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Modify to make UniversalIsomorphismTester usable in a threaded enviro…
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…nment. Remove keyword static from variables start and timeout. Remove keyword static from methods isIsomorph, getIsomorphMap, getIsomorphAtomsMap, getIsomorphMaps, getSubgraphMaps, getSubgraphMap, getSubgraphAtomsMaps, getSubgraphAtomsMap, isSubgraph, getOverlaps, search, getMaximum, setTimeout. Added constructor.
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@yapchunwei @egonw
yapchunwei authored and egonw committed Jul 27, 2012
1 parent 510a753 commit c241461
Showing 1 changed file with 26 additions and 21 deletions.
47 changes: 26 additions & 21 deletions src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
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Expand Up @@ -111,8 +111,13 @@ public class UniversalIsomorphismTester {

final static int ID1 = 0;
final static int ID2 = 1;
private static long start;
private static long timeout=-1;
private long start;
private long timeout=-1;

public UniversalIsomorphismTester()
{

}

///////////////////////////////////////////////////////////////////////////
// Query Methods
Expand All @@ -134,7 +139,7 @@ public class UniversalIsomorphismTester {
* @return true if the 2 molecule are isomorph
* @throws CDKException if the first molecule is an instance of IQueryAtomContainer
*/
public static boolean isIsomorph(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public boolean isIsomorph(IAtomContainer g1, IAtomContainer g2) throws CDKException{
if (g1 instanceof IQueryAtomContainer)
throw new CDKException(
"The first IAtomContainer must not be an IQueryAtomContainer"
Expand Down Expand Up @@ -167,7 +172,7 @@ public static boolean isIsomorph(IAtomContainer g1, IAtomContainer g2) throws C
* @param g2 second molecule. May be an {@link IQueryAtomContainer}.
* @return the first isomorph mapping found projected of g1. This is a List of RMap objects containing Ids of matching bonds.
*/
public static List<RMap> getIsomorphMap(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public List<RMap> getIsomorphMap(IAtomContainer g1, IAtomContainer g2) throws CDKException{
if (g1 instanceof IQueryAtomContainer)
throw new CDKException(
"The first IAtomContainer must not be an IQueryAtomContainer"
Expand All @@ -194,15 +199,15 @@ public static List<RMap> getIsomorphMap(IAtomContainer g1, IAtomContainer g2) t
* This is a List of RMap objects containing Ids of matching atoms.
* @throws CDKException if the first molecules is not an instance of {@link IQueryAtomContainer}
*/
public static List<RMap> getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g2) throws CDKException {
public List<RMap> getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g2) throws CDKException {
if (g1 instanceof IQueryAtomContainer)
throw new CDKException(
"The first IAtomContainer must not be an IQueryAtomContainer"
);

List<RMap> list = checkSingleAtomCases(g1, g2);
if (list == null) {
return makeAtomsMapOfBondsMap(UniversalIsomorphismTester.getIsomorphMap(g1, g2), g1, g2);
return makeAtomsMapOfBondsMap(getIsomorphMap(g1, g2), g1, g2);
} else if (list.isEmpty()) {
return null;
} else {
Expand All @@ -219,7 +224,7 @@ public static List<RMap> getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g
* @param g2 second molecule. May be an {@link IQueryAtomContainer}.
* @return the list of all the 'mappings'
*/
public static List<List<RMap>> getIsomorphMaps(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public List<List<RMap>> getIsomorphMaps(IAtomContainer g1, IAtomContainer g2) throws CDKException{
return search(g1, g2, getBitSet(g1), getBitSet(g2), true, true);
}

Expand All @@ -246,7 +251,7 @@ public static List<List<RMap>> getIsomorphMaps(IAtomContainer g1, IAtomContainer
*
* @see #makeAtomsMapsOfBondsMaps(List, IAtomContainer, IAtomContainer)
*/
public static List<List<RMap>> getSubgraphMaps(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public List<List<RMap>> getSubgraphMaps(IAtomContainer g1, IAtomContainer g2) throws CDKException{
return search(g1, g2, new BitSet(), getBitSet(g2), true, true);
}

Expand All @@ -259,7 +264,7 @@ public static List<List<RMap>> getSubgraphMaps(IAtomContainer g1, IAtomContainer
* @return the first subgraph bond mapping found projected on g1. This is a {@link List} of
* {@link RMap} objects containing Ids of matching bonds.
*/
public static List<RMap> getSubgraphMap(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public List<RMap> getSubgraphMap(IAtomContainer g1, IAtomContainer g2) throws CDKException{
List<RMap> result = null;
List<List<RMap>> rMapsList = search(g1, g2, new BitSet(), getBitSet(g2), false, false);

