net.sf.octet.query
Class AllCyclesMoleculeQuery

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

All Implemented Interfaces:

MoleculeQuery

public class AllCyclesMoleculeQuery

extends java.lang.Object

implements MoleculeQuery

Queries the set of all cycles in a Molecule. AllCyclesMoleculeQuery can be used with any instance of CycleTraverser to implement custom cycle-perception strategies. HanserCycleTraverser is used by default.

Author:

Richard Apodaca

Constructor Summary

AllCyclesMoleculeQuery()
Constructs a fully-functional AllCyclesMoleculeQuery that uses a HanserCycleTraverser for cycle perception.

AllCyclesMoleculeQuery(CycleTraverser traverser)
Constructs a fully-functional AllCyclesMoleculequery that delegates cycle perception to traverser.

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

AllCyclesMoleculeQuery

public AllCyclesMoleculeQuery()

Constructs a fully-functional AllCyclesMoleculeQuery that uses a HanserCycleTraverser for cycle perception.

AllCyclesMoleculeQuery

public AllCyclesMoleculeQuery(CycleTraverser traverser)

Constructs a fully-functional AllCyclesMoleculequery that delegates cycle perception to traverser.

Parameters:

traverser - the CycleTraverser that will be used for cycle perception

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