net.sf.octet.query
Class BilateralQueryStrategy

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

All Implemented Interfaces:

ConfigurationComparator, ConformationComparator, IsomorphismTraverser, MoleculeQueryStrategy

public class BilateralQueryStrategy

extends java.lang.Object

implements MoleculeQueryStrategy

A MoleculeQueryStrategy consistent with exact structure matching. BilateralQueryStrategy requires a reciprocal one-to-one correspondence between all features in two Molecules.

Author:

Richard Apodaca

Nested Class Summary

Nested classes inherited from class net.sf.octet.traversal.IsomorphismTraverser

IsomorphismTraverser.Handler

Constructor Summary

BilateralQueryStrategy()
Constructs a fully-functional BilateralQueryStrategy.

BilateralQueryStrategy(IsomorphismTraverser traverser)
Constructs a fully functional BilateralQueryStrategy that delegates traversal operations to traverser.

Method Summary

boolean	compare(Configuration input, Configuration model, AtomMap map) Compares input with model using map to correlate Atoms between the two.
boolean	compare(Conformation input, Conformation model, AtomMap map) Compares input to model, using the specified AtomMap to correlate Atoms between the two.
AtomQuery	createAtomQuery(Atom atom, Molecule molecule) Creates an AtomQuery for atom in the context of molecule.
void	traverse(AtomGraph input, AtomGraph model, IsomorphismTraverser.Handler handler) Traverses the Atoms and AtomPairs in model that are isomorphic with those contained in input while forwarding traversal events to handler.

Methods inherited from class java.lang.Object

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

Constructor Detail

BilateralQueryStrategy

public BilateralQueryStrategy()

Constructs a fully-functional BilateralQueryStrategy.

BilateralQueryStrategy

public BilateralQueryStrategy(IsomorphismTraverser traverser)

Constructs a fully functional BilateralQueryStrategy that delegates traversal operations to traverser.

Parameters:

traverser - the IsomorphismTraverser to which this BilateralQueryStrategy will delegate traversal responsibilities

Method Detail

createAtomQuery

public AtomQuery createAtomQuery(Atom atom,
                                 Molecule molecule)

Description copied from interface: MoleculeQueryStrategy

Creates an AtomQuery for atom in the context of molecule.

Specified by:

createAtomQuery in interface MoleculeQueryStrategy

Parameters:

atom - the atom after which the AtomQuery will be modeled

molecule - the context of atom

Returns:

a fully-functional AtomQuery based on the properties of atom

traverse

public void traverse(AtomGraph input,
                     AtomGraph model,
                     IsomorphismTraverser.Handler handler)

Description copied from interface: IsomorphismTraverser

Traverses the Atoms and AtomPairs in model that are isomorphic with those contained in input while forwarding traversal events to handler.

Specified by:

traverse in interface IsomorphismTraverser

Parameters:

input - the AtomGraph whose elements will be compared to model

model - the AtomGraph whose elements that are isomorphic to model will be traversed

handler - receives traversal events

compare

public boolean compare(Configuration input,
                       Configuration model,
                       AtomMap map)

Description copied from interface: ConfigurationComparator

Compares input with model using map to correlate Atoms between the two. Returns true if commonality was detected, or false otherwise.

Specified by:

compare in interface ConfigurationComparator

Parameters:

input - the Configuration whose features will be compared with those of model using map

model - the reference Configuration

map - the mapping of the atoms of input onto map

Returns:

true if the comparison was positive or false otherwise

compare

public boolean compare(Conformation input,
                       Conformation model,
                       AtomMap map)

Description copied from interface: ConformationComparator

Compares input to model, using the specified AtomMap to correlate Atoms between the two. Returns true if a match was detected, or false otherwise.

Specified by:

compare in interface ConformationComparator

Parameters:

input - the Conformation whose features will be compared with those of model using map

model - the reference Conformation

map - the mapping of the atoms of input onto map

Returns:

true if the comparison was positive or false otherwise