net.sf.octet.query
Class TemplateMoleculeQuery

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

All Implemented Interfaces:

MoleculeQuery

public class TemplateMoleculeQuery

extends java.lang.Object

implements MoleculeQuery

A query that uses a Molecule as a template. TemplateMoleculeQuery allows for a variety of implementation modifications through the use of custom MoleculeQueryStrategies.

Author:

Richard Apodaca

Constructor Summary

TemplateMoleculeQuery(Molecule molecule, MoleculeQueryStrategy strategy)
Constructs a fully-functional TemplateMoleculeQuery using the indicated Molecule as a template and the specified Strategy.

Method Summary

int	countMatches(Molecule molecule) Returns the number of non-degenerate occurrences of this query in the specified Molecule.
AtomGraphCollection	getMatches(Molecule molecule) Returns a mapping of all occurrences of this query onto the specified Molecule.
boolean	match(Molecule molecule) Returns true if this MoleculeQuery matches molecule, or false otherwise.

Methods inherited from class java.lang.Object

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

Constructor Detail

TemplateMoleculeQuery

public TemplateMoleculeQuery(Molecule molecule,
                             MoleculeQueryStrategy strategy)

Constructs a fully-functional TemplateMoleculeQuery using the indicated Molecule as a template and the specified Strategy. This TemplateMoleculeQuery will delegate all Strategy specific methods to strategy. Clients interested in customizing TemplateMoleculeQuery behavior should implement a customized Strategy.

Parameters:

molecule - the template

strategy - the Strategy

Method Detail

match

public boolean match(Molecule molecule)

Description copied from interface: MoleculeQuery

Returns true if this MoleculeQuery matches molecule, or false otherwise.

Specified by:

match in interface MoleculeQuery

Parameters:

molecule - the Molecule to query

Returns:

true if a match was found, or false otherwise

countMatches

public int countMatches(Molecule molecule)

Description copied from interface: MoleculeQuery

Returns the number of non-degenerate occurrences of this query in the specified Molecule.

Specified by:

countMatches in interface MoleculeQuery

Parameters:

molecule - the Molecule to query

Returns:

the number of non-degenerate occurrences of this query in molecule

getMatches

public AtomGraphCollection getMatches(Molecule molecule)

Description copied from interface: MoleculeQuery

Returns a mapping of all occurrences of this query onto the specified Molecule.

Specified by:

getMatches in interface MoleculeQuery

Parameters:

molecule - the Molecule to query

Returns:

the mapping of all occurrences of this query in molecule