Package etomica.atom.iterator

Class AtomIteratorBasis

java.lang.Object

etomica.atom.iterator.AtomIteratorArrayListSimple

etomica.atom.iterator.AtomIteratorBasis

All Implemented Interfaces:

AtomIterator, AtomIteratorBasisDependent, AtomLeafsetIterator, AtomsetIterator, AtomsetIteratorBasisDependent, AtomsetIteratorTargetable

Direct Known Subclasses:

AtomIteratorBasisFilteredType, AtomIteratorBasisFilteredType2

public class AtomIteratorBasis
extends AtomIteratorArrayListSimple
implements AtomIteratorBasisDependent

Elementary basis-dependent iterator that gives atoms meeting specification of a basis and a target. Iterates are determined as follows:

• the basis atom determines the set of atoms (basis-set) that are candidates for iteration. If the basis is an atom group, iterates (if any) will always be the child atoms of the basis; if the basis is a leaf atom, the single iterate (if any) will be the basis atom itself.
• the target atom narrows down the iterates from the basis-set. Possibilities are:
  • no target atom is specified: all basis-set atoms will be given on iteration
  • the target atom is the same as the basis atom: this is equivalent to specifying no target
  • the target atom is in the species hierarchy above the basis atom, and the basis atom is descended from it: this is equivalent to specifying no target
  • the target atom is a child of the basis atom: the target atom will be the only iterate
  • the target atom is descended from the basis atom, but is not a direct child of it: the only iterate will be the child atom of the basis through which the target is descended
  • the target and basis are in different branches of the species hierarchy, such that the target atom is not descended from the basis atom, and the basis atom is not descended from the target atom: no iterates will be given

See Also:

Serialized Form

Field Summary

Fields inherited from class etomica.atom.iterator.AtomIteratorArrayListSimple

atomSetSinglet, cursor, list

Constructor Summary

Constructors

Constructor	Description
AtomIteratorBasis()	Constructor makes iterator in an unset condition; must set basis and call reset before beginning iteration.

Method Summary

Modifier and Type	Method	Description
int	basisSize()	Returns 1, indicating that only a single-atom basis is appropriate.
boolean	haveTarget(IAtom target)	Returns true if the given target with the present basis could yield an iterate.
void	reset()	Puts iterator in a state ready to begin iteration.
void	setBasis(IMoleculeList atoms)	Sets the basis for iteration, such that the childList atoms of the given atom will be subject to iteration (within any specifications given by a prior or subsequent call to setTarget).
void	setTarget(IAtom newTargetAtom)	Method to specify a target atom.

Methods inherited from interface etomica.atom.iterator.AtomIterator

nextAtom

Methods inherited from class etomica.atom.iterator.AtomIteratorArrayListSimple

getList, nBody, next, nextAtom, setList, size, unset

Methods inherited from interface etomica.atom.iterator.AtomLeafsetIterator

next

Methods inherited from interface etomica.atom.iterator.AtomsetIterator

nBody, size, unset

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomIteratorBasis

public AtomIteratorBasis()

Constructor makes iterator in an unset condition; must set basis and call reset before beginning iteration.

Method Detail

setTarget

public void setTarget(IAtom newTargetAtom)

Method to specify a target atom. Specifying a zero-length AtomSet or a length-1 AtomSet with a null atom releases any target restrictions, and specifies that the iterator should give all of the basis-set atoms. Call to this method leaves iterator unset; call to reset is required before beginning iteration.

Specified by:

setTarget in interface AtomsetIteratorTargetable

setBasis

public void setBasis(IMoleculeList atoms)

Sets the basis for iteration, such that the childList atoms of the given atom will be subject to iteration (within any specifications given by a prior or subsequent call to setTarget). If given atom is a leaf, it will itself be the sole candidate iterate given by the iterator. If argument is null or otherwise does not specify an atom, iterator will be conditioned to give no iterates until a new basis is specified. The given AtomSet, if not null, must have a size of 1.

Specified by:

setBasis in interface AtomsetIteratorBasisDependent

Parameters:

atoms - The basis atoms; a null basis will condition the iterator to give no iterates until a valid basis is specified via another call to this method.

Throws:

java.lang.IllegalArgumentException - if atoms.count() is not 0 or 1

haveTarget

public boolean haveTarget(IAtom target)

Returns true if the given target with the present basis could yield an iterate. Assumes that the basis -- if it is a group -- has child atoms.

Specified by:

haveTarget in interface AtomsetIteratorBasisDependent

reset

public void reset()

Puts iterator in a state ready to begin iteration.

Specified by:

reset in interface AtomsetIterator

Overrides:

reset in class AtomIteratorArrayListSimple

basisSize

public int basisSize()

Returns 1, indicating that only a single-atom basis is appropriate.

Specified by:

basisSize in interface AtomsetIteratorBasisDependent

Returns:

the size of the basis for this iterator.