org.jmol.modelset
Class AtomIteratorWithinModel

java.lang.Object
  extended by org.jmol.modelset.AtomIteratorWithinModel
All Implemented Interfaces:
AtomIndexIterator
Direct Known Subclasses:
AtomIteratorWithinModelSet

public class AtomIteratorWithinModel
extends java.lang.Object
implements AtomIndexIterator


Field Summary
private  int atomIndex
           
private  Atom[] atoms
           
protected  Bspf bspf
           
private  java.util.BitSet bsSelected
           
private  boolean checkGreater
           
protected  CubeIterator cubeIterator
           
private  float distanceSquared
           
private  boolean hemisphereOnly
           
private  int iNext
           
private  boolean isGreaterOnly
           
private  boolean isVdw
           
private  boolean isZeroBased
           
protected  int modelIndex
           
private  RadiusData radiusData
           
private  boolean threadSafe
           
private  float vdw1
           
private  Viewer viewer
           
private  int zeroBase
           
 
Constructor Summary
AtomIteratorWithinModel()
           
 
Method Summary
 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(ModelCollection modelSet, int modelIndex, int firstModelAtom, int atomIndex, javax.vecmath.Point3f center, float distance, RadiusData rd)
           
 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

cubeIterator

protected CubeIterator cubeIterator

bspf

protected Bspf bspf

threadSafe

private boolean threadSafe

hemisphereOnly

private boolean hemisphereOnly

isZeroBased

private boolean isZeroBased

modelIndex

protected int modelIndex

atomIndex

private int atomIndex

zeroBase

private int zeroBase

distanceSquared

private float distanceSquared

bsSelected

private java.util.BitSet bsSelected

isGreaterOnly

private boolean isGreaterOnly

checkGreater

private boolean checkGreater

radiusData

private RadiusData radiusData

vdw1

private float vdw1

isVdw

private boolean isVdw

atoms

private Atom[] atoms

viewer

private Viewer viewer

iNext

private int iNext
Constructor Detail

AtomIteratorWithinModel

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(ModelCollection modelSet,
                int modelIndex,
                int firstModelAtom,
                int atomIndex,
                javax.vecmath.Point3f center,
                float distance,
                RadiusData rd)
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