net.sf.octet.query
Class TemplateAtomQuery

java.lang.Object
  net.sf.octet.query.TemplateAtomQuery

All Implemented Interfaces:

AtomQuery

public class TemplateAtomQuery

extends java.lang.Object

implements AtomQuery

An implementation of the AtomQuery interface in which an existing Atom is used as a template for comparing other Atoms. TemplateAtomQuery will match Atoms in molecules that are either identical to the one in which the template is hosted, or which are superstructures of the molecule hosting the template.

This implementation ignores the Configuration of Atoms. To perform queries in which configuration is defined, use a MoleculeQueryBuilder .

Author:

Richard Apodaca

Constructor Summary

TemplateAtomQuery(Atom atom, Molecule molecule)
Constructs a TemplateAtomQuery using atom as the templateAtom.

Method Summary

boolean

match(Atom atom, Molecule molecule) Returns true if this AtomQuery matches atom, or false otherwise.

Methods inherited from class java.lang.Object

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

Constructor Detail

TemplateAtomQuery

public TemplateAtomQuery(Atom atom,
                         Molecule molecule)

Constructs a TemplateAtomQuery using atom as the templateAtom.

Parameters:

atom - the template Atom

molecule - the Molecule in which atom resides

Throws:

java.lang.NullPointerException - if atom is null

Method Detail

match

public boolean match(Atom atom,
                     Molecule molecule)

Description copied from interface: AtomQuery

Returns true if this AtomQuery matches atom, or false otherwise.

Specified by:

match in interface AtomQuery

Parameters:

atom - the Atom to match

molecule - the Molecule in which atom resides

Returns:

true if a match was found, or false otherwise