lang.Double[] getMultipliers()
           
 boolean getNotification()
           
 java.util.Map getProperties()
           
 java.lang.Object getProperty(java.lang.Object description)
           
 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(java.lang.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(java.lang.String identifier)
           
 boolean setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0, java.lang.Double arg1)
           
 void setMultiplier(int position, java.lang.Double multiplier)
           
 boolean setMultipliers(java.lang.Double[] newMultipliers)
           
 void setNotification(boolean arg0)
           
 void setProperties(java.util.Map<java.lang.Object,java.lang.Object> properties)
           
 void setProperty(java.lang.Object description, java.lang.Object property)
           
 void sortAtomContainers(java.util.Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)
           
 
Methods inherited from class java.util.ArrayList
add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize
 
Methods inherited from class java.util.AbstractList
equals, hashCode, iterator, listIterator, listIterator, subList
 
Methods inherited from class java.util.AbstractCollection
containsAll, removeAll, retainAll, toString
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
clone, toString
 
Methods inherited from interface java.util.List
containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList
 

Field Detail

logger

protected transient TTLogger logger

id

protected java.lang.String id

properties

protected java.util.Map properties
Constructor Detail

ListOfAtomContainers

public ListOfAtomContainers()

ListOfAtomContainers

public ListOfAtomContainers(int arg0)

ListOfAtomContainers

public ListOfAtomContainers(java.util.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,
                          java.lang.Double multiplier)
Specified by:
setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public java.lang.Double getMultiplier(int arg0)
Specified by:
getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultipliers

public java.lang.Double[] getMultipliers()
Specified by:
getMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultipliers

public boolean setMultipliers(java.lang.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 java.lang.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,
                             java.lang.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(java.lang.Object description,
                        java.lang.Object property)
Specified by:
setProperty in interface org.openscience.cdk.interfaces.IChemObject

removeProperty

public void removeProperty(java.lang.Object description)
Specified by:
removeProperty in interface org.openscience.cdk.interfaces.IChemObject

getProperty

public java.lang.Object getProperty(java.lang.Object description)
Specified by:
getProperty in interface org.openscience.cdk.interfaces.IChemObject

getProperties

public java.util.Map getProperties()
Specified by:
getProperties in interface org.openscience.cdk.interfaces.IChemObject

getID

public java.lang.String getID()
Specified by:
getID in interface org.openscience.cdk.interfaces.IChemObject

setID

public void setID(java.lang.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(java.util.Map<java.lang.Object,java.lang.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 java.lang.Iterable<org.openscience.cdk.interfaces.IAtomContainer> atomContainers()
Specified by:
atomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

sortAtomContainers

public void sortAtomContainers(java.util.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


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