- clean up during documentation

src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java

@@ -103,7 +103,6 @@ public class ClassHierarchy {
         return model.getOntClass( childrenNodes.get(index).getURI() );          //returns the class from the position that we have selected -> the random number
     }
 
-    //modifies the class hierarchy after we have flattened it
     public void flattenClassHierarchy( OntModel model, int level, ArrayList<OntClass> childClasses,
                                         ArrayList<OntClass> parentClasses, ArrayList<OntClass> superLevelClasses) {
         List<URITree> childrenNodes = root.getNodesFromLevel( level );
@@ -138,7 +137,7 @@ public class ClassHierarchy {
 	    }
 	    System.err.println();
 	    */
-            childNode.setParent( parentNode.getParent() );			//change the parent of my superclass to the [parent of the "parent node"]
+            childNode.setParent( superNode );			//change the parent of my superclass to the [parent of the "parent node"]
 	    // JE : likely wrong in multiple inheritance
             childNode.setDepth( parentNode.getDepth() );			//change it's depth
             parentNode.getChildrenList().remove( childNode );			//remove it from the children list of parentNode

src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java

@@ -30,7 +30,7 @@ import java.util.Properties;
  * OntologyNetworkWeakener
  *
  * A interface which alters ontology networks.
- * NOTE: These two primitives would benefit from the hability to declare static in ineterfaces...
+ * NOTE: These two primitives would benefit from the hability to declare static in interfaces...
  * Now we have to create instances of the implementing classes.
  *
  */

src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java

@@ -46,8 +46,7 @@ public class AddClassLevel extends BasicAlterator {
 	int nbClasses = Integer.valueOf( p.substring(index+1, p.length()) );
 	if ( debug ) System.err.println( "level " + level );
 	if ( debug ) System.err.println( "nbClasses " + nbClasses );
-	float percentage = 1.00f;
-        String classURI;
+	//float percentage = 1.00f;
         //the parent class -> if level is 1 then we create a new class
         //else we get a random class from the level : level-1 to be the parent of the class
         OntClass parentClass;
@@ -57,28 +56,22 @@ public class AddClassLevel extends BasicAlterator {
 
         buildClassHierarchy();                                                  //check if the class hierarchy is built
         if ( level == 1 ) {                                                     //the parent of the class is Thing, we add the class and then the rest of the classes
-           classURI = getRandomString();
-           parentClass = modifiedModel.createClass( modifiedOntologyNS + classURI );//create a new class to the model
-           classHierarchy.addClass( modifiedOntologyNS + classURI, "Thing" );  //add the node in the hierarchy of classes
-           childClasses.add(parentClass);
-        }
-        else {
-            parentClasses = classHierarchy.getClassesFromLevel(modifiedModel, level);
-            int nbParentClasses = parentClasses.size();                         //number of classes from the Ontology
-            int toAdd = Math.round( percentage*nbClasses );                       // 1 can be replaced by percentage
-
+	    String classURI = getRandomString();
+	    parentClass = modifiedModel.createClass( modifiedOntologyNS + classURI );//create a new class to the model
+	    classHierarchy.addClass( modifiedOntologyNS + classURI, "Thing" );  //add the node in the hierarchy of classes
+	    childClasses.add(parentClass);
+        } else {
+            parentClasses = classHierarchy.getClassesFromLevel( modifiedModel, level );
+            //int nbParentClasses = parentClasses.size();                         //number of classes from the Ontology
+            //int toAdd = Math.round( percentage*nbClasses );                       // 1 can be replaced by percentage
             for ( OntClass pClass : parentClasses ) {
-                classURI = getRandomString();
-                childClass = addClass (pClass, classURI );
-                pClass = childClass;
-                childClasses.add( childClass );
+                childClasses.add( addClass( pClass, getRandomString() ) );
             }
         }
-
         for ( OntClass pClass : childClasses ) {
-	    classURI = "IS_" + getLocalName( pClass.getURI() );
-            for ( int i=level+1; i<level + nbClasses; i++ ) {
-                childClass = addClass (pClass, classURI);
+	    String classURI = "IS_" + getLocalName( pClass.getURI() );
+            for ( int i = 1; i < nbClasses; i++ ) {
+                childClass = addClass( pClass, classURI );
                 pClass = childClass;
             }	//this.classHierarchy.printClassHierarchy();
         }

src/fr/inrialpes/exmo/align/gen/alt/SuppressHierarchy.java

@@ -39,16 +39,15 @@ public class SuppressHierarchy extends BasicAlterator {
     public Alterator modify( Properties params ) {
 	String p = params.getProperty( ParametersIds.NO_HIERARCHY );
 	if ( p == null ) return null;
-        int level = getMaxLevel();
-        while ( getMaxLevel() != 1 ) { // JE: dangerous to not use level
-            //this.classHierarchy.printClassHierarchy();
+        buildClassHierarchy();                                                  //builds the class hierarchy if necessary
+        for( int level = classHierarchy.getMaxLevel(); level > 1; level-- ) {
             noHierarchy ( level );
-            level--;
         }
 	return this; // useless
     };
 
-    // flatten level
+    // This suppress attach all classes of a level to the level above
+    // JE: why not directly attach all classes to Thing (or the root) and set childs to all these classes but root to null?
     public void noHierarchy ( int level ) {
         if ( level == 1 ) return;
         ArrayList<OntClass> levelClasses = new ArrayList<OntClass>();		//the list of classes from that level
@@ -69,11 +68,4 @@ public class SuppressHierarchy extends BasicAlterator {
 	    parentClass.removeSubClass( childClass );
         }
     }
-
-    //must have the max level of the class hierarchy
-    public int getMaxLevel() {
-        buildClassHierarchy();                                                  //check if the class hierarchy is built
-        return classHierarchy.getMaxLevel();
-    }
-
 }