Merge lp:~yrke/tapaal/drawcode-cleanup-extreme into lp:tapaal

[Kenneth Yrke Jørgensen]

Merged branch drawcode-cleanup-extreme

Large changes in the pipe gui, making it more consistent with "the TAPAAL way", and how the new TAPN model layer.
The code has been Audited with state of the art tool fixing found problems and optimizing the code

Large changes in the pipe gui, making it more consistent with "the TAPAAL way", and how the new TAPN model layer.
The code has been Audited with state of the art tool fixing found problems and optimizing the code

[Kenneth Yrke Jørgensen (yrke)]

review: Approve

[Jiri Srba (srba)]

review: Approve

[lp:~yrke/tapaal/drawcode-cleanup-extreme]

640. By Kenneth Yrke Jørgensen on 2011-10-14

Merged dracode-cleanup

641. By Kenneth Yrke Jørgensen on 2011-10-14

Merged with trunk

=== modified file 'src/dk/aau/cs/TCTL/Parsing/TAPAALQueryParser.java'
--- src/dk/aau/cs/TCTL/Parsing/TAPAALQueryParser.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/TCTL/Parsing/TAPAALQueryParser.java	2011-10-14 12:17:24 +0000
@@ -36,26 +36,26 @@
 	private static final String ERROR_PARSING_QUERY_MESSAGE = "TAPAAL countered an error trying to parse the query";
 
 	public interface SymbolConstants {
-		final int SYMBOL_EOF                =  0;  // (EOF)
-	       final int SYMBOL_ERROR              =  1;  // (Error)
-	       final int SYMBOL_WHITESPACE         =  2;  // (Whitespace)
-	       final int SYMBOL_EXCLAM             =  3;  // '!'
-	       final int SYMBOL_AMPAMP             =  4;  // '&&'
-	       final int SYMBOL_LPARAN             =  5;  // '('
-	       final int SYMBOL_RPARAN             =  6;  // ')'
-	       final int SYMBOL_DOT                =  7;  // '.'
-	       final int SYMBOL_PIPEPIPE           =  8;  // '||'
-	       final int SYMBOL_LT                 =  9;  // '<'
-	       final int SYMBOL_LTEQ               = 10;  // '<='
-	       final int SYMBOL_EQ                 = 11;  // '='
-	       final int SYMBOL_EQEQ               = 12;  // '=='
-	       final int SYMBOL_GT                 = 13;  // '>'
-	       final int SYMBOL_GTEQ               = 14;  // '>='
-	       final int SYMBOL_ALBRACKETRBRACKET  = 15;  // 'A[]'
-	       final int SYMBOL_ALTGT              = 16;  // 'A<>'
-	       final int SYMBOL_AF                 = 17;  // AF
-	       final int SYMBOL_AG                 = 18;  // AG
-	       final int SYMBOL_AND                = 19;  // and
+		int SYMBOL_EOF                =  0;  // (EOF)
+	       int SYMBOL_ERROR              =  1;  // (Error)
+	       int SYMBOL_WHITESPACE         =  2;  // (Whitespace)
+	       int SYMBOL_EXCLAM             =  3;  // '!'
+	       int SYMBOL_AMPAMP             =  4;  // '&&'
+	       int SYMBOL_LPARAN             =  5;  // '('
+	       int SYMBOL_RPARAN             =  6;  // ')'
+	       int SYMBOL_DOT                =  7;  // '.'
+	       int SYMBOL_PIPEPIPE           =  8;  // '||'
+	       int SYMBOL_LT                 =  9;  // '<'
+	       int SYMBOL_LTEQ               = 10;  // '<='
+	       int SYMBOL_EQ                 = 11;  // '='
+	       int SYMBOL_EQEQ               = 12;  // '=='
+	       int SYMBOL_GT                 = 13;  // '>'
+	       int SYMBOL_GTEQ               = 14;  // '>='
+	       int SYMBOL_ALBRACKETRBRACKET  = 15;  // 'A[]'
+	       int SYMBOL_ALTGT              = 16;  // 'A<>'
+	       int SYMBOL_AF                 = 17;  // AF
+	       int SYMBOL_AG                 = 18;  // AG
+	       int SYMBOL_AND                = 19;  // and
 	       final int SYMBOL_ELBRACKETRBRACKET  = 20;  // 'E[]'
 	       final int SYMBOL_ELTGT              = 21;  // 'E<>'
 	       final int SYMBOL_EF                 = 22;  // EF
@@ -146,7 +146,7 @@
 			temp.deleteOnExit();
 			PrintStream out = new PrintStream(temp);
 			out.append(textToParse);
-			out.append("\n");
+			out.append('\n');
 			out.close();
 
 			// open temp file

=== modified file 'src/dk/aau/cs/TCTL/TCTLAFNode.java'
--- src/dk/aau/cs/TCTL/TCTLAFNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLAFNode.java	2011-10-14 12:17:24 +0000
@@ -21,8 +21,8 @@
 	}
 
 	public TCTLAFNode() {
-		this.property = new TCTLStatePlaceHolder();
-		this.property.setParent(this);
+		property = new TCTLStatePlaceHolder();
+		property.setParent(this);
 	}
 
 	@Override

=== modified file 'src/dk/aau/cs/TCTL/TCTLAGNode.java'
--- src/dk/aau/cs/TCTL/TCTLAGNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLAGNode.java	2011-10-14 12:17:24 +0000
@@ -21,8 +21,8 @@
 	}
 
 	public TCTLAGNode() {
-		this.property = new TCTLStatePlaceHolder();
-		this.property.setParent(this);
+		property = new TCTLStatePlaceHolder();
+		property.setParent(this);
 	}
 
 	@Override

=== modified file 'src/dk/aau/cs/TCTL/TCTLAndListNode.java'
--- src/dk/aau/cs/TCTL/TCTLAndListNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLAndListNode.java	2011-10-14 12:17:24 +0000
@@ -30,14 +30,14 @@
 
 	public TCTLAndListNode(TCTLAbstractStateProperty property1,
 			TCTLAbstractStateProperty property2) {
-		this.properties = new ArrayList<TCTLAbstractStateProperty>();
+		properties = new ArrayList<TCTLAbstractStateProperty>();
 
 		addConjunct(property1);
 		addConjunct(property2);
 	}
 
 	public TCTLAndListNode(TCTLAndListNode andListNode) {
-		this.properties = new ArrayList<TCTLAbstractStateProperty>();
+		properties = new ArrayList<TCTLAbstractStateProperty>();
 
 		for (TCTLAbstractStateProperty p : andListNode.properties) {
 			addConjunct(p.copy());
@@ -45,13 +45,13 @@
 	}
 
 	public TCTLAndListNode() {
-		this.properties = new ArrayList<TCTLAbstractStateProperty>();
+		properties = new ArrayList<TCTLAbstractStateProperty>();
 		TCTLStatePlaceHolder ph = new TCTLStatePlaceHolder();
 		ph.setParent(this);
-		this.properties.add(ph);
+		properties.add(ph);
 		ph = new TCTLStatePlaceHolder();
 		ph.setParent(this);
-		this.properties.add(ph);
+		properties.add(ph);
 	}
 
 	public void addConjunct(TCTLAbstractStateProperty conjunct) {
@@ -146,7 +146,7 @@
 			TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			for (int i = 0; i < properties.size(); i++) {

=== modified file 'src/dk/aau/cs/TCTL/TCTLAtomicPropositionNode.java'
--- src/dk/aau/cs/TCTL/TCTLAtomicPropositionNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLAtomicPropositionNode.java	2011-10-14 12:17:24 +0000
@@ -65,9 +65,9 @@
 			TCTLAtomicPropositionNode node = (TCTLAtomicPropositionNode) o;
 			// TODO: Not sure if this is intentional but this is reference
 			// equals and not equality
-			return this.template == node.template
-					&& this.place == node.getPlace() && this.op == node.getOp()
-					&& this.n == node.getN();
+			return template.equals(node.template)
+					&& place.equals(node.getPlace()) && op.equals(node.getOp())
+					&& n == node.getN();
 		}
 		return false;
 	}
@@ -77,7 +77,7 @@
 			TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			return this;
@@ -87,7 +87,7 @@
 	@Override
 	public String toString() {
 		String value = place + "" + op + "" + n;
-		return template == null || template.isEmpty() ? value : template + "."
+		return (template == null || template.isEmpty()) ? value : template + "."
 				+ value;
 	}
 
@@ -113,7 +113,7 @@
 	}
 
 	public void setTemplate(String string) {
-		this.template = string;
+		template = string;
 	}
 	
 	public boolean containsAtomicPropositionWithSpecificPlaceInTemplate(String templateName, String placeName) {

=== modified file 'src/dk/aau/cs/TCTL/TCTLEFNode.java'
--- src/dk/aau/cs/TCTL/TCTLEFNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLEFNode.java	2011-10-14 12:17:24 +0000
@@ -21,8 +21,8 @@
 	}
 
 	public TCTLEFNode() {
-		this.property = new TCTLStatePlaceHolder();
-		this.property.setParent(this);
+		property = new TCTLStatePlaceHolder();
+		property.setParent(this);
 	}
 
 	@Override

=== modified file 'src/dk/aau/cs/TCTL/TCTLEGNode.java'
--- src/dk/aau/cs/TCTL/TCTLEGNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLEGNode.java	2011-10-14 12:17:24 +0000
@@ -21,8 +21,8 @@
 	}
 
 	public TCTLEGNode() {
-		this.property = new TCTLStatePlaceHolder();
-		this.property.setParent(this);
+		property = new TCTLStatePlaceHolder();
+		property.setParent(this);
 	}
 
 	@Override

=== modified file 'src/dk/aau/cs/TCTL/TCTLFalseNode.java'
--- src/dk/aau/cs/TCTL/TCTLFalseNode.java	2011-05-14 11:11:41 +0000
+++ src/dk/aau/cs/TCTL/TCTLFalseNode.java	2011-10-14 12:17:24 +0000
@@ -11,7 +11,7 @@
 	public TCTLAbstractStateProperty replace(TCTLAbstractProperty object1, TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			return this;

=== modified file 'src/dk/aau/cs/TCTL/TCTLNotNode.java'
--- src/dk/aau/cs/TCTL/TCTLNotNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLNotNode.java	2011-10-14 12:17:24 +0000
@@ -62,7 +62,7 @@
 			TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			property = property.replace(object1, object2);

=== modified file 'src/dk/aau/cs/TCTL/TCTLOrListNode.java'
--- src/dk/aau/cs/TCTL/TCTLOrListNode.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLOrListNode.java	2011-10-14 12:17:24 +0000
@@ -29,7 +29,7 @@
 	}
 
 	public TCTLOrListNode(TCTLOrListNode orListNode) {
-		this.properties = new ArrayList<TCTLAbstractStateProperty>();
+		properties = new ArrayList<TCTLAbstractStateProperty>();
 
 		for (TCTLAbstractStateProperty p : orListNode.properties) {
 			addDisjunct(p.copy());
@@ -38,20 +38,20 @@
 
 	public TCTLOrListNode(TCTLAbstractStateProperty property1,
 			TCTLAbstractStateProperty property2) {
-		this.properties = new ArrayList<TCTLAbstractStateProperty>();
+		properties = new ArrayList<TCTLAbstractStateProperty>();
 
 		addDisjunct(property1);
 		addDisjunct(property2);
 	}
 
 	public TCTLOrListNode() {
-		this.properties = new ArrayList<TCTLAbstractStateProperty>();
+		properties = new ArrayList<TCTLAbstractStateProperty>();
 		TCTLStatePlaceHolder ph = new TCTLStatePlaceHolder();
 		ph.setParent(this);
-		this.properties.add(ph);
+		properties.add(ph);
 		ph = new TCTLStatePlaceHolder();
 		ph.setParent(this);
-		this.properties.add(ph);
+		properties.add(ph);
 	}
 
 	public void addDisjunct(TCTLAbstractStateProperty disjunct) {
@@ -146,7 +146,7 @@
 			TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			for (int i = 0; i < properties.size(); i++) {

=== modified file 'src/dk/aau/cs/TCTL/TCTLStatePlaceHolder.java'
--- src/dk/aau/cs/TCTL/TCTLStatePlaceHolder.java	2011-02-11 18:11:16 +0000
+++ src/dk/aau/cs/TCTL/TCTLStatePlaceHolder.java	2011-10-14 12:17:24 +0000
@@ -39,7 +39,7 @@
 			TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			return this;

=== modified file 'src/dk/aau/cs/TCTL/TCTLTrueNode.java'
--- src/dk/aau/cs/TCTL/TCTLTrueNode.java	2011-05-12 18:07:24 +0000
+++ src/dk/aau/cs/TCTL/TCTLTrueNode.java	2011-10-14 12:17:24 +0000
@@ -11,7 +11,7 @@
 	public TCTLAbstractStateProperty replace(TCTLAbstractProperty object1, TCTLAbstractProperty object2) {
 		if (this == object1 && object2 instanceof TCTLAbstractStateProperty) {
 			TCTLAbstractStateProperty obj2 = (TCTLAbstractStateProperty) object2;
-			obj2.setParent(this.parent);
+			obj2.setParent(parent);
 			return obj2;
 		} else {
 			return this;

