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a)IMatch to Match and constructor call for state used TargetPropertie…
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…s for faster processing Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>
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@asad @egonw
asad authored and egonw committed Aug 30, 2010
1 parent a420b61 commit 4a2f9c1
Showing 1 changed file with 35 additions and 33 deletions.
68 changes: 35 additions & 33 deletions src/test/org/openscience/cdk/smsd/algorithm/vflib/VFLibTest.java
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Expand Up @@ -38,19 +38,20 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties;
import org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper;
import org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode;
import org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery;
import org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState;
import org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMatch;
import org.openscience.cdk.smsd.algorithm.vflib.map.Match;
import org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper;
import org.openscience.cdk.smsd.algorithm.vflib.map.VFState;
import org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler;
import org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

/**
* Unit testing for the {@link VFMapper}, {@link VFState}, {@link IMatch} class.
* Unit testing for the {@link VFMapper}, {@link VFState}, {@link Match} class.
* @author Syed Asad Rahman <asad@ebi.ac.uk>
* @cdk.module test-smsd
*/
Expand All @@ -68,18 +69,19 @@ public static void setUp() throws CDKException {
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(hexane);
hexane = ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(hexane);
CDKHueckelAromaticityDetector.detectAromaticity(hexane);
hexaneQuery = QueryCompiler.compile(hexane, true);
hexaneQuery = new QueryCompiler(hexane, true).compile();
Assert.assertEquals(6, hexaneQuery.countNodes());
benzene = createBenzene();
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(benzene);
hexane = ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(benzene);
CDKHueckelAromaticityDetector.detectAromaticity(benzene);
benzeneQuery = QueryCompiler.compile(benzene, true);
benzeneQuery = new QueryCompiler(benzene, true).compile();
}

@Test
public void testItShouldFindAllMatchCandidatesInTheRootState() {
IState state = new VFState(benzeneQuery, benzene);

IState state = new VFState(benzeneQuery, new TargetProperties(benzene));
int count = 0;

while (state.hasNextCandidate()) {
Expand All @@ -91,10 +93,10 @@ public void testItShouldFindAllMatchCandidatesInTheRootState() {

@Test
public void testItShoudFindAllMatchCandidatesInThePrimaryState() {
IState state = new VFState(benzeneQuery, benzene);
IMatch match = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState newState = state.nextState(match);
List<IMatch> candidates = new ArrayList<IMatch>();
List<Match> candidates = new ArrayList<Match>();

while (newState.hasNextCandidate()) {
candidates.add(newState.nextCandidate());
Expand All @@ -105,12 +107,12 @@ public void testItShoudFindAllMatchCandidatesInThePrimaryState() {

@Test
public void testItShouldFindAllMatchCandidatesInTheSecondaryState() {
IState state0 = new VFState(benzeneQuery, benzene);
IMatch match0 = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state0 = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match0 = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state1 = state0.nextState(match0);
IMatch match1 = new IMatch(benzeneQuery.getNode(1), benzene.getAtom(1));
Match match1 = new Match(benzeneQuery.getNode(1), benzene.getAtom(1));
IState state2 = state1.nextState(match1);
List<IMatch> candidates = new ArrayList<IMatch>();
List<Match> candidates = new ArrayList<Match>();

while (state2.hasNextCandidate()) {
candidates.add(state2.nextCandidate());
Expand All @@ -121,10 +123,10 @@ public void testItShouldFindAllMatchCandidatesInTheSecondaryState() {

@Test
public void testItShouldMapAllAtomsInTheSecondaryState() {
IState state0 = new VFState(benzeneQuery, benzene);
IMatch match0 = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state0 = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match0 = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state1 = state0.nextState(match0);
IMatch match1 = new IMatch(benzeneQuery.getNode(1), benzene.getAtom(1));
Match match1 = new Match(benzeneQuery.getNode(1), benzene.getAtom(1));
IState state2 = state1.nextState(match1);