Expand All @@ -281,13 +286,13 @@ public static List<RMap> getSubgraphMap(IAtomContainer g1, IAtomContainer g2) t
* @return all subgraph atom mappings found projected on g1. This is a
* {@link List} of {@link RMap} objects containing Ids of matching atoms.
*/
public static List<List<RMap>> getSubgraphAtomsMaps(IAtomContainer g1,
public List<List<RMap>> getSubgraphAtomsMaps(IAtomContainer g1,
IAtomContainer g2)
throws CDKException {
List<RMap> list = checkSingleAtomCases(g1, g2);
if (list == null) {
return makeAtomsMapsOfBondsMaps(
UniversalIsomorphismTester.getSubgraphMaps(g1, g2), g1, g2
getSubgraphMaps(g1, g2), g1, g2
);
} else {
List<List<RMap>> atomsMap = new ArrayList<List<RMap>>();
Expand All @@ -305,12 +310,12 @@ public static List<List<RMap>> getSubgraphAtomsMaps(IAtomContainer g1,
* @return the first subgraph atom mapping found projected on g1.
* This is a {@link List} of {@link RMap} objects containing Ids of matching atoms.
*/
public static List<RMap> getSubgraphAtomsMap(IAtomContainer g1,
public List<RMap> getSubgraphAtomsMap(IAtomContainer g1,
IAtomContainer g2)
throws CDKException {
List<RMap> list = checkSingleAtomCases(g1, g2);
if (list == null) {
return makeAtomsMapOfBondsMap(UniversalIsomorphismTester.getSubgraphMap(g1, g2), g1, g2);
return makeAtomsMapOfBondsMap(getSubgraphMap(g1, g2), g1, g2);
} else if (list.isEmpty()) {
return null;
} else {
Expand All @@ -325,7 +330,7 @@ public static List<RMap> getSubgraphAtomsMap(IAtomContainer g1,
* @param g2 second molecule. May be an {@link IQueryAtomContainer}.
* @return true if g2 a subgraph on g1
*/
public static boolean isSubgraph(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public boolean isSubgraph(IAtomContainer g1, IAtomContainer g2) throws CDKException{
if (g1 instanceof IQueryAtomContainer)
throw new CDKException(
"The first IAtomContainer must not be an IQueryAtomContainer"
Expand Down Expand Up @@ -365,7 +370,7 @@ public static boolean isSubgraph(IAtomContainer g1, IAtomContainer g2) throws C
* @return the list of all the maximal common substructure
* found projected of g1 (list of AtomContainer )
*/
public static List<IAtomContainer> getOverlaps(IAtomContainer g1, IAtomContainer g2) throws CDKException{
public List<IAtomContainer> getOverlaps(IAtomContainer g1, IAtomContainer g2) throws CDKException{
start=System.currentTimeMillis();
List<List<RMap>> rMapsList = search(g1, g2, new BitSet(), new BitSet(), true, false);

Expand Down Expand Up @@ -438,7 +443,7 @@ public static RGraph buildRGraph(IAtomContainer g1, IAtomContainer g2) throws C
* structure
* @return a List of Lists of {@link RMap} objects that represent the search solutions
*/
public static List<List<RMap>> search(IAtomContainer g1, IAtomContainer g2, BitSet c1,
public List<List<RMap>> search(IAtomContainer g1, IAtomContainer g2, BitSet c1,
BitSet c2, boolean findAllStructure, boolean findAllMap) throws CDKException{
// remember start time
start = System.currentTimeMillis();
Expand Down Expand Up @@ -476,8 +481,8 @@ public static List<List<RMap>> search(IAtomContainer g1, IAtomContainer g2, BitS
// build the RGraph corresponding to this problem
RGraph rGraph = buildRGraph(g1, g2);
// Set time data
rGraph.setTimeout(UniversalIsomorphismTester.timeout);
rGraph.setStart(UniversalIsomorphismTester.start);
rGraph.setTimeout(timeout);
rGraph.setStart(start);
// parse the RGraph with the given constrains and options
rGraph.parse(c1, c2, findAllStructure, findAllMap);
List<BitSet> solutionList = rGraph.getSolutions();
Expand Down Expand Up @@ -579,7 +584,7 @@ public static List<IAtomContainer> projectList(List<List<RMap>> rMapsList, IAtom
* @return the list cleaned
* @throws CDKException if there is a problem in obtaining subgraphs
*/
private static List<IAtomContainer> getMaximum(List<IAtomContainer> graphList) throws CDKException {
private List<IAtomContainer> getMaximum(List<IAtomContainer> graphList) throws CDKException {
List<IAtomContainer> reducedGraphList = new ArrayList<IAtomContainer>();
reducedGraphList.addAll(graphList);

Expand Down Expand Up @@ -1087,8 +1092,8 @@ private static boolean testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer
* @param timeout
* Time in milliseconds. -1 to ignore the timeout.
*/
public static void setTimeout(long timeout) {
UniversalIsomorphismTester.timeout = timeout;
public void setTimeout(long timeout) {
this.timeout = timeout;
}

}
Expand Down

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