meshi.energy.hydrogenBondsPairs
Class PairsOfHBEElementsList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<PairOfHydrogenBondsElements>
              meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<PairOfHydrogenBondsElements>, java.util.Collection<PairOfHydrogenBondsElements>, java.util.List<PairOfHydrogenBondsElements>, java.util.RandomAccess, Updateable

public class PairsOfHBEElementsList
extends java.util.ArrayList<PairOfHydrogenBondsElements>
implements Updateable

See Also:

Serialized Form

Nested Class Summary

(package private) static class	PairsOfHBEElementsList.IsWithInRmax
private class	PairsOfHBEElementsList.WithinRmaxPairsIterator

Field Summary

private boolean	debug
int	deletions
protected HBondList	hBondList
int	insertion
private PairsOfHBEElementsList.IsWithInRmax	isWithinRmax
private int	numberOfUpdates

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

PairsOfHBEElementsList()

PairsOfHBEElementsList(HydrogenBondsEnergy hbe)

Method Summary

void	cleanList() save only the live elements inthis list
private void	createPairsList(DistanceList hBonbds)
private void	doNothing()
HBondList	hBondList()
void	update()
void	update(int numberOfUpdates)
void	updateNew(DistanceList newlist, int lastIndexBeforeNewElements)
java.util.Iterator	withinRmaxPairsIterator()

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 java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

insertion

public int insertion

deletions

public int deletions

hBondList

protected HBondList hBondList

numberOfUpdates

private int numberOfUpdates

debug

private boolean debug

isWithinRmax

private PairsOfHBEElementsList.IsWithInRmax isWithinRmax

Constructor Detail

PairsOfHBEElementsList

public PairsOfHBEElementsList()

PairsOfHBEElementsList

public PairsOfHBEElementsList(HydrogenBondsEnergy hbe)

Method Detail

hBondList

public final HBondList hBondList()

update

public void update(int numberOfUpdates)

Specified by:

update in interface Updateable

update

public void update()

doNothing

private void doNothing()

createPairsList

private void createPairsList(DistanceList hBonbds)

updateNew

public void updateNew(DistanceList newlist,
                      int lastIndexBeforeNewElements)

cleanList

public void cleanList()

save only the live elements inthis list

withinRmaxPairsIterator

public java.util.Iterator withinRmaxPairsIterator()