Map<INode, IAtom> map = state2.getMap();
Expand All @@ -136,14 +138,14 @@ public void testItShouldMapAllAtomsInTheSecondaryState() {

@Test
public void testItShouldFindAllMatchCandidatesFromTheTeriaryState() {
IState state0 = new VFState(benzeneQuery, benzene);
IMatch match0 = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state0 = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match0 = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state1 = state0.nextState(match0);
IMatch match1 = new IMatch(benzeneQuery.getNode(1), benzene.getAtom(1));
Match match1 = new Match(benzeneQuery.getNode(1), benzene.getAtom(1));
IState state2 = state1.nextState(match1);
IMatch match2 = new IMatch(benzeneQuery.getNode(2), benzene.getAtom(2));
Match match2 = new Match(benzeneQuery.getNode(2), benzene.getAtom(2));
IState state3 = state2.nextState(match2);
List<IMatch> candidates = new ArrayList<IMatch>();
List<Match> candidates = new ArrayList<Match>();

while (state3.hasNextCandidate()) {
candidates.add(state3.nextCandidate());
Expand All @@ -154,12 +156,12 @@ public void testItShouldFindAllMatchCandidatesFromTheTeriaryState() {

@Test
public void testItShouldMapAllAtomsInTheTertiaryState() {
IState state0 = new VFState(benzeneQuery, benzene);
IMatch match0 = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state0 = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match0 = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state1 = state0.nextState(match0);
IMatch match1 = new IMatch(benzeneQuery.getNode(1), benzene.getAtom(1));
Match match1 = new Match(benzeneQuery.getNode(1), benzene.getAtom(1));
IState state2 = state1.nextState(match1);
IMatch match2 = new IMatch(benzeneQuery.getNode(2), benzene.getAtom(2));
Match match2 = new Match(benzeneQuery.getNode(2), benzene.getAtom(2));
IState state3 = state2.nextState(match2);
Map<INode, IAtom> map = state3.getMap();

Expand All @@ -171,30 +173,30 @@ public void testItShouldMapAllAtomsInTheTertiaryState() {

@Test
public void testItShouldReachGoalWhenAllAtomsAreMapped() {
IState state0 = new VFState(benzeneQuery, benzene);
IMatch match0 = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state0 = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match0 = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state1 = state0.nextState(match0);
IMatch match1 = new IMatch(benzeneQuery.getNode(1), benzene.getAtom(1));
Match match1 = new Match(benzeneQuery.getNode(1), benzene.getAtom(1));
IState state2 = state1.nextState(match1);
IMatch match2 = new IMatch(benzeneQuery.getNode(2), benzene.getAtom(2));
Match match2 = new Match(benzeneQuery.getNode(2), benzene.getAtom(2));
IState state3 = state2.nextState(match2);
IMatch match3 = new IMatch(benzeneQuery.getNode(3), benzene.getAtom(3));
Match match3 = new Match(benzeneQuery.getNode(3), benzene.getAtom(3));
IState state4 = state3.nextState(match3);
IMatch match4 = new IMatch(benzeneQuery.getNode(4), benzene.getAtom(4));
Match match4 = new Match(benzeneQuery.getNode(4), benzene.getAtom(4));
IState state5 = state4.nextState(match4);

Assert.assertFalse(state5.isGoal());

IMatch match5 = new IMatch(benzeneQuery.getNode(5), benzene.getAtom(5));
Match match5 = new Match(benzeneQuery.getNode(5), benzene.getAtom(5));
IState state6 = state5.nextState(match5);

Assert.assertTrue(state6.isGoal());
}

@Test
public void testItShouldHaveANextCandidateInTheSecondaryState() {
IState state = new VFState(benzeneQuery, benzene);
IMatch match = new IMatch(benzeneQuery.getNode(0), benzene.getAtom(0));
IState state = new VFState(benzeneQuery, new TargetProperties(benzene));
Match match = new Match(benzeneQuery.getNode(0), benzene.getAtom(0));
IState nextState = state.nextState(match);
Assert.assertTrue(nextState.hasNextCandidate());
}
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