org.jmol.modelset

Class AtomIteratorWithinModel

java.lang.Object

org.jmol.modelset.AtomIteratorWithinModel

All Implemented Interfaces:

AtomIndexIterator

public class AtomIteratorWithinModel
extends java.lang.Object
implements AtomIndexIterator

Field Summary

Fields

Modifier and Type	Field and Description
private int	atomIndex
private Bspf	bspf
private CubeIterator	bsptIter
private java.util.BitSet	bsSelected
private float	distanceSquared
private boolean	hemisphereOnly
private int	iNext
private boolean	isGreaterOnly
private boolean	isZeroBased
private int	modelIndex
private boolean	threadSafe
private int	zeroBase

Constructor Summary

Constructors

Constructor and Description
AtomIteratorWithinModel()

Method Summary

Methods

Modifier and Type	Method and Description
void	addAtoms(java.util.BitSet bsResult) turns this into a SPHERICAL iterator for "within Distance" measures
float	foundDistance2()
boolean	hasNext()
(package private) void	initialize(Bspf bspf, java.util.BitSet bsSelected, boolean isGreaterOnly, boolean isZeroBased, boolean hemisphereOnly, boolean threadSafe) ############## ITERATOR SHOULD BE RELEASED #################
int	next()
void	release()
void	set(int modelIndex, int firstModelAtom, int atomIndex, javax.vecmath.Point3f center, float distance)
void	set(javax.vecmath.Point3f center, float distance)

Methods inherited from class java.lang.Object

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

Field Detail

bsptIter

private CubeIterator bsptIter

bspf

private Bspf bspf

threadSafe

private boolean threadSafe

hemisphereOnly

private boolean hemisphereOnly

isZeroBased

private boolean isZeroBased

modelIndex

private int modelIndex

atomIndex

private int atomIndex

zeroBase

private int zeroBase

distanceSquared

private float distanceSquared

bsSelected

private java.util.BitSet bsSelected

isGreaterOnly

private boolean isGreaterOnly

iNext

private int iNext

Constructor Detail

AtomIteratorWithinModel

public AtomIteratorWithinModel()

Method Detail

initialize

void initialize(Bspf bspf,
              java.util.BitSet bsSelected,
              boolean isGreaterOnly,
              boolean isZeroBased,
              boolean hemisphereOnly,
              boolean threadSafe)

############## ITERATOR SHOULD BE RELEASED #################

Parameters:

bspf -

bsSelected -

isGreaterOnly -

isZeroBased -

hemisphereOnly - TODO

threadSafe -

set

public void set(int modelIndex,
       int firstModelAtom,
       int atomIndex,
       javax.vecmath.Point3f center,
       float distance)

Specified by:

set in interface AtomIndexIterator

firstModelAtom - an offset used in the AtomIteratorWithinSet only

set

public void set(javax.vecmath.Point3f center,
       float distance)

Specified by:

set in interface AtomIndexIterator

hasNext

public boolean hasNext()

Specified by:

hasNext in interface AtomIndexIterator

next

public int next()

Specified by:

next in interface AtomIndexIterator

foundDistance2

public float foundDistance2()

Specified by:

foundDistance2 in interface AtomIndexIterator

addAtoms

public void addAtoms(java.util.BitSet bsResult)

turns this into a SPHERICAL iterator for "within Distance" measures

Specified by:

addAtoms in interface AtomIndexIterator

Parameters:

bsResult -

release

public void release()

Specified by:

release in interface AtomIndexIterator