Merge branch 'MajorCoreUpdate' of

https://github.com/AgreementMakerLight/AML-Project.git into
MajorCoreUpdate

Conflicts:
	AgreementMakerLight/src/aml/ontology/Ontology.java

AgreementMakerLight/src/aml/AML.java

@@ -234,6 +234,11 @@ public class AML
 		}
 		selectedSources = new Vector<String>(bkSources);
 		
+		//Custom Match
+		matchSteps = new Vector<MatchStep>();
+		for(MatchStep s : MatchStep.values())
+			matchSteps.add(s);
+		
 		matchClasses = hasClasses();
 		double sourceRatio = (source.count(EntityType.DATA) + source.count(EntityType.OBJECT)) * 1.0 / source.count(EntityType.CLASS);
 		double targetRatio = (target.count(EntityType.DATA) + target.count(EntityType.OBJECT)) * 1.0 / target.count(EntityType.CLASS);

AgreementMakerLight/src/aml/ontology/Ontology.java

@@ -1407,7 +1407,6 @@ public class Ontology
 			if(sv == null)
 				continue;
 			Vector<Integer> cl = new Vector<Integer>(sv);
-
 			for(int i = 0; i < cl.size() - 1; i++)
 			{
 				int c1 = objectSomeValues.get(prop, cl.get(i));

AgreementMakerLight/src/aml/util/StringParser.java

@@ -63,24 +63,24 @@ public class StringParser
 	 */
 	public static boolean isNumericId(String name)
 	{
-				//just digits
+		//just digits
 		return name.matches("[0-9]*")
-				//digits with an intervening separator
-				|| name.matches("[0-9]+[_:\\.\\-][0-9]+")
-				//a single letter
-				|| name.matches("[a-zA-Z]{1}")
-				//a single letter followed by digits
-				|| name.matches("[a-zA-Z]{1}[0-9]{1,3}")
-				//OBO Foundry style (e.g., "GO:000001")
-				|| name.matches("[a-zA-Z]{2,}[_:][0-9\\.]{4,}")
-				//akin to OBO Foundry style (e.g., "C_A00001")
-				|| name.matches("[a-zA-Z]+[_:]?[a-zA-Z]?[0-9\\.]{5,}")
-				//simple letters-dash-numbers-dash-numbers pattern
-				|| name.matches("[a-zA-Z]{1,3}-[0-9]{3,}-[0-9]{3,}")
-				//specific letters-and-numbers separated by dashes pattern
-				|| name.matches("[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}")
-				//another specific letters-and-numbers separated by dashes pattern
-				|| name.matches("sid-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}");
+			//digits with an intervening separator
+			|| name.matches("[0-9]+[_:\\.\\-][0-9]+")
+			//a single letter
+			|| name.matches("[a-zA-Z]{1}")
+			//a single letter followed by digits
+			|| name.matches("[a-zA-Z]{1}[0-9]{1,3}")
+			//OBO Foundry style (e.g., "GO:000001")
+			|| name.matches("[a-zA-Z]{2,}[_:][0-9\\.]{4,}")
+			//akin to OBO Foundry style (e.g., "C_A00001")
+			|| name.matches("[a-zA-Z]+[_:]?[a-zA-Z]?[0-9\\.]{5,}")
+			//simple letters-dash-numbers-dash-numbers pattern
+			|| name.matches("[a-zA-Z]{1,3}-[0-9]{3,}-[0-9]{3,}")
+			//specific letters-and-numbers separated by dashes pattern
+			|| name.matches("[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}")
+			//another specific letters-and-numbers separated by dashes pattern
+			|| name.matches("sid-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}-[a-zA-Z0-9]{4,}");
 	}
 
 	/**

AgreementMakerLight/store/config.ini

-#AgreementMakerLight OAEI Configuration File
-
-#Instance Matching Classes (options: leave empty if no restriction, or list local names of classes to match separated by ';', or use * if target_classes = source_classes)
-source_classes=Transition
-target_classes=Transition
\ No newline at end of file