Debugged code for the detection of already existing alignments in the source ontology

AgreementMakerLight/pom.xml

@@ -37,8 +37,8 @@
 		</repository>
 	</repositories>
   <properties>
-    <maven.compiler.source>1.6</maven.compiler.source>
-    <maven.compiler.target>1.6</maven.compiler.target>
+    <maven.compiler.source>1.7</maven.compiler.source>
+    <maven.compiler.target>1.7</maven.compiler.target>
   </properties>
   <build>
     <sourceDirectory>${basedir}/src</sourceDirectory>
@@ -101,14 +101,14 @@
       <artifactId>gephi-toolkit</artifactId>
       <version>0.8.2</version>
       <scope>system</scope>
-      <systemPath>${project.basedir}/src/lib/gephi-toolkit.jar</systemPath>
+     <systemPath>${project.basedir}/src/lib/gephi-toolkit.jar</systemPath> 
     </dependency>
     <dependency>
       <groupId>edu.smu.tspell.wordnet</groupId>
       <artifactId>jaws</artifactId>
       <version>1.3.3</version>
       <scope>system</scope>
-      <systemPath>${project.basedir}/src/lib/jaws.jar</systemPath>
+      <systemPath>${project.basedir}/src/lib/jaws.jar</systemPath> 
     </dependency>
     <dependency>
       <groupId>log4j</groupId>
@@ -144,4 +144,4 @@
       <version>1.6.4</version>
     </dependency>
   </dependencies>
-</project>
\ No newline at end of file
+</project>

AgreementMakerLight/src/aml/match/Alignment.java

@@ -131,12 +131,15 @@ public class Alignment implements Collection<Mapping>
 		nbExistingMatch = 0;
 
 //cpichotjv2020		for (int i=0; i< source.classCount();i++){
-		for (int i=0; i< source.count();i++){
+		//cpichotMarch2020 for (int i=0; i< source.count();i++){
+		for (int i=1; i< source.count()+1;i++){
 			Set<String> matchesTable = source.getExistingMatches(i);
 			if (matchesTable.size() > 0){
 				for (int matchIndex = 0; matchIndex < matchesTable.size(); matchIndex++){
+					//String existingMatch = matchesTable.toArray()[matchIndex].toString();
 					String existingMatch = matchesTable.toArray()[matchIndex].toString();
 					
+					
 					//check if the class (i) belongs to the present mapping					
 					for(Mapping m : maps){
 						if (m.getSourceId() == i){							

AgreementMakerLight/src/aml/ontology/ExistingMatches.java

@@ -102,11 +102,12 @@ public class ExistingMatches
 		String s;
 		Provenance p;
 		
-		int index = 0;//cpichotjv2020
-/* cpichotjv2020
-		//Get the type of the entity
+//		int index = 0;//cpichotjv2020
+				//Get the type of the entity
 		EntityType e = uris.getType(id);
 		int index = getIndex(e);
+		
+/* cpichotjv2020
 
 		//If the name is not in english we parse it as a formula
 		if(!language.equals("en"))
@@ -122,7 +123,8 @@ public class ExistingMatches
 				return;
 			//If it is a formula, parse it and label it as such
 			else if(StringParser.isFormula(name))
- cpichotjv2020	*/
+ cpichotjv2020	*/		
+		
 			if(StringParser.isFormula(name))	
 			{
 				s = StringParser.normalizeFormula(name);
@@ -138,13 +140,14 @@ public class ExistingMatches
 			//Otherwise, parse it normally
 			else
 			{
-				s = StringParser.normalizeName(name);
+//cpichotjv2020				s = StringParser.normalizeName(name);
+				s = name ;
 //cpichotjv2020				p = new Provenance(type, source, language, weight);
-				p = new Provenance(LexicalType.FORMULA, source, "en", 1.0);
-				
-				
+				p = new Provenance(LexicalType.FORMULA, source, "en", 1.0);							
 			}
 		//cpichotjv2020}
+			
+			
 		//Then update the tables
 		entityDefinitions[index].add(s,id,p);
 		definitionEntities[index].add(id,s,p);
@@ -579,7 +582,7 @@ public class ExistingMatches
 	 * @return the list of names associated with the entity
 	 */
 	public Set<String> getNames(int id)
-	{
+	{	
 		int index = getIndex(uris.getType(id));
 		if(definitionEntities[index].contains(id))
 			return definitionEntities[index].keySet(id);
@@ -860,7 +863,7 @@ public class ExistingMatches
 	
 	private int getIndex(EntityType e)
 	{
-		EntityType[] types = EntityType.values();
+		EntityType[] types = EntityType.values();		
 		for(int i = 0; i < types.length; i++)
 			if(types[i].equals(e))
 				return i;

AgreementMakerLight/src/aml/ontology/Ontology.java

@@ -545,7 +545,6 @@ public class Ontology
 	            		//OWLNamedIndividual ni = factory.getOWLNamedIndividual((IRI) annotation.getValue());
 	            		//existingMatch = ni.toString();
 	            		existingMatch = annotation.getValue().toString();
-	            		//System.out.println(existingMatch);
 	            	}
 	            	existingMatches.add(id, existingMatch, source);	            	
             	}//cpichotjv2020