=== modified file 'src/dk/aau/cs/TCTL/visitors/BooleanResult.java'
--- src/dk/aau/cs/TCTL/visitors/BooleanResult.java	2011-03-27 09:10:43 +0000
+++ src/dk/aau/cs/TCTL/visitors/BooleanResult.java	2011-10-14 12:17:24 +0000
@@ -8,7 +8,7 @@
 	}
 	
 	public BooleanResult(boolean initialValue){
-		this.result = initialValue;
+		result = initialValue;
 	}
 
 	public boolean result(){

=== modified file 'src/dk/aau/cs/TCTL/visitors/BroadcastTranslationQueryVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/BroadcastTranslationQueryVisitor.java	2011-02-03 19:03:15 +0000
+++ src/dk/aau/cs/TCTL/visitors/BroadcastTranslationQueryVisitor.java	2011-10-14 12:17:24 +0000
@@ -27,7 +27,7 @@
 			append("(i).");
 			append(atomicPropositionNode.getPlace());
 			append(") ");
-			append(OperatorConversion(atomicPropositionNode.getOp()));
+			append(operatorConversion(atomicPropositionNode.getOp()));
 			append(" ");
 			append(atomicPropositionNode.getN());
 		} else if (totalTokens == 0) {
@@ -36,7 +36,7 @@
 			append(".");
 			append(atomicPropositionNode.getPlace());
 			append(") ");
-			append(OperatorConversion(atomicPropositionNode.getOp()));
+			append(operatorConversion(atomicPropositionNode.getOp()));
 			append(" ");
 			append(atomicPropositionNode.getN());
 		} else {
@@ -52,7 +52,7 @@
 				append(atomicPropositionNode.getPlace());
 			}
 			append(") ");
-			append(OperatorConversion(atomicPropositionNode.getOp()));
+			append(operatorConversion(atomicPropositionNode.getOp()));
 			append(" ");
 			append(atomicPropositionNode.getN());
 		}

=== modified file 'src/dk/aau/cs/TCTL/visitors/OptimizedStandardTranslationQueryVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/OptimizedStandardTranslationQueryVisitor.java	2011-05-22 12:57:23 +0000
+++ src/dk/aau/cs/TCTL/visitors/OptimizedStandardTranslationQueryVisitor.java	2011-10-14 12:17:24 +0000
@@ -29,13 +29,13 @@
 			append("(i).");
 			append(atomicPropositionNode.getPlace());
 			append(") ");
-			append(OperatorConversion(atomicPropositionNode.getOp()));
+			append(operatorConversion(atomicPropositionNode.getOp()));
 			append(" ");
 			append(atomicPropositionNode.getN());
 		} else {
 			append("(");
 			append(createAtomicPropositionSum(atomicPropositionNode.getPlace()));
-			append(OperatorConversion(atomicPropositionNode.getOp()));
+			append(operatorConversion(atomicPropositionNode.getOp()));
 			append(" ");
 			append(atomicPropositionNode.getN());
 			append(")");
@@ -64,7 +64,7 @@
 				sum.append(" + ");
 			}
 		}
-		sum.append(")");
+		sum.append(')');
 		return sum.toString();
 	}
 }

=== modified file 'src/dk/aau/cs/TCTL/visitors/QueryVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/QueryVisitor.java	2011-05-12 18:07:24 +0000
+++ src/dk/aau/cs/TCTL/visitors/QueryVisitor.java	2011-10-14 12:17:24 +0000
@@ -34,7 +34,7 @@
 	}
 
 	public String getUppaalQueryFor(TAPNQuery tapnQuery) {
-		this.uppaalQuery = new StringBuffer();
+		uppaalQuery = new StringBuffer();
 		tapnQuery.getProperty().accept(this, null);
 		return uppaalQuery.toString();
 	}
@@ -64,7 +64,7 @@
 	}
 
 	public void visit(TCTLAndListNode andListNode, Object context) {
-		uppaalQuery.append("(");
+		uppaalQuery.append('(');
 		boolean firstTime = true;
 
 		for (TCTLAbstractStateProperty p : andListNode.getProperties()) {
@@ -76,12 +76,12 @@
 			firstTime = false;
 		}
 
-		uppaalQuery.append(")");
+		uppaalQuery.append(')');
 
 	}
 
 	public void visit(TCTLOrListNode orListNode, Object context) {
-		uppaalQuery.append("(");
+		uppaalQuery.append('(');
 		boolean firstTime = true;
 
 		for (TCTLAbstractStateProperty p : orListNode.getProperties()) {
@@ -93,15 +93,15 @@
 			firstTime = false;
 		}
 
-		uppaalQuery.append(")");
+		uppaalQuery.append(')');
 
 	}
 
 	public void visit(TCTLNotNode notNode, Object context) {
-		uppaalQuery.append("!");
-		uppaalQuery.append("(");
+		uppaalQuery.append('!');
+		uppaalQuery.append('(');
 		notNode.getProperty().accept(this, context);
-		uppaalQuery.append(")");
+		uppaalQuery.append(')');
 	}
 
 	public void visit(TCTLStatePlaceHolder statePlaceHolderNode, Object context) {
@@ -119,7 +119,7 @@
 		uppaalQuery.append(tctlFalseNode.toString());
 	}
 
-	protected String OperatorConversion(String op) {
+	protected String operatorConversion(String op) {
 		if (op.equals("="))
 			return "==";
 

=== modified file 'src/dk/aau/cs/TCTL/visitors/RenamePlaceTCTLVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/RenamePlaceTCTLVisitor.java	2011-05-12 18:07:24 +0000
+++ src/dk/aau/cs/TCTL/visitors/RenamePlaceTCTLVisitor.java	2011-10-14 12:17:24 +0000
@@ -20,8 +20,8 @@
 	private String newPlaceName;
 
 	public RenamePlaceTCTLVisitor(String oldName, String newName) {
-		this.oldPlaceName = oldName;
-		this.newPlaceName = newName;
+		oldPlaceName = oldName;
+		newPlaceName = newName;
 	}
 
 	public void visit(TCTLAFNode afNode, Object context) {

=== modified file 'src/dk/aau/cs/TCTL/visitors/SimplifyPropositionsVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/SimplifyPropositionsVisitor.java	2011-05-12 18:07:24 +0000
+++ src/dk/aau/cs/TCTL/visitors/SimplifyPropositionsVisitor.java	2011-10-14 12:17:24 +0000
@@ -12,7 +12,7 @@
 	List<TCTLAtomicPropositionNode> truePropositions = new ArrayList<TCTLAtomicPropositionNode>();
 	List<TCTLAtomicPropositionNode> falsePropositions = new ArrayList<TCTLAtomicPropositionNode>();
 	
-	public void FindAndReplaceTrueAndFalsePropositions(TCTLAbstractProperty query) {
+	public void findAndReplaceTrueAndFalsePropositions(TCTLAbstractProperty query) {
 		query.accept(this, null);
 		
 		for(TCTLAtomicPropositionNode node : truePropositions)

=== modified file 'src/dk/aau/cs/TCTL/visitors/StandardSymmetryTranslationQueryVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/StandardSymmetryTranslationQueryVisitor.java	2011-03-27 08:57:51 +0000
+++ src/dk/aau/cs/TCTL/visitors/StandardSymmetryTranslationQueryVisitor.java	2011-10-14 12:17:24 +0000
@@ -21,7 +21,7 @@
 		append("(i).");
 		append(atomicPropositionNode.getPlace());
 		append(") ");
-		append(OperatorConversion(atomicPropositionNode.getOp()));
+		append(operatorConversion(atomicPropositionNode.getOp()));
 		append(" ");
 		append(atomicPropositionNode.getN());
 	}

=== modified file 'src/dk/aau/cs/TCTL/visitors/StandardTranslationQueryVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/StandardTranslationQueryVisitor.java	2011-05-21 13:32:34 +0000
+++ src/dk/aau/cs/TCTL/visitors/StandardTranslationQueryVisitor.java	2011-10-14 12:17:24 +0000
@@ -24,7 +24,7 @@
 
 		append("(");
 		append(createAtomicPropositionSum(atomicPropositionNode.getPlace()));
-		append(OperatorConversion(atomicPropositionNode.getOp()));
+		append(operatorConversion(atomicPropositionNode.getOp()));
 		append(" ");
 		append(atomicPropositionNode.getN());
 		append(")");
@@ -49,7 +49,7 @@
 				sum.append(" + ");
 			}
 		}
-		sum.append(")");
+		sum.append(')');
 		return sum.toString();
 	}
 }

=== modified file 'src/dk/aau/cs/TCTL/visitors/VerifyPlaceNamesVisitor.java'
--- src/dk/aau/cs/TCTL/visitors/VerifyPlaceNamesVisitor.java	2011-05-12 18:07:24 +0000
+++ src/dk/aau/cs/TCTL/visitors/VerifyPlaceNamesVisitor.java	2011-10-14 12:17:24 +0000
@@ -27,7 +27,7 @@
 		this.templatePlaceNames = templatePlaceNames;
 	}
 
-	public Context VerifyPlaceNames(TCTLAbstractProperty query) {
+	public Context verifyPlaceNames(TCTLAbstractProperty query) {
 		Context c = new Context();
 
 		query.accept(this, c);
@@ -54,7 +54,7 @@
 	public void visit(TCTLAtomicPropositionNode atomicPropositionNode, Object context) {
 		Context c = (Context) context;
 		if (!templatePlaceNames.contains(new Tuple<String,String>(atomicPropositionNode.getTemplate(), atomicPropositionNode.getPlace()))) {
-			c.AddIncorrectPlaceName(atomicPropositionNode.getTemplate() + "." + atomicPropositionNode.getPlace());
+			c.addIncorrectPlaceName(atomicPropositionNode.getTemplate() + "." + atomicPropositionNode.getPlace());
 			c.setResult(false);
 		}
 	}
@@ -98,13 +98,13 @@
 			return incorrectPlaceNames;
 		}
 
-		public void AddIncorrectPlaceName(String incorrectPlaceName) {
+		public void addIncorrectPlaceName(String incorrectPlaceName) {
 			incorrectPlaceNames.add(incorrectPlaceName);
 		}
 
 		public Context() {
-			this.result = true;
-			this.incorrectPlaceNames = new HashSet<String>();
+			result = true;
+			incorrectPlaceNames = new HashSet<String>();
 		}
 	}
 

=== modified file 'src/dk/aau/cs/gui/BatchProcessingDialog.java'
--- src/dk/aau/cs/gui/BatchProcessingDialog.java	2011-10-09 20:16:40 +0000
+++ src/dk/aau/cs/gui/BatchProcessingDialog.java	2011-10-14 12:17:24 +0000
@@ -188,7 +188,7 @@
 		fileList.addListSelectionListener(new ListSelectionListener() {
 
 			public void valueChanged(ListSelectionEvent e) {
-				if (e.getValueIsAdjusting() == false) {
+				if (!(e.getValueIsAdjusting())) {
 					if (fileList.getSelectedIndex() == -1) {
 						removeFileButton.setEnabled(false);
 					} else {

=== modified file 'src/dk/aau/cs/gui/Context.java'
--- src/dk/aau/cs/gui/Context.java	2011-05-05 18:02:09 +0000
+++ src/dk/aau/cs/gui/Context.java	2011-10-14 12:17:24 +0000
@@ -16,10 +16,10 @@
 	
 	public Context(TabContent tab) {
 		Require.that(tab != null, "tab cannot be null");
-		this.currentTab = tab;
-		this.network = tab.network();
-		this.selectedTemplate = tab.currentTemplate();
-		this.undoManager = tab.drawingSurface().getUndoManager();
+		currentTab = tab;
+		network = tab.network();
+		selectedTemplate = tab.currentTemplate();
+		undoManager = tab.drawingSurface().getUndoManager();
 	}
 	
 	public TimedArcPetriNetNetwork network(){

=== modified file 'src/dk/aau/cs/gui/SharedPlaceNamePanel.java'
--- src/dk/aau/cs/gui/SharedPlaceNamePanel.java	2011-10-04 18:07:57 +0000
+++ src/dk/aau/cs/gui/SharedPlaceNamePanel.java	2011-10-14 12:17:24 +0000
@@ -37,7 +37,7 @@
 	
 	public SharedPlaceNamePanel(JRootPane rootPane, SharedPlacesListModel sharedPlacesListModel, Context context, SharedPlace placeToEdit) {
 		this.rootPane = rootPane;
-		this.listModel = sharedPlacesListModel;
+		listModel = sharedPlacesListModel;
 		this.placeToEdit = placeToEdit;
 		this.context = context;
 		initComponents();		
@@ -60,7 +60,7 @@
 		GridBagConstraints gbc = new GridBagConstraints();
 		namePanel.add(label, gbc);
 		
-		String initialText = placeToEdit == null ? "" : placeToEdit.name();
+		String initialText = (placeToEdit == null) ? "" : placeToEdit.name();
 		nameField = new JTextField(initialText);
 		nameField.setMinimumSize(new Dimension(150,27));
 		nameField.setPreferredSize(new Dimension(200, 27));

=== modified file 'src/dk/aau/cs/gui/SharedPlacesAndTransitionsPanel.java'
--- src/dk/aau/cs/gui/SharedPlacesAndTransitionsPanel.java	2011-08-30 08:42:12 +0000
+++ src/dk/aau/cs/gui/SharedPlacesAndTransitionsPanel.java	2011-10-14 12:17:24 +0000
@@ -30,18 +30,17 @@
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
-import pipe.dataLayer.Arc;
 import pipe.dataLayer.TAPNQuery;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.TimedInhibitorArcComponent;
-import pipe.dataLayer.TimedInputArcComponent;
-import pipe.dataLayer.TimedOutputArcComponent;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.dataLayer.TimedTransitionComponent;
-import pipe.dataLayer.TimedTransportArcComponent;
 import pipe.gui.CreateGui;
 import pipe.gui.DrawingSurfaceImpl;
-import pipe.gui.Pipe;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.tapn.TimedInhibitorArcComponent;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedOutputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
 import pipe.gui.undo.DeleteTimedInhibitorArcCommand;
 import pipe.gui.undo.DeleteTimedInputArcCommand;
 import pipe.gui.undo.DeleteTimedOutputArcCommand;
@@ -92,8 +91,8 @@
 	public SharedPlacesAndTransitionsPanel(TabContent tab){
 		Require.that(tab != null, "tab cannot be null");
 
-		this.undoManager = tab.drawingSurface().getUndoManager();
-		this.nameGenerator = tab.drawingSurface().getNameGenerator();
+		undoManager = tab.drawingSurface().getUndoManager();
+		nameGenerator = tab.drawingSurface().getNameGenerator();
 		this.tab = tab;
 
 		sharedPlacesListModel = new SharedPlacesListModel(tab.network());

=== modified file 'src/dk/aau/cs/gui/SharedTransitionNamePanel.java'
--- src/dk/aau/cs/gui/SharedTransitionNamePanel.java	2011-10-04 18:07:57 +0000
+++ src/dk/aau/cs/gui/SharedTransitionNamePanel.java	2011-10-14 12:17:24 +0000
@@ -38,7 +38,7 @@
 	
 	public SharedTransitionNamePanel(JRootPane rootPane, SharedTransitionsListModel sharedTransitionsListModel, UndoManager undoManager, NameGenerator nameGenerator, SharedTransition transitionToEdit) {
 		this.rootPane = rootPane;
-		this.listModel = sharedTransitionsListModel;
+		listModel = sharedTransitionsListModel;
 		this.undoManager = undoManager;
 		this.nameGenerator = nameGenerator;
 		this.transitionToEdit = transitionToEdit;
@@ -62,7 +62,7 @@
 		GridBagConstraints gbc = new GridBagConstraints();
 		namePanel.add(label, gbc);
 		
-		String initialText = transitionToEdit == null ? "" : transitionToEdit.name();
+		String initialText = (transitionToEdit == null) ? "" : transitionToEdit.name();
 		nameField = new JTextField(initialText);
 		nameField.setMinimumSize(new Dimension(150,27));
 		nameField.setPreferredSize(new Dimension(200, 27));

=== modified file 'src/dk/aau/cs/gui/TabComponent.java'
--- src/dk/aau/cs/gui/TabComponent.java	2011-08-22 13:31:50 +0000
+++ src/dk/aau/cs/gui/TabComponent.java	2011-10-14 12:17:24 +0000
@@ -151,7 +151,7 @@
 
 	}
 
-	private final static MouseListener buttonMouseListener = new MouseAdapter() {
+	private static final MouseListener buttonMouseListener = new MouseAdapter() {
 		@Override
 		public void mouseEntered(MouseEvent e) {
 			Component component = e.getComponent();

=== modified file 'src/dk/aau/cs/gui/TabContent.java'
--- src/dk/aau/cs/gui/TabContent.java	2011-10-13 12:32:31 +0000
+++ src/dk/aau/cs/gui/TabContent.java	2011-10-14 12:17:24 +0000
@@ -71,7 +71,7 @@
 			zoomLevels.put(net, new Zoomer());
 		}
 
-		this.drawingSurface = new DrawingSurfaceImpl(new DataLayer(), this);
+		drawingSurface = new DrawingSurfaceImpl(new DataLayer(), this);
 		drawingSurfaceScroller = new JScrollPane(drawingSurface);
 		// make it less bad on XP
 		drawingSurfaceScroller.setBorder(new BevelBorder(BevelBorder.LOWERED));
@@ -392,7 +392,7 @@
 
 	public void setNetwork(TimedArcPetriNetNetwork network, Collection<Template> templates) {
 		Require.that(network != null, "network cannot be null");
-		this.tapnNetwork = network;
+		tapnNetwork = network;
 		
 		guiModels.clear();
 		for(Template template : templates){

=== modified file 'src/dk/aau/cs/gui/TemplateExplorer.java'
--- src/dk/aau/cs/gui/TemplateExplorer.java	2011-10-13 13:26:34 +0000
+++ src/dk/aau/cs/gui/TemplateExplorer.java	2011-10-14 12:17:24 +0000
@@ -287,7 +287,7 @@
 				s.append("The following queries are associated with the currently selected objects:\n\n");
 				for (TAPNQuery q : queriesToDelete) {
 					s.append(q.getName());
-					s.append("\n");
+					s.append('\n');
 				}
 				s.append("\nAre you sure you want to remove the current selection and all associated queries?");
 				return s;
@@ -489,7 +489,7 @@
 		
 		
 		public TemplateListCellRenderer(ListCellRenderer renderer) {
-			this.cellRenderer = renderer;
+			cellRenderer = renderer;
 			setLayout(new BorderLayout()); 
 	        setOpaque(false); 
 	        activeCheckbox.setOpaque(false);
@@ -521,7 +521,7 @@
 		
 		public TemplateListManager(JList list) {
 			this.list = list;
-			this.selectionModel = list.getSelectionModel();
+			selectionModel = list.getSelectionModel();
 			this.list.registerKeyboardAction(this, KeyStroke.getKeyStroke(KeyEvent.VK_SPACE, 0), JComponent.WHEN_FOCUSED);
 		}
 		
@@ -597,7 +597,7 @@
 		}
 
 		public void valueChanged(ListSelectionEvent e) {
-			if (e.getValueIsAdjusting() == false) {
+			if (!(e.getValueIsAdjusting())) {
 				int index = templateList.getSelectedIndex();
 				if (index == -1) {
 					removeTemplateButton.setEnabled(false);

=== modified file 'src/dk/aau/cs/gui/components/BatchProcessingResultsTableModel.java'
--- src/dk/aau/cs/gui/components/BatchProcessingResultsTableModel.java	2011-08-28 14:43:51 +0000
+++ src/dk/aau/cs/gui/components/BatchProcessingResultsTableModel.java	2011-10-14 12:17:24 +0000
@@ -18,7 +18,7 @@
 		results = new ArrayList<BatchProcessingVerificationResult>();
 	}
 	
-	public void AddResult(BatchProcessingVerificationResult result){
+	public void addResult(BatchProcessingVerificationResult result){
 		int lastRow = results.size();
 		results.add(result);
 		fireTableRowsInserted(lastRow, lastRow);

=== modified file 'src/dk/aau/cs/gui/components/ConstantsListModel.java'
--- src/dk/aau/cs/gui/components/ConstantsListModel.java	2011-07-15 12:40:18 +0000
+++ src/dk/aau/cs/gui/components/ConstantsListModel.java	2011-10-14 12:17:24 +0000
@@ -16,15 +16,15 @@
 
 	public ConstantsListModel(TimedArcPetriNetNetwork network){
 		listener = new ConstantsListener() {
-			public void ConstantRemoved(ConstantEvent e) {
+			public void constantRemoved(ConstantEvent e) {
 				fireIntervalRemoved(this, e.index(), e.index());
 			}
 			
-			public void ConstantChanged(ConstantChangedEvent e) {
+			public void constantChanged(ConstantChangedEvent e) {
 				fireContentsChanged(this, e.index(), e.index());
 			}
 			
-			public void ConstantAdded(ConstantEvent e) {
+			public void constantAdded(ConstantEvent e) {
 				fireIntervalAdded(this, e.index(), e.index());
 			}
 		};
@@ -34,11 +34,11 @@
 	// TODO: Due to stupid programming, we have to allow it to be set later
 	//       since the Network is sometimes set after the TabContent is created.
 	public void setNetwork(TimedArcPetriNetNetwork newNetwork){
-		if(this.network != null){
-			this.network.removeConstantsListener(listener);
+		if(network != null){
+			network.removeConstantsListener(listener);
 		}
-		this.network = newNetwork;
-		this.network.addConstantsListener(listener);	
+		network = newNetwork;
+		network.addConstantsListener(listener);	
 		fireContentsChanged(this,0, Integer.MAX_VALUE);
 	}
 	

=== modified file 'src/dk/aau/cs/gui/components/MultiLineAutoWrappingTooltipUI.java'
--- src/dk/aau/cs/gui/components/MultiLineAutoWrappingTooltipUI.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/gui/components/MultiLineAutoWrappingTooltipUI.java	2011-10-14 12:17:24 +0000
@@ -61,7 +61,7 @@
 			
 			int width = 400;
 			Dimension dim = textArea.getPreferredSize();
-			dim.width = originalDim.width > width ? width : originalDim.width+10;
+			dim.width = (originalDim.width > width) ? width : originalDim.width + 10;
 			dim.height++;
 			textArea.setSize(dim);
 			

=== modified file 'src/dk/aau/cs/gui/components/TextLabel.java'
--- src/dk/aau/cs/gui/components/TextLabel.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/gui/components/TextLabel.java	2011-10-14 12:17:24 +0000
@@ -74,7 +74,7 @@
 		private Component targetComponent;
 
 		public MouseWheelAndClickPassThroughHandler(Component target) {
-			this.targetComponent = target;
+			targetComponent = target;
 		}
 
 		@Override

=== modified file 'src/dk/aau/cs/gui/components/TimedPlaceControl.java'
--- src/dk/aau/cs/gui/components/TimedPlaceControl.java	2011-03-07 18:53:27 +0000
+++ src/dk/aau/cs/gui/components/TimedPlaceControl.java	2011-10-14 12:17:24 +0000
@@ -86,7 +86,7 @@
 
 	public void setAttributesVisible(boolean value) {
 		if (value != attributesVisible) {
-			this.attributesVisible = value;
+			attributesVisible = value;
 			if (value) {
 				addChildControls();
 			} else {

=== modified file 'src/dk/aau/cs/gui/undo/MakePlaceSharedCommand.java'
--- src/dk/aau/cs/gui/undo/MakePlaceSharedCommand.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/gui/undo/MakePlaceSharedCommand.java	2011-10-14 12:17:24 +0000
@@ -4,7 +4,7 @@
 import java.util.List;
 
 import pipe.dataLayer.TAPNQuery;
-import pipe.dataLayer.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
 import dk.aau.cs.TCTL.visitors.BooleanResult;
 import dk.aau.cs.TCTL.visitors.MakePlaceSharedVisitor;
 import dk.aau.cs.gui.TabContent;
@@ -39,9 +39,9 @@
 		this.sharedPlace = sharedPlace;
 		this.place = place;
 		this.placeComponent = placeComponent;
-		this.oldTokens = place.tokens();
+		oldTokens = place.tokens();
 		this.currentTab = currentTab;
-		this.newQueryToOldQueryMapping = new Hashtable<TAPNQuery, TAPNQuery>();
+		newQueryToOldQueryMapping = new Hashtable<TAPNQuery, TAPNQuery>();
 	}
 	
 	@Override

=== modified file 'src/dk/aau/cs/gui/undo/MakeTransitionSharedCommand.java'
--- src/dk/aau/cs/gui/undo/MakeTransitionSharedCommand.java	2011-02-26 15:56:34 +0000
+++ src/dk/aau/cs/gui/undo/MakeTransitionSharedCommand.java	2011-10-14 12:17:24 +0000
@@ -11,7 +11,7 @@
 	public MakeTransitionSharedCommand(SharedTransition sharedTransition, TimedTransition timedTransition){
 		this.sharedTransition = sharedTransition;
 		this.timedTransition = timedTransition;
-		this.oldName = timedTransition.name();
+		oldName = timedTransition.name();
 	}
 	
 	@Override

=== modified file 'src/dk/aau/cs/gui/undo/TimedPlaceMarkingEdit.java'
--- src/dk/aau/cs/gui/undo/TimedPlaceMarkingEdit.java	2011-02-26 15:56:34 +0000
+++ src/dk/aau/cs/gui/undo/TimedPlaceMarkingEdit.java	2011-10-14 12:17:24 +0000
@@ -1,6 +1,6 @@
 package dk.aau.cs.gui.undo;
 
-import pipe.dataLayer.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
 
 // TODO: Fix this to work on the model class instead of the GUI class
 public class TimedPlaceMarkingEdit extends Command {
@@ -8,7 +8,7 @@
 	private final TimedPlaceComponent timedPlaceComponent;
 
 	public TimedPlaceMarkingEdit(TimedPlaceComponent tpc, int numberOfTokens) {
-		this.timedPlaceComponent = tpc;
+		timedPlaceComponent = tpc;
 		this.numberOfTokens = numberOfTokens;
 	}
 

=== modified file 'src/dk/aau/cs/gui/undo/UnsharePlaceCommand.java'
--- src/dk/aau/cs/gui/undo/UnsharePlaceCommand.java	2011-03-10 19:01:57 +0000
+++ src/dk/aau/cs/gui/undo/UnsharePlaceCommand.java	2011-10-14 12:17:24 +0000
@@ -1,6 +1,6 @@
 package dk.aau.cs.gui.undo;
 
-import pipe.dataLayer.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
 import dk.aau.cs.model.tapn.SharedPlace;
 import dk.aau.cs.model.tapn.TimedArcPetriNet;
 import dk.aau.cs.model.tapn.TimedInhibitorArc;

=== modified file 'src/dk/aau/cs/io/TapnLegacyXmlLoader.java'
--- src/dk/aau/cs/io/TapnLegacyXmlLoader.java	2011-10-14 11:36:08 +0000
+++ src/dk/aau/cs/io/TapnLegacyXmlLoader.java	2011-10-14 12:17:24 +0000
@@ -18,32 +18,31 @@
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
-import pipe.dataLayer.AnnotationNote;
-import pipe.dataLayer.Arc;
-import pipe.dataLayer.DataLayer;
-import pipe.dataLayer.Note;
-import pipe.dataLayer.PetriNetObject;
-import pipe.dataLayer.Place;
-import pipe.dataLayer.PlaceTransitionObject;
 import pipe.dataLayer.TAPNQuery;
 import pipe.dataLayer.TAPNQuery.ExtrapolationOption;
 import pipe.dataLayer.TAPNQuery.HashTableSize;
 import pipe.dataLayer.TAPNQuery.SearchOption;
 import pipe.dataLayer.TAPNQuery.TraceOption;
+import pipe.dataLayer.DataLayer;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.TimedInhibitorArcComponent;
-import pipe.dataLayer.TimedInputArcComponent;
-import pipe.dataLayer.TimedOutputArcComponent;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.dataLayer.TimedTransitionComponent;
-import pipe.dataLayer.Transition;
-import pipe.dataLayer.TimedTransportArcComponent;
 import pipe.gui.CreateGui;
 import pipe.gui.DrawingSurfaceImpl;
 import pipe.gui.Grid;
 import pipe.gui.Pipe;
-import pipe.gui.Zoomable;
 import pipe.gui.Zoomer;
+import pipe.gui.graphicElements.AnnotationNote;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.Note;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.Place;
+import pipe.gui.graphicElements.PlaceTransitionObject;
+import pipe.gui.graphicElements.Transition;
+import pipe.gui.graphicElements.tapn.TimedInhibitorArcComponent;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedOutputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
 import pipe.gui.handler.AnimationHandler;
 import pipe.gui.handler.AnnotationNoteHandler;
 import pipe.gui.handler.ArcHandler;
@@ -102,7 +101,7 @@
 		transportArcsTimeIntervals = new HashMap<TimedTransportArcComponent, TimeInterval>();
 		queries = new ArrayList<TAPNQuery>();
 		constants = new ConstantStore();
-		this.drawingSurface = drawingSurfaceImpl;
+		drawingSurface = drawingSurfaceImpl;
 	}
 	
 	public LoadedModel load(InputStream file) throws FormatException {
@@ -286,7 +285,7 @@
 				TimedPlace sourcePlace = tapn.getPlaceByName(presetTransportArc.getSource().getName());
 				TimedTransition trans = tapn.getTransitionByName(sourceIn.getName());
 				TimedPlace destPlace = tapn.getPlaceByName(targetIn.getName());
-				TimeInterval interval = transportArcsTimeIntervals.get((TimedTransportArcComponent) presetTransportArc);
+				TimeInterval interval = transportArcsTimeIntervals.get(presetTransportArc);
 
 				assert (sourcePlace != null);
 				assert (trans != null);
@@ -304,7 +303,7 @@
 				tapn.add(transArc);
 
 				presetArcs.remove((TimedTransitionComponent) sourceIn);
-				transportArcsTimeIntervals.remove((TimedTransportArcComponent) presetTransportArc);
+				transportArcsTimeIntervals.remove(presetTransportArc);
 			} else {
 				postsetArcs.put((TimedTransitionComponent) sourceIn, (TimedTransportArcComponent) tempArc);
 			}
@@ -499,7 +498,7 @@
 	private boolean doesPlacesUsedInQueryExist(TAPNQuery query, ArrayList<Tuple<String, String>> templatePlaceNames) {
 		VerifyPlaceNamesVisitor nameChecker = new VerifyPlaceNamesVisitor(templatePlaceNames);
 
-		VerifyPlaceNamesVisitor.Context c = nameChecker.VerifyPlaceNames(query.getProperty());
+		VerifyPlaceNamesVisitor.Context c = nameChecker.verifyPlaceNames(query.getProperty());
 		
 		return c.getResult();
 	}
@@ -615,7 +614,7 @@
 
 		Place place = null;
 
-		if (invariant == null || invariant == "") {
+		if (invariant == null || invariant.equals("")) {
 			place = new Place(positionXInput, positionYInput, idInput,
 					nameInput, nameOffsetXInput, nameOffsetYInput,
 					initialMarkingInput, markingOffsetXInput,
@@ -753,10 +752,7 @@
 	private boolean getSymmetryAsOldFormat(Element queryElement) {
 		String reductionString = queryElement.getAttribute("reductionOption");
 		
-		if(reductionString.contains(SYMMETRY))
-			return true;
-		else
-			return false;
+		return reductionString.contains(SYMMETRY);
 	}
 
 	private TCTLAbstractProperty parseQueryPropertyAsOldFormat(Element queryElement) throws FormatException {
@@ -958,9 +954,9 @@
 					((Note) newObject).getNote().addMouseListener(noteHandler);
 					((Note) newObject).getNote().addMouseMotionListener(noteHandler);
 				}
-				if (newObject instanceof Zoomable) {
-					newObject.zoomUpdate(drawingSurface.getZoom());
-				}
+				
+				newObject.zoomUpdate(drawingSurface.getZoom());
+				
 			}
 			newObject.setGuiModel(guiModel);
 		}

=== modified file 'src/dk/aau/cs/io/TapnXmlLoader.java'
--- src/dk/aau/cs/io/TapnXmlLoader.java	2011-10-14 11:36:08 +0000
+++ src/dk/aau/cs/io/TapnXmlLoader.java	2011-10-14 12:17:24 +0000
@@ -19,32 +19,31 @@
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
-import pipe.dataLayer.AnnotationNote;
-import pipe.dataLayer.Arc;
-import pipe.dataLayer.DataLayer;
-import pipe.dataLayer.Note;
-import pipe.dataLayer.PetriNetObject;
-import pipe.dataLayer.Place;
-import pipe.dataLayer.PlaceTransitionObject;
 import pipe.dataLayer.TAPNQuery;
 import pipe.dataLayer.TAPNQuery.ExtrapolationOption;
 import pipe.dataLayer.TAPNQuery.HashTableSize;
 import pipe.dataLayer.TAPNQuery.SearchOption;
 import pipe.dataLayer.TAPNQuery.TraceOption;
+import pipe.dataLayer.DataLayer;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.TimedInhibitorArcComponent;
-import pipe.dataLayer.TimedInputArcComponent;
-import pipe.dataLayer.TimedOutputArcComponent;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.dataLayer.TimedTransitionComponent;
-import pipe.dataLayer.Transition;
-import pipe.dataLayer.TimedTransportArcComponent;
 import pipe.gui.CreateGui;
 import pipe.gui.DrawingSurfaceImpl;
 import pipe.gui.Grid;
 import pipe.gui.Pipe;
-import pipe.gui.Zoomable;
 import pipe.gui.Zoomer;
+import pipe.gui.graphicElements.AnnotationNote;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.Note;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.Place;
+import pipe.gui.graphicElements.PlaceTransitionObject;
+import pipe.gui.graphicElements.Transition;
+import pipe.gui.graphicElements.tapn.TimedInhibitorArcComponent;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedOutputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
 import pipe.gui.handler.AnimationHandler;
 import pipe.gui.handler.AnnotationNoteHandler;
 import pipe.gui.handler.ArcHandler;
@@ -248,7 +247,7 @@
 	private boolean doesPlacesUsedInQueryExist(TAPNQuery query, ArrayList<Tuple<String, String>> templatePlaceNames) {
 		VerifyPlaceNamesVisitor nameChecker = new VerifyPlaceNamesVisitor(templatePlaceNames);
 
-		VerifyPlaceNamesVisitor.Context c = nameChecker.VerifyPlaceNames(query.getProperty());
+		VerifyPlaceNamesVisitor.Context c = nameChecker.verifyPlaceNames(query.getProperty());
 		
 		return c.getResult();
 		
@@ -636,8 +635,8 @@
 
 				postsetArcs.remove((TimedTransitionComponent) targetIn);
 			} else {
-				presetArcs.put((TimedTransitionComponent) targetIn,	(TimedTransportArcComponent) tempArc);
-				transportArcsTimeIntervals.put((TimedTransportArcComponent) tempArc, TimeInterval.parse(inscriptionSplit[0], constants));
+				presetArcs.put((TimedTransitionComponent) targetIn,	tempArc);
+				transportArcsTimeIntervals.put(tempArc, TimeInterval.parse(inscriptionSplit[0], constants));
 			}
 		} else {
 			if (presetArcs.containsKey((TimedTransitionComponent) sourceIn)) {
@@ -645,7 +644,7 @@
 				TimedPlace sourcePlace = template.model().getPlaceByName(presetTransportArc.getSource().getName());
 				TimedTransition trans = template.model().getTransitionByName(sourceIn.getName());
 				TimedPlace destPlace = template.model().getPlaceByName(targetIn.getName());
-				TimeInterval interval = transportArcsTimeIntervals.get((TimedTransportArcComponent) presetTransportArc);
+				TimeInterval interval = transportArcsTimeIntervals.get(presetTransportArc);
 
 				assert (sourcePlace != null);
 				assert (trans != null);
@@ -662,9 +661,9 @@
 				template.model().add(transArc);
 
 				presetArcs.remove((TimedTransitionComponent) sourceIn);
-				transportArcsTimeIntervals.remove((TimedTransportArcComponent) presetTransportArc);
+				transportArcsTimeIntervals.remove(presetTransportArc);
 			} else {
-				postsetArcs.put((TimedTransitionComponent) sourceIn, (TimedTransportArcComponent) tempArc);
+				postsetArcs.put((TimedTransitionComponent) sourceIn, tempArc);
 			}
 		}
 		return tempArc;
@@ -1004,9 +1003,9 @@
 					((Note) newObject).getNote().addMouseListener(noteHandler);
 					((Note) newObject).getNote().addMouseMotionListener(noteHandler);
 				}
-				if (newObject instanceof Zoomable) {
-					newObject.zoomUpdate(drawingSurface.getZoom());
-				}
+				
+				newObject.zoomUpdate(drawingSurface.getZoom());
+				
 			}
 			newObject.setGuiModel(template.guiModel());
 		}

=== modified file 'src/dk/aau/cs/io/TimedArcPetriNetNetworkWriter.java'
--- src/dk/aau/cs/io/TimedArcPetriNetNetworkWriter.java	2011-08-30 09:20:01 +0000
+++ src/dk/aau/cs/io/TimedArcPetriNetNetworkWriter.java	2011-10-14 12:17:24 +0000
@@ -20,20 +20,20 @@
 import org.w3c.dom.Element;
 import org.w3c.dom.Text;
 
-import pipe.dataLayer.AnnotationNote;
-import pipe.dataLayer.Arc;
 import pipe.dataLayer.DataLayer;
 import pipe.dataLayer.PNMLWriter;
-import pipe.dataLayer.Place;
 import pipe.dataLayer.TAPNQuery;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.TimedInhibitorArcComponent;
-import pipe.dataLayer.TimedInputArcComponent;
-import pipe.dataLayer.TimedOutputArcComponent;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.dataLayer.TimedTransitionComponent;
-import pipe.dataLayer.Transition;
-import pipe.dataLayer.TimedTransportArcComponent;
+import pipe.gui.graphicElements.AnnotationNote;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.Place;
+import pipe.gui.graphicElements.Transition;
+import pipe.gui.graphicElements.tapn.TimedInhibitorArcComponent;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedOutputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
 import pipe.gui.widgets.InclusionPlaces.InclusionPlacesOption;
 import dk.aau.cs.model.tapn.Constant;
 import dk.aau.cs.model.tapn.SharedPlace;
@@ -265,7 +265,7 @@
 		boolean first = true;
 		StringBuilder s = new StringBuilder();
 		for(TimedPlace p : query.inclusionPlaces().inclusionPlaces()) {
-			if(!first) s.append(",");
+			if(!first) s.append(',');
 			
 			s.append(p.toString());
 			if(first) first = false;
@@ -326,9 +326,9 @@
 		transitionElement.setAttribute("nameOffsetY", (inputTransition.getNameOffsetYObject() != null ? String.valueOf(inputTransition.getNameOffsetYObject()) : ""));
 		transitionElement.setAttribute("name", inputTransition.underlyingTransition().name());
 		transitionElement.setAttribute("id", (inputTransition.getId() != null ? inputTransition.getId()	: "error"));
-		transitionElement.setAttribute("infiniteServer", String.valueOf(inputTransition.isInfiniteServer()));
+		transitionElement.setAttribute("infiniteServer", "false");
 		transitionElement.setAttribute("angle", String.valueOf(inputTransition.getAngle()));
-		transitionElement.setAttribute("priority", String.valueOf(inputTransition.getPriority()));
+		transitionElement.setAttribute("priority", "0");
 
 		return transitionElement;
 	}
@@ -350,7 +350,7 @@
 				arcElement.setAttribute("inscription", getGuardAsString((TimedInputArcComponent)inputArc));	
 			} else {
 				arcElement.setAttribute("type", "normal");
-				arcElement.setAttribute("inscription", Integer.toString((inputArc != null ? inputArc.getWeight() : 1)));
+				arcElement.setAttribute("inscription", "");
 			}
 		} 
 		return arcElement;

=== modified file 'src/dk/aau/cs/io/batchProcessing/BatchProcessingLegacyLoader.java'
--- src/dk/aau/cs/io/batchProcessing/BatchProcessingLegacyLoader.java	2011-10-02 13:59:04 +0000
+++ src/dk/aau/cs/io/batchProcessing/BatchProcessingLegacyLoader.java	2011-10-14 12:17:24 +0000
@@ -359,7 +359,7 @@
 	private boolean doesPlacesUsedInQueryExist(TAPNQuery query, ArrayList<Tuple<String, String>> templatePlaceNames) {
 		VerifyPlaceNamesVisitor nameChecker = new VerifyPlaceNamesVisitor(templatePlaceNames);
 
-		VerifyPlaceNamesVisitor.Context c = nameChecker.VerifyPlaceNames(query.getProperty());
+		VerifyPlaceNamesVisitor.Context c = nameChecker.verifyPlaceNames(query.getProperty());
 		
 		return c.getResult();
 	}
@@ -469,10 +469,7 @@
 	private boolean getSymmetryAsOldFormat(Element queryElement) {
 		String reductionString = queryElement.getAttribute("reductionOption");
 		
-		if(reductionString.contains(SYMMETRY))
-			return true;
-		else
-			return false;
+		return reductionString.contains(SYMMETRY);
 	}
 
 	private TCTLAbstractProperty parseQueryPropertyAsOldFormat(Element queryElement) throws FormatException {

=== modified file 'src/dk/aau/cs/io/batchProcessing/BatchProcessingLoader.java'
--- src/dk/aau/cs/io/batchProcessing/BatchProcessingLoader.java	2011-10-03 15:53:02 +0000
+++ src/dk/aau/cs/io/batchProcessing/BatchProcessingLoader.java	2011-10-14 12:17:24 +0000
@@ -183,7 +183,7 @@
 	private boolean doesPlacesUsedInQueryExist(TAPNQuery query, ArrayList<Tuple<String, String>> templatePlaceNames) {
 		VerifyPlaceNamesVisitor nameChecker = new VerifyPlaceNamesVisitor(templatePlaceNames);
 
-		VerifyPlaceNamesVisitor.Context c = nameChecker.VerifyPlaceNames(query.getProperty());
+		VerifyPlaceNamesVisitor.Context c = nameChecker.verifyPlaceNames(query.getProperty());
 		
 		return c.getResult();
 		

=== modified file 'src/dk/aau/cs/io/batchProcessing/BatchProcessingResultsExporter.java'
--- src/dk/aau/cs/io/batchProcessing/BatchProcessingResultsExporter.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/io/batchProcessing/BatchProcessingResultsExporter.java	2011-10-14 12:17:24 +0000
@@ -44,7 +44,7 @@
 			
 			s.append(result.modelFile());
 			s.append(DELIMITER);
-			s.append(query != null ? query.getName() : "");
+			s.append((query != null) ? query.getName() : "");
 			s.append(DELIMITER);
 			s.append(result.verificationResult());
 			s.append(DELIMITER);
@@ -56,15 +56,15 @@
 			s.append(DELIMITER);
 			s.append(result.hasStats() ? result.stats().storedStates() : "");
 			s.append(DELIMITER);
-			s.append(query != null ? query.getProperty().toString() : "");
-			s.append(DELIMITER);
-			s.append(query != null ? query.getCapacity() : "");
-			s.append(DELIMITER);
-			s.append(query != null ? getSearchOrder(query) : "");
-			s.append(DELIMITER);
-			s.append(query != null ? (query.useSymmetry() ? "Yes" : "No") : "");
-			s.append(DELIMITER);
-			s.append(query != null ? getVerificationMethod(query) : "");
+			s.append((query != null) ? query.getProperty().toString() : "");
+			s.append(DELIMITER);
+			s.append((query != null) ? query.getCapacity() : "");
+			s.append(DELIMITER);
+			s.append((query != null) ? getSearchOrder(query) : "");
+			s.append(DELIMITER);
+			s.append((query != null) ? (query.useSymmetry() ? "Yes" : "No") : "");
+			s.append(DELIMITER);
+			s.append((query != null) ? getVerificationMethod(query) : "");
 			
 			writer.println(s.toString());
 		}

=== modified file 'src/dk/aau/cs/model/NTA/StandardUPPAALQuery.java'
--- src/dk/aau/cs/model/NTA/StandardUPPAALQuery.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/model/NTA/StandardUPPAALQuery.java	2011-10-14 12:17:24 +0000
@@ -19,7 +19,7 @@
 		file.append(pathQuantifier);
 		file.append(nodeQuantifier);
 		file.append(query);
-		file.append("\n");
+		file.append('\n');
 	}
 
 	public void setPathQuantifier(String pathQuantifier) {

=== modified file 'src/dk/aau/cs/model/NTA/SupQuery.java'
--- src/dk/aau/cs/model/NTA/SupQuery.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/model/NTA/SupQuery.java	2011-10-14 12:17:24 +0000
@@ -27,11 +27,11 @@
 		boolean first = true;
 		for (String elem : elements) {
 			if (!first) {
-				file.append(",");
+				file.append(',');
 			}
 			file.append(elem);
 		}
-		file.append("\n");
+		file.append('\n');
 	}
 
 }

=== modified file 'src/dk/aau/cs/model/NTA/trace/SymbolicState.java'
--- src/dk/aau/cs/model/NTA/trace/SymbolicState.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/model/NTA/trace/SymbolicState.java	2011-10-14 12:17:24 +0000
@@ -18,7 +18,7 @@
 			HashMap<String, String> locations,
 			HashMap<String, HashMap<String, ValueRange>> localClocksAndVariables,
 			HashMap<String, ValueRange> globalClocksAndVariables) {
-		this.automataLocations = locations;
+		automataLocations = locations;
 		this.localClocksAndVariables = localClocksAndVariables;
 		this.globalClocksAndVariables = globalClocksAndVariables;
 	}
@@ -41,7 +41,7 @@
 		return automataLocations.get(automata);
 	}
 
-	public boolean IsConcreteState() {
+	public boolean isConcreteState() {
 		for (ValueRange range : globalClocksAndVariables.values()) {
 			if (!range.hasExactValue())
 				return false;

=== modified file 'src/dk/aau/cs/model/NTA/trace/TimeDelayFiringAction.java'
--- src/dk/aau/cs/model/NTA/trace/TimeDelayFiringAction.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/model/NTA/trace/TimeDelayFiringAction.java	2011-10-14 12:17:24 +0000
@@ -23,7 +23,7 @@
 
 	public TimeDelayFiringAction(SymbolicState state, BigDecimal delay) {
 		this.state = state;
-		this.timedelay = delay;
+		timedelay = delay;
 	}
 
 	public BigDecimal getDelay() {

=== modified file 'src/dk/aau/cs/model/NTA/trace/TransitionFiring.java'
--- src/dk/aau/cs/model/NTA/trace/TransitionFiring.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/model/NTA/trace/TransitionFiring.java	2011-10-14 12:17:24 +0000
@@ -24,7 +24,7 @@
 
 	public TransitionFiring(SymbolicState state, String channel,
 			Participant... participants) {
-		this.previousState = state;
+		previousState = state;
 		this.channel = channel;
 		this.participants = participants;
 	}

=== modified file 'src/dk/aau/cs/model/NTA/trace/UppaalTrace.java'
--- src/dk/aau/cs/model/NTA/trace/UppaalTrace.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/model/NTA/trace/UppaalTrace.java	2011-10-14 12:17:24 +0000
@@ -52,13 +52,13 @@
 		return length() == 0 && numberOfStates() == 0;
 	}
 
-	public List<SymbolicState> States() {
+	public List<SymbolicState> getStates() {
 		return states;
 	}
 
 	public boolean isConcreteTrace() {
 		for (SymbolicState state : states) {
-			if (!state.IsConcreteState()) {
+			if (!state.isConcreteState()) {
 				return false;
 			}
 		}

=== modified file 'src/dk/aau/cs/model/tapn/Bound.java'
--- src/dk/aau/cs/model/tapn/Bound.java	2011-02-23 19:01:49 +0000
+++ src/dk/aau/cs/model/tapn/Bound.java	2011-10-14 12:17:24 +0000
@@ -7,9 +7,9 @@
 	boolean equals(Object other);
 	int hashCode();
 	
-	public static Bound Infinity = new InfBound();
+	Bound Infinity = new InfBound();
 
-	public class InfBound implements Bound {
+	class InfBound implements Bound {
 		public int value() {
 			return -1;
 		}

=== modified file 'src/dk/aau/cs/model/tapn/Constant.java'
--- src/dk/aau/cs/model/tapn/Constant.java	2011-03-19 15:32:14 +0000
+++ src/dk/aau/cs/model/tapn/Constant.java	2011-10-14 12:17:24 +0000
@@ -23,17 +23,17 @@
 	public Constant(Constant constant) {
 		Require.that(constant != null, "Constant cannot be null");
 
-		this.name = constant.name;
-		this.value = constant.value;
-		this.lowerBound = constant.lowerBound;
-		this.upperBound = constant.upperBound;
-		this.isUsed = constant.isUsed;
+		name = constant.name;
+		value = constant.value;
+		lowerBound = constant.lowerBound;
+		upperBound = constant.upperBound;
+		isUsed = constant.isUsed;
 	}
 
 	public void setName(String newName) {
 		Require.that(newName != null && !newName.isEmpty(), "A constant must have a name");
 		Require.that(isValid(newName), "name must match regular expression [a-zA-Z_][a-zA-Z0-9_]*");
-		this.name = newName;
+		name = newName;
 	}
 
 	private boolean isValid(String newName) {

=== modified file 'src/dk/aau/cs/model/tapn/ConstantBound.java'
--- src/dk/aau/cs/model/tapn/ConstantBound.java	2011-03-12 13:43:46 +0000
+++ src/dk/aau/cs/model/tapn/ConstantBound.java	2011-10-14 12:17:24 +0000
@@ -30,7 +30,7 @@
 	public void setConstant(Constant newConstant) {
 		Require.that(newConstant != null, "Constant cannot be null");
 
-		this.constant = newConstant;
+		constant = newConstant;
 	}
 
 	public String toString() {

=== modified file 'src/dk/aau/cs/model/tapn/LocalTimedMarking.java'
--- src/dk/aau/cs/model/tapn/LocalTimedMarking.java	2011-03-27 10:57:57 +0000
+++ src/dk/aau/cs/model/tapn/LocalTimedMarking.java	2011-10-14 12:17:24 +0000
@@ -19,7 +19,7 @@
 	}
 
 	public void setNetworkMarking(NetworkMarking marking){
-		this.parent = marking;
+		parent = marking;
 	}
 
 	public void add(TimedToken token) {

=== modified file 'src/dk/aau/cs/model/tapn/LocalTimedPlace.java'
--- src/dk/aau/cs/model/tapn/LocalTimedPlace.java	2011-10-02 13:30:45 +0000
+++ src/dk/aau/cs/model/tapn/LocalTimedPlace.java	2011-10-14 12:17:24 +0000
@@ -51,7 +51,7 @@
 
 	public void setCurrentMarking(TimedMarking marking) {
 		Require.that(marking != null, "marking cannot be null");
-		this.currentMarking = marking;
+		currentMarking = marking;
 		fireMarkingChanged();
 	}
 
@@ -137,9 +137,9 @@
 	}
 
 	public LocalTimedPlace copy() {
-		LocalTimedPlace p = new LocalTimedPlace(this.name);
+		LocalTimedPlace p = new LocalTimedPlace(name);
 
-		p.invariant = this.invariant.copy();
+		p.invariant = invariant.copy();
 
 		return p;
 	}

=== modified file 'src/dk/aau/cs/model/tapn/SharedPlace.java'
--- src/dk/aau/cs/model/tapn/SharedPlace.java	2011-10-04 15:24:12 +0000
+++ src/dk/aau/cs/model/tapn/SharedPlace.java	2011-10-14 12:17:24 +0000
@@ -35,7 +35,7 @@
 	public void setName(String newName) {
 		Require.that(newName != null && !newName.isEmpty(), "A timed transition must have a name");
 		Require.that(isValid(newName) && !newName.toLowerCase().equals("true") && !newName.toLowerCase().equals("false"), "The specified name must conform to the pattern [a-zA-Z_][a-zA-Z0-9_]*");
-		this.name = newName;
+		name = newName;
 		fireNameChanged();
 	}
 	

=== modified file 'src/dk/aau/cs/model/tapn/SharedTransition.java'
--- src/dk/aau/cs/model/tapn/SharedTransition.java	2011-10-08 16:55:12 +0000
+++ src/dk/aau/cs/model/tapn/SharedTransition.java	2011-10-14 12:17:24 +0000
@@ -30,7 +30,7 @@
 	public void setName(String newName) {
 		Require.that(newName != null && !newName.isEmpty(), "A timed transition must have a name");
 		Require.that(isValid(newName), "The specified name must conform to the pattern [a-zA-Z_][a-zA-Z0-9_]*");
-		this.name = newName;
+		name = newName;
 		for(TimedTransition transition : transitions){
 			transition.setName(newName);
 		}

=== modified file 'src/dk/aau/cs/model/tapn/TAPNQuery.java'
--- src/dk/aau/cs/model/tapn/TAPNQuery.java	2011-05-21 13:00:05 +0000
+++ src/dk/aau/cs/model/tapn/TAPNQuery.java	2011-10-14 12:17:24 +0000
@@ -15,7 +15,7 @@
 	}
 
 	public TAPNQuery(TCTLAbstractProperty inputProperty, int extraTokens) {
-		this.property = inputProperty;
+		property = inputProperty;
 		this.extraTokens = extraTokens;
 	}
 

=== modified file 'src/dk/aau/cs/model/tapn/TimeInterval.java'
--- src/dk/aau/cs/model/tapn/TimeInterval.java	2011-05-20 18:26:51 +0000
+++ src/dk/aau/cs/model/tapn/TimeInterval.java	2011-10-14 12:17:24 +0000
@@ -31,10 +31,10 @@
 	public TimeInterval(TimeInterval interval) {
 		Require.that(interval != null, "Interval cannot be null");
 
-		this.isLowerIncluded = interval.isLowerIncluded;
-		this.isUpperIncluded = interval.isUpperIncluded;
-		this.lower = interval.lower.copy();
-		this.upper = interval.upper.copy();
+		isLowerIncluded = interval.isLowerIncluded;
+		isUpperIncluded = interval.isUpperIncluded;
+		lower = interval.lower.copy();
+		upper = interval.upper.copy();
 	}
 
 	private boolean isValidInterval() {
@@ -55,7 +55,7 @@
 		StringBuffer buffer = new StringBuffer();
 		buffer.append(isLowerIncluded ? "[" : "(");
 		buffer.append(lower);
-		buffer.append(",");
+		buffer.append(',');
 		buffer.append(upper);
 		buffer.append(isUpperIncluded ? "]" : ")");
 		return buffer.toString();
@@ -65,7 +65,7 @@
 		StringBuffer buffer = new StringBuffer();
 		buffer.append(isLowerIncluded ? "[" : "(");
 		buffer.append(displayConstantNames ? lower : lower.value());
-		buffer.append(",");
+		buffer.append(',');
 		buffer.append(displayConstantNames || upper instanceof InfBound ? upper : upper.value());
 		buffer.append(isUpperIncluded ? "]" : ")");
 		return buffer.toString();
@@ -160,12 +160,12 @@
 	
 		int invariantUpper = invariant.upperBound().value();
 		
-		if (invariantUpper < this.lower.value() || (invariantUpper == this.lower.value() && !isLowerIncluded) || (invariantUpper == this.lower.value() && !invariant.isUpperNonstrict())) {
+		if (invariantUpper < lower.value() || (invariantUpper == lower.value() && !isLowerIncluded) || (invariantUpper == lower.value() && !invariant.isUpperNonstrict())) {
 			return new TimeInterval(false, new IntBound(0), new IntBound(0), false); // intersection is empty, so return an empty interval
-		} else if (invariantUpper > this.upper.value()) {
+		} else if (invariantUpper > upper.value()) {
 			return this.copy();
 		} else {
-			return new TimeInterval(this.isLowerIncluded, this.lower.copy(), invariant.upperBound().copy(), invariant.isUpperNonstrict());
+			return new TimeInterval(isLowerIncluded, lower.copy(), invariant.upperBound().copy(), invariant.isUpperNonstrict());
 		}
 	}
 	

=== modified file 'src/dk/aau/cs/model/tapn/TimeInvariant.java'
--- src/dk/aau/cs/model/tapn/TimeInvariant.java	2011-05-20 18:26:51 +0000
+++ src/dk/aau/cs/model/tapn/TimeInvariant.java	2011-10-14 12:17:24 +0000
@@ -70,14 +70,14 @@
 	}
 	
 	public TimeInvariant copy() {
-		return new TimeInvariant(this.isUpperIncluded, upper.copy());
+		return new TimeInvariant(isUpperIncluded, upper.copy());
 	}
 
 	@Override
 	public String toString() {
 		StringBuffer buffer = new StringBuffer();
 		buffer.append(isUpperIncluded ? "<=" : "<");
-		buffer.append(" ");
+		buffer.append(' ');
 		buffer.append(upper);
 		return buffer.toString();
 	};
@@ -85,8 +85,8 @@
 	public String toString(boolean displayConstantNames) {
 		StringBuffer buffer = new StringBuffer();
 		buffer.append(isUpperIncluded ? "<=" : "<");
-		buffer.append(" ");
-		buffer.append(displayConstantNames || upper instanceof InfBound ? upper	: upper.value());
+		buffer.append(' ');
+		buffer.append((displayConstantNames || upper instanceof InfBound) ? upper	: upper.value());
 		return buffer.toString();
 	}
 

=== modified file 'src/dk/aau/cs/model/tapn/TimedArcPetriNet.java'
--- src/dk/aau/cs/model/tapn/TimedArcPetriNet.java	2011-08-23 13:14:47 +0000
+++ src/dk/aau/cs/model/tapn/TimedArcPetriNet.java	2011-10-14 12:17:24 +0000
@@ -30,7 +30,7 @@
 	}
 
 	public void setParentNetwork(TimedArcPetriNetNetwork network){
-		this.parentNetwork = network;
+		parentNetwork = network;
 	}
 
 	public TimedArcPetriNetNetwork parentNetwork(){
@@ -232,7 +232,7 @@
 
 	public void setMarking(TimedMarking marking) {
 		Require.that(marking != null, "marking must not be null");
-		this.currentMarking = marking;
+		currentMarking = marking;
 
 		for (TimedPlace p : places) {
 			p.setCurrentMarking(marking);
@@ -264,9 +264,9 @@
 	}
 
 	public TimedArcPetriNet copy() {
-		TimedArcPetriNet tapn = new TimedArcPetriNet(this.name);
+		TimedArcPetriNet tapn = new TimedArcPetriNet(name);
 
-		for(TimedPlace p : this.places) {
+		for(TimedPlace p : places) {
 			TimedPlace copy = p.copy();
 			tapn.add(copy);
 			if(!p.isShared()){
@@ -276,7 +276,7 @@
 			}
 		}
 
-		for(TimedTransition t : this.transitions){
+		for(TimedTransition t : transitions){
 			TimedTransition copy = t.copy();
 			tapn.add(copy);
 			if(t.isShared()){
@@ -284,16 +284,16 @@
 			}
 		}
 
-		for(TimedInputArc inputArc : this.inputArcs)
+		for(TimedInputArc inputArc : inputArcs)
 			tapn.add(inputArc.copy(tapn));
 
-		for(TimedOutputArc outputArc : this.outputArcs)
+		for(TimedOutputArc outputArc : outputArcs)
 			tapn.add(outputArc.copy(tapn));
 
-		for(TransportArc transArc : this.transportArcs)
+		for(TransportArc transArc : transportArcs)
 			tapn.add(transArc.copy(tapn));
 
-		for(TimedInhibitorArc inhibArc : this.inhibitorArcs)
+		for(TimedInhibitorArc inhibArc : inhibitorArcs)
 			tapn.add(inhibArc.copy(tapn));
 
 		return tapn;

=== modified file 'src/dk/aau/cs/model/tapn/TimedArcPetriNetNetwork.java'
--- src/dk/aau/cs/model/tapn/TimedArcPetriNetNetwork.java	2011-08-23 13:14:47 +0000
+++ src/dk/aau/cs/model/tapn/TimedArcPetriNetNetwork.java	2011-10-14 12:17:24 +0000
@@ -27,7 +27,7 @@
 	
 	public TimedArcPetriNetNetwork(ConstantStore constants){
 		this.constants = constants;
-		this.currentMarking = new NetworkMarking();
+		currentMarking = new NetworkMarking();
 		buildConstraints();
 	}
 	
@@ -166,7 +166,7 @@
 
 	private void fireConstantAdded(Constant constant) {
 		for(ConstantsListener listener : constantsListeners){
-			listener.ConstantAdded(new ConstantEvent(constant, constants.getIndexOf(constant)));
+			listener.constantAdded(new ConstantEvent(constant, constants.getIndexOf(constant)));
 		}
 	}
 
@@ -176,7 +176,7 @@
 		int index = constants.getIndexOf(constant);
 		Command cmd = constants.removeConstant(name);
 		for(ConstantsListener listener : constantsListeners){
-			listener.ConstantRemoved(new ConstantEvent(constant, index));
+			listener.constantRemoved(new ConstantEvent(constant, index));
 		}
 		return cmd;
 	}
@@ -189,7 +189,7 @@
 		if (edit != null) {
 			updateGuardsWithNewConstant(oldName, constant);
 			for(ConstantsListener listener : constantsListeners){
-				listener.ConstantChanged(new ConstantChangedEvent(old, constant, index));
+				listener.constantChanged(new ConstantChangedEvent(old, constant, index));
 			}
 		}
 

=== modified file 'src/dk/aau/cs/model/tapn/TimedInputArc.java'
--- src/dk/aau/cs/model/tapn/TimedInputArc.java	2011-03-19 15:09:41 +0000
+++ src/dk/aau/cs/model/tapn/TimedInputArc.java	2011-10-14 12:17:24 +0000
@@ -69,7 +69,7 @@
 	// This method should ONLY be called in relation to sharing/unsharing a place
 	public void setSource(TimedPlace place) {
 		Require.that(place != null, "place cannot be null");
-		this.source = place;		
+		source = place;		
 	}
 	
 	@Override

=== modified file 'src/dk/aau/cs/model/tapn/TimedMarking.java'
--- src/dk/aau/cs/model/tapn/TimedMarking.java	2011-03-07 18:53:27 +0000
+++ src/dk/aau/cs/model/tapn/TimedMarking.java	2011-10-14 12:17:24 +0000
@@ -6,24 +6,24 @@
 import dk.aau.cs.model.tapn.simulation.FiringMode;
 
 public interface TimedMarking {
-	public abstract void add(TimedToken token);
-	public abstract void remove(TimedToken token);
+	void add(TimedToken token);
+	void remove(TimedToken token);
 
 //	public abstract void removePlaceFromMarking(TimedPlace place);
 //	public abstract void removePlaceFromMarking(SharedPlace place);
-	public abstract void removePlaceFromMarking(TimedPlace place);
+	void removePlaceFromMarking(TimedPlace place);
 	
-	public abstract List<TimedToken> getTokensFor(TimedPlace place);
+	List<TimedToken> getTokensFor(TimedPlace place);
 //	public abstract List<TimedToken> getTokensFor(TimedPlace place);
 //	public abstract List<TimedToken> getTokensFor(SharedPlace place);
 	
-	public abstract TimedMarking clone();
-
-	public abstract boolean isDelayPossible(BigDecimal delay);
-	public abstract TimedMarking delay(BigDecimal amount);
-
-	public abstract TimedMarking fireTransition(TimedTransition transition, List<TimedToken> tokensToConsume);
-	public abstract TimedMarking fireTransition(TimedTransition transition, FiringMode firingMode);
-
-	public abstract int size();
+	TimedMarking clone();
+
+	boolean isDelayPossible(BigDecimal delay);
+	TimedMarking delay(BigDecimal amount);
+
+	TimedMarking fireTransition(TimedTransition transition, List<TimedToken> tokensToConsume);
+	TimedMarking fireTransition(TimedTransition transition, FiringMode firingMode);
+
+	int size();
 }
\ No newline at end of file

=== modified file 'src/dk/aau/cs/model/tapn/TimedOutputArc.java'
--- src/dk/aau/cs/model/tapn/TimedOutputArc.java	2011-03-19 15:09:41 +0000
+++ src/dk/aau/cs/model/tapn/TimedOutputArc.java	2011-10-14 12:17:24 +0000
@@ -33,7 +33,7 @@
 
 	public void setDestination(TimedPlace place) {
 		Require.that(place != null, "place cannot be null");
-		this.destination = place;		
+		destination = place;		
 	}
 	
 	@Override

=== modified file 'src/dk/aau/cs/model/tapn/TimedPlace.java'
--- src/dk/aau/cs/model/tapn/TimedPlace.java	2011-03-07 18:53:27 +0000
+++ src/dk/aau/cs/model/tapn/TimedPlace.java	2011-10-14 12:17:24 +0000
@@ -5,21 +5,21 @@
 import dk.aau.cs.model.tapn.event.TimedPlaceListener;
 
 public interface TimedPlace {
-	public abstract void addTimedPlaceListener(TimedPlaceListener listener);
-	public abstract void removeTimedPlaceListener(TimedPlaceListener listener);
-
-	public abstract boolean isShared();
-
-	public abstract String name();
-	public abstract void setName(String newName);
-
-	public abstract TimeInvariant invariant();
-	public abstract void setInvariant(TimeInvariant invariant);
-
-	public abstract List<TimedToken> tokens();
-	public abstract int numberOfTokens();
-
-	public abstract void setCurrentMarking(TimedMarking marking);
+	void addTimedPlaceListener(TimedPlaceListener listener);
+	void removeTimedPlaceListener(TimedPlaceListener listener);
+
+	boolean isShared();
+
+	String name();
+	void setName(String newName);
+
+	TimeInvariant invariant();
+	void setInvariant(TimeInvariant invariant);
+
+	List<TimedToken> tokens();
+	int numberOfTokens();
+
+	void setCurrentMarking(TimedMarking marking);
 	
 	public abstract void addToken(TimedToken timedToken);
 	public abstract void addTokens(Iterable<TimedToken> tokens);

=== modified file 'src/dk/aau/cs/model/tapn/TimedToken.java'
--- src/dk/aau/cs/model/tapn/TimedToken.java	2011-05-08 15:02:45 +0000
+++ src/dk/aau/cs/model/tapn/TimedToken.java	2011-10-14 12:17:24 +0000
@@ -44,7 +44,7 @@
 		buffer.append(place.toString());
 		buffer.append(", ");
 		buffer.append(df.format(age));
-		buffer.append(")");
+		buffer.append(')');
 		return buffer.toString();
 	}
 

=== modified file 'src/dk/aau/cs/model/tapn/TimedTransition.java'
--- src/dk/aau/cs/model/tapn/TimedTransition.java	2011-10-08 16:55:12 +0000
+++ src/dk/aau/cs/model/tapn/TimedTransition.java	2011-10-14 12:17:24 +0000
@@ -70,7 +70,7 @@
 	public void setName(String newName) {
 		Require.that(newName != null && !newName.isEmpty(), "A timed transition must have a name");
 		Require.that(isValid(newName), "The specified name must conform to the pattern [a-zA-Z_][a-zA-Z0-9_]*");
-		this.name = newName;
+		name = newName;
 		fireNameChanged();
 	}
 
@@ -250,7 +250,7 @@
 	}
 
 	public TimedTransition copy() {
-		return new TimedTransition(this.name);
+		return new TimedTransition(name);
 	}
 
 	@Override

=== modified file 'src/dk/aau/cs/model/tapn/TransportArc.java'
--- src/dk/aau/cs/model/tapn/TransportArc.java	2011-03-19 15:09:41 +0000
+++ src/dk/aau/cs/model/tapn/TransportArc.java	2011-10-14 12:17:24 +0000
@@ -83,13 +83,13 @@
 	// Should ONLY be called in relation to sharing/unsharing places
 	public void setSource(TimedPlace place) {
 		Require.that(place != null, "place cannot be null");
-		this.source = place;		
+		source = place;		
 	}
 	
 	// Should ONLY be called in relation to sharing/unsharing places
 	public void setDestination(TimedPlace place) {
 		Require.that(place != null, "place cannot be null");
-		this.destination = place;		
+		destination = place;		
 	}
 	
 	@Override

=== modified file 'src/dk/aau/cs/model/tapn/event/ConstantsListener.java'
--- src/dk/aau/cs/model/tapn/event/ConstantsListener.java	2011-07-12 18:10:29 +0000
+++ src/dk/aau/cs/model/tapn/event/ConstantsListener.java	2011-10-14 12:17:24 +0000
@@ -1,7 +1,7 @@
 package dk.aau.cs.model.tapn.event;
 
 public interface ConstantsListener {
-	void ConstantChanged(ConstantChangedEvent e);
-	void ConstantAdded(ConstantEvent e);
-	void ConstantRemoved(ConstantEvent e);
+	void constantChanged(ConstantChangedEvent e);
+	void constantAdded(ConstantEvent e);
+	void constantRemoved(ConstantEvent e);
 }

=== modified file 'src/dk/aau/cs/translations/Pairing.java'
--- src/dk/aau/cs/translations/Pairing.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/translations/Pairing.java	2011-10-14 12:17:24 +0000
@@ -15,7 +15,7 @@
 	protected Hashtable<TimedInputArc,TimedOutputArc> inputArcToOutputArc = new Hashtable<TimedInputArc, TimedOutputArc>();
 	
 	public Pairing(TimedTransition t) {
-		this.transition = t;
+		transition = t;
 		generatePairing();
 	}
 

=== modified file 'src/dk/aau/cs/translations/TranslationNamingScheme.java'
--- src/dk/aau/cs/translations/TranslationNamingScheme.java	2011-02-03 19:03:15 +0000
+++ src/dk/aau/cs/translations/TranslationNamingScheme.java	2011-10-14 12:17:24 +0000
@@ -12,7 +12,7 @@
 
 	boolean isIgnoredAutomata(String automata);
 
-	public class TransitionTranslation {
+	class TransitionTranslation {
 		private int startsAt;
 		private String originalTransitionName;
 		private int endsAt;

=== modified file 'src/dk/aau/cs/translations/tapn/BroadcastTranslation.java'
--- src/dk/aau/cs/translations/tapn/BroadcastTranslation.java	2011-06-09 17:56:03 +0000
+++ src/dk/aau/cs/translations/tapn/BroadcastTranslation.java	2011-10-14 12:17:24 +0000
@@ -154,7 +154,7 @@
 				builder.append(TOKEN_TEMPLATE_NAME);
 				builder.append(i);
 			}
-			builder.append(";");
+			builder.append(';');
 
 			return builder.toString();
 		}
@@ -185,7 +185,7 @@
 			} else if (isTransitionDegree1(t) && !t.hasInhibitorArcs()) {
 				builder.append("broadcast chan ");
 				builder.append(t.name());
-				builder.append(";");
+				builder.append(';');
 			} else if (isTransitionDegree2(t) && !t.hasInhibitorArcs()) {
 				builder.append("chan ");
 				builder.append(t.name());
@@ -193,7 +193,7 @@
 			} else {
 				builder.append("broadcast chan ");
 				builder.append(String.format(TEST_CHANNEL_NAME, t.name(), ""));
-				builder.append(",");
+				builder.append(',');
 				builder.append(String.format(FIRE_CHANNEL_NAME, t.name(), ""));
 				builder.append(";\n");
 			}
@@ -364,7 +364,7 @@
 			String counter = inhibitorArcsToCounters.get(inhib);
 			builder.append(counter);
 			builder.append(inhibComparison);
-			builder.append("0");
+			builder.append('0');
 		}
 
 		return builder.toString();

=== modified file 'src/dk/aau/cs/translations/tapn/Degree2BroadcastKBoundOptimizeTranslation.java'
--- src/dk/aau/cs/translations/tapn/Degree2BroadcastKBoundOptimizeTranslation.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/translations/tapn/Degree2BroadcastKBoundOptimizeTranslation.java	2011-10-14 12:17:24 +0000
@@ -15,8 +15,8 @@
 public class Degree2BroadcastKBoundOptimizeTranslation extends Degree2BroadcastTranslation {
 	private final String usedExtraTokens = "usedExtraTokens";
 	private int tokens = 0;
-	private final int SUBTRACT = 0;
-	private final int ADD = 1;
+	private final int subtract = 0;
+	private final int add = 1;
 
 	public Degree2BroadcastKBoundOptimizeTranslation() {
 		super(true);
@@ -42,10 +42,10 @@
 		for (Edge e : ta.getTransitions()) {
 			if (e.getSource() == pcapacity && isNotInitializationEdge(e) && isNotTestingEdge(e)) {
 
-				String newUpdate = createUpdate(e.getUpdate(), ADD);
+				String newUpdate = createUpdate(e.getUpdate(), add);
 				e.setUpdate(newUpdate);
 			} else if (e.getDestination() == pcapacity && isNotTestingEdge(e)) {
-				String newUpdate = createUpdate(e.getUpdate(), SUBTRACT);
+				String newUpdate = createUpdate(e.getUpdate(), subtract);
 				e.setUpdate(newUpdate);
 			}
 		}
@@ -69,7 +69,7 @@
 			newUpdate += ",";
 		}
 		newUpdate += usedExtraTokens;
-		if (method == ADD) {
+		if (method == add) {
 			newUpdate += "++";
 		} else {
 			newUpdate += "--";
@@ -82,7 +82,7 @@
 	protected String createGlobalDeclarations(TimedArcPetriNet degree2Net,TimedArcPetriNet originalModel) {
 		StringBuilder builder = new StringBuilder("int[");
 		builder.append(-(tokens + extraTokens));
-		builder.append(",");
+		builder.append(',');
 		builder.append(tokens + extraTokens);
 		builder.append("] ");
 		builder.append(usedExtraTokens);

=== modified file 'src/dk/aau/cs/translations/tapn/Degree2BroadcastTranslation.java'
--- src/dk/aau/cs/translations/tapn/Degree2BroadcastTranslation.java	2011-06-09 17:56:03 +0000
+++ src/dk/aau/cs/translations/tapn/Degree2BroadcastTranslation.java	2011-10-14 12:17:24 +0000
@@ -162,7 +162,7 @@
 				builder.append(TOKEN_TEMPLATE_NAME);
 				builder.append(i);
 			}
-			builder.append(";");
+			builder.append(';');
 
 			return builder.toString();
 		}

=== modified file 'src/dk/aau/cs/translations/tapn/OptimizedStandardTranslation.java'
--- src/dk/aau/cs/translations/tapn/OptimizedStandardTranslation.java	2011-05-22 12:57:23 +0000
+++ src/dk/aau/cs/translations/tapn/OptimizedStandardTranslation.java	2011-10-14 12:17:24 +0000
@@ -149,7 +149,7 @@
 				builder.append(TOKEN_TEMPLATE_NAME);
 				builder.append(i);
 			}
-			builder.append(";");
+			builder.append(';');
 
 			return builder.toString();
 		}
@@ -478,10 +478,7 @@
 
 	
 	public boolean supportsModel(TimedArcPetriNet model) {
-		if(model.hasInhibitorArcs())
-			return false;
-		else
-			return true;
+		return !(model.hasInhibitorArcs());
 	}
 
 	

=== modified file 'src/dk/aau/cs/translations/tapn/StandardTranslation.java'
--- src/dk/aau/cs/translations/tapn/StandardTranslation.java	2011-06-09 17:24:10 +0000
+++ src/dk/aau/cs/translations/tapn/StandardTranslation.java	2011-10-14 12:17:24 +0000
@@ -147,7 +147,7 @@
 				builder.append(TOKEN_TEMPLATE_NAME);
 				builder.append(i);
 			}
-			builder.append(";");
+			builder.append(';');
 
 			return builder.toString();
 		}
@@ -433,17 +433,11 @@
 
 
 	public boolean supportsModel(TimedArcPetriNet model) {
-		if(model.hasInhibitorArcs())
-			return false;
-		else
-			return true;
+		return !(model.hasInhibitorArcs());
 	}
 
 
 	public boolean supportsQuery(TimedArcPetriNet model, TAPNQuery query) {
-		if(query.getProperty() instanceof TCTLEGNode || query.getProperty() instanceof TCTLAFNode)
-			return false;
-		else
-			return true;
+		return !(query.getProperty() instanceof TCTLEGNode || query.getProperty() instanceof TCTLAFNode);
 	}
 }

=== modified file 'src/dk/aau/cs/verification/TAPNComposer.java'
--- src/dk/aau/cs/verification/TAPNComposer.java	2011-10-08 17:17:27 +0000
+++ src/dk/aau/cs/verification/TAPNComposer.java	2011-10-14 12:17:24 +0000
@@ -58,23 +58,23 @@
 		System.out.println("Composed Model:");
 		System.out.println("PLACES:");
 		for(TimedPlace place : tapn.places()){
-			System.out.print("\t");
+			System.out.print('\t');
 			System.out.print(place.name());
 			System.out.print(", invariant: ");
 			System.out.print(place.invariant().toString());
 			System.out.print(" (Original: ");
 			System.out.print(mapping.map(place.name()));
-			System.out.println(")");
+			System.out.println(')');
 		}
 
 		System.out.println();
 		System.out.println("TRANSITIONS:");
 		for(TimedTransition transition : tapn.transitions()){
-			System.out.print("\t");
+			System.out.print('\t');
 			System.out.print(transition.name());
 			System.out.print(" (Original: ");
 			System.out.print(mapping.map(transition.name()).toString());
-			System.out.println(")");
+			System.out.println(')');
 		}
 
 		System.out.println();

=== modified file 'src/dk/aau/cs/verification/UPPAAL/Verifyta.java'
--- src/dk/aau/cs/verification/UPPAAL/Verifyta.java	2011-06-29 10:48:23 +0000
+++ src/dk/aau/cs/verification/UPPAAL/Verifyta.java	2011-10-14 12:17:24 +0000
@@ -184,9 +184,9 @@
 
 	private String createArgumentString(String modelFile, String queryFile, VerificationOptions options) {
 		StringBuffer buffer = new StringBuffer(options.toString());
-		buffer.append(" ");
+		buffer.append(' ');
 		buffer.append(modelFile);
-		buffer.append(" ");
+		buffer.append(' ');
 		buffer.append(queryFile);
 
 		return buffer.toString();

=== modified file 'src/dk/aau/cs/verification/UPPAAL/VerifytaOptions.java'
--- src/dk/aau/cs/verification/UPPAAL/VerifytaOptions.java	2011-06-18 14:41:17 +0000
+++ src/dk/aau/cs/verification/UPPAAL/VerifytaOptions.java	2011-10-14 12:17:24 +0000
@@ -20,8 +20,8 @@
 
 	public VerifytaOptions(TraceOption trace, SearchOption search,
 			boolean untimedTrace, ReductionOption reduction, boolean symmetry) {
-		this.traceOption = trace;
-		this.searchOption = search;
+		traceOption = trace;
+		searchOption = search;
 		this.untimedTrace = untimedTrace;
 		this.reduction = reduction;
 		this.symmetry = symmetry;

=== modified file 'src/dk/aau/cs/verification/UPPAAL/VerifytaTraceInterpreter.java'
--- src/dk/aau/cs/verification/UPPAAL/VerifytaTraceInterpreter.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/verification/UPPAAL/VerifytaTraceInterpreter.java	2011-10-14 12:17:24 +0000
@@ -26,7 +26,7 @@
 	private final TranslationNamingScheme namingScheme;
 
 	public VerifytaTraceInterpreter(TimedArcPetriNet model, TranslationNamingScheme namingScheme) {
-		this.tapn = model;
+		tapn = model;
 		this.namingScheme = namingScheme;
 	}
 

=== modified file 'src/dk/aau/cs/verification/UPPAAL/VerifytaTraceParser.java'
--- src/dk/aau/cs/verification/UPPAAL/VerifytaTraceParser.java	2011-04-02 17:43:38 +0000
+++ src/dk/aau/cs/verification/UPPAAL/VerifytaTraceParser.java	2011-10-14 12:17:24 +0000
@@ -20,7 +20,7 @@
 				StringBuffer buffer = new StringBuffer();
 				while ((line = reader.readLine()) != null && !line.isEmpty()) {
 					buffer.append(line);
-					buffer.append("\n");
+					buffer.append('\n');
 				}
 
 				String element = buffer.toString();

=== modified file 'src/dk/aau/cs/verification/VerificationResult.java'
--- src/dk/aau/cs/verification/VerificationResult.java	2011-06-11 14:41:11 +0000
+++ src/dk/aau/cs/verification/VerificationResult.java	2011-10-14 12:17:24 +0000
@@ -23,7 +23,7 @@
 	}
 
 	public VerificationResult(String outputMessage, long verificationTime) {
-		this.errorMessage = outputMessage;
+		errorMessage = outputMessage;
 		this.verificationTime = verificationTime;
 	}
 

=== modified file 'src/dk/aau/cs/verification/VerifyTAPN/VerifyTAPN.java'
--- src/dk/aau/cs/verification/VerifyTAPN/VerifyTAPN.java	2011-10-09 11:38:38 +0000
+++ src/dk/aau/cs/verification/VerifyTAPN/VerifyTAPN.java	2011-10-14 12:17:24 +0000
@@ -268,9 +268,9 @@
 
 	private String createArgumentString(String modelFile, String queryFile, VerificationOptions options) {
 		StringBuffer buffer = new StringBuffer(options.toString());
-		buffer.append(" ");
+		buffer.append(' ');
 		buffer.append(modelFile);
-		buffer.append(" ");
+		buffer.append(' ');
 		buffer.append(queryFile);
 
 		return buffer.toString();

=== modified file 'src/dk/aau/cs/verification/VerifyTAPN/VerifyTAPNOptions.java'
--- src/dk/aau/cs/verification/VerifyTAPN/VerifyTAPNOptions.java	2011-06-18 14:51:13 +0000
+++ src/dk/aau/cs/verification/VerifyTAPN/VerifyTAPNOptions.java	2011-10-14 12:17:24 +0000
@@ -34,7 +34,7 @@
 	public VerifyTAPNOptions(int extraTokens, TraceOption traceOption, SearchOption search, boolean symmetry, boolean discreteInclusion, InclusionPlaces inclusionPlaces) {
 		this.extraTokens = extraTokens;
 		this.traceOption = traceOption;
-		this.searchOption = search;
+		searchOption = search;
 		this.symmetry = symmetry;
 		this.discreteInclusion = discreteInclusion;
 		this.inclusionPlaces = inclusionPlaces;
@@ -53,7 +53,7 @@
 	}
 	
 	public void setTokensInModel(int tokens){ // TODO: Get rid of this method when verifytapn refactored
-		this.tokensInModel = tokens;
+		tokensInModel = tokens;
 	}
 
 	@Override
@@ -62,13 +62,13 @@
 
 		result.append("-k ");
 		result.append(extraTokens+tokensInModel);
-		result.append(" ");
+		result.append(' ');
 		result.append(traceMap.get(traceOption));
-		result.append(" ");
+		result.append(' ');
 		result.append(searchMap.get(searchOption));
-		result.append(" ");
+		result.append(' ');
 		result.append(symmetry ? "" : "-s"); // symmetry is on by default in verifyTAPN so "-s" disables it
-		result.append(" ");
+		result.append(' ');
 		result.append(discreteInclusion ? " -f 1" : "");
 		result.append(discreteInclusion ? " -i " + generateDiscretePlacesList() : "");
 		return result.toString();
@@ -81,7 +81,7 @@
 		StringBuilder s = new StringBuilder();
 		boolean first = true;
 		for(TimedPlace p : inclusionPlaces.inclusionPlaces()) {
-			if(!first) s.append(",");
+			if(!first) s.append(',');
 			
 			s.append(p.name());
 			if(first) first = false;

=== modified file 'src/dk/aau/cs/verification/batchProcessing/BatchProcessingVerificationResult.java'
--- src/dk/aau/cs/verification/batchProcessing/BatchProcessingVerificationResult.java	2011-06-28 16:30:37 +0000
+++ src/dk/aau/cs/verification/batchProcessing/BatchProcessingVerificationResult.java	2011-10-14 12:17:24 +0000
@@ -15,7 +15,7 @@
 		this.file = file;
 		this.query = query;
 		this.verificationResult = verificationResult;
-		this.verificationTimeInMs = verificationTime;
+		verificationTimeInMs = verificationTime;
 		this.stats = stats;
 	}
 	
@@ -46,10 +46,7 @@
 
 
 	public boolean hasStats() {
-		if(stats instanceof NullStats)
-			return false;
-		else
-			return true;
+		return !(stats instanceof NullStats);
 	}
 	
 	

=== modified file 'src/dk/aau/cs/verification/batchProcessing/BatchProcessingWorker.java'
--- src/dk/aau/cs/verification/batchProcessing/BatchProcessingWorker.java	2011-10-10 10:11:23 +0000
+++ src/dk/aau/cs/verification/batchProcessing/BatchProcessingWorker.java	2011-10-14 12:17:24 +0000
@@ -187,14 +187,11 @@
 	
 	private void simplifyQuery(pipe.dataLayer.TAPNQuery query) {
 		SimplifyPropositionsVisitor visitor = new SimplifyPropositionsVisitor();
-		visitor.FindAndReplaceTrueAndFalsePropositions(query.getProperty());
+		visitor.findAndReplaceTrueAndFalsePropositions(query.getProperty());
 	}
 
 	private boolean getSymmetryFromBatchProcessingOptions() {
-		if(batchProcessingVerificationOptions.symmetry() == SymmetryOption.Yes)
-			return true;
-		else
-			return false;
+		return batchProcessingVerificationOptions.symmetry() == SymmetryOption.Yes;
 	}
 
 	private Tuple<TimedArcPetriNet, NameMapping> composeModel(LoadedBatchProcessingModel model) {
@@ -320,7 +317,7 @@
 	@Override
 	protected void process(List<BatchProcessingVerificationResult> chunks) {
 		for(BatchProcessingVerificationResult result : chunks){
-			tableModel.AddResult(result);
+			tableModel.addResult(result);
 		}
 	}
 	

=== modified file 'src/net/tapaal/TAPAAL.java'
--- src/net/tapaal/TAPAAL.java	2011-08-29 23:00:27 +0000
+++ src/net/tapaal/TAPAAL.java	2011-10-14 12:17:24 +0000
@@ -9,7 +9,6 @@
 import org.apache.commons.cli.PosixParser;
 
 import pipe.gui.CreateGui;
-import pipe.gui.Pipe;
 import dk.aau.cs.debug.Logger;
 
 public class TAPAAL {

=== modified file 'src/pipe/dataLayer/DataLayer.java'
--- src/pipe/dataLayer/DataLayer.java	2011-08-30 09:04:54 +0000
+++ src/pipe/dataLayer/DataLayer.java	2011-10-14 12:17:24 +0000
@@ -5,6 +5,19 @@
 import java.util.Iterator;
 import java.util.Observable;
 
+import pipe.gui.graphicElements.AnnotationNote;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.Place;
+import pipe.gui.graphicElements.PlaceTransitionObject;
+import pipe.gui.graphicElements.Transition;
+import pipe.gui.graphicElements.tapn.TimedInhibitorArcComponent;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedOutputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
+
 import dk.aau.cs.model.tapn.TimeInvariant;
 import dk.aau.cs.model.tapn.TimedArcPetriNet;
 import dk.aau.cs.util.Require;
@@ -31,7 +44,7 @@
 	 * An ArrayList used to point to either the Arc, Place or Transition
 	 * ArrayLists when these ArrayLists are being update
 	 */
-	private ArrayList changeArrayList = null;
+	private ArrayList<? extends PetriNetObject> changeArrayList = null;
 
 	/** Used to determine whether the matrixes have been modified */
 	static boolean initialMarkingVectorChanged = true;
@@ -391,12 +404,7 @@
 				addTransition((Transition) pnObject);
 			} else if (pnObject instanceof AnnotationNote) {
 				addAnnotation((AnnotationNote)pnObject);				
-			} else { // arrows, other labels.
-				changeArrayList.add(pnObject);
-				setChanged();
-
-				notifyObservers(pnObject);
-			}
+			} 
 		}
 		// we reset to null so that the wrong ArrayList can't get added to
 		changeArrayList = null;
@@ -875,7 +883,7 @@
 		}
 
 		for (Arc arc : arcsArray) {
-			arc.updateWeightLabel(displayConstantNames);
+			arc.updateLabel(displayConstantNames);
 			arc.repaint();
 		}
 

=== modified file 'src/pipe/dataLayer/PNMLWriter.java'
--- src/pipe/dataLayer/PNMLWriter.java	2011-02-03 19:03:15 +0000
+++ src/pipe/dataLayer/PNMLWriter.java	2011-10-14 12:17:24 +0000
@@ -10,7 +10,7 @@
 import org.w3c.dom.DOMException;
 
 public interface PNMLWriter {
-	public void savePNML(File file) throws NullPointerException, IOException,
+	void savePNML(File file) throws NullPointerException, IOException,
 			ParserConfigurationException, DOMException,
 			TransformerConfigurationException, TransformerException;
 }

=== modified file 'src/pipe/dataLayer/TAPNQuery.java'
--- src/pipe/dataLayer/TAPNQuery.java	2011-06-28 16:30:37 +0000
+++ src/pipe/dataLayer/TAPNQuery.java	2011-10-14 12:17:24 +0000
@@ -52,7 +52,7 @@
 	}
 
 	public void setDiscreteInclusion(boolean value){
-		this.discreteInclusion = value;
+		discreteInclusion = value;
 	}
 	
 	public boolean discreteInclusion(){
@@ -193,17 +193,17 @@
 	}
 
 	public void set(TAPNQuery newQuery) {
-		this.name = newQuery.getName();
-		this.capacity = newQuery.getCapacity();
-		this.property = newQuery.getProperty();
-		this.traceOption = newQuery.getTraceOption();
-		this.searchOption = newQuery.getSearchOption();
-		this.reductionOption = newQuery.getReductionOption();
-		this.symmetry = newQuery.useSymmetry();
-		this.hashTableSize = newQuery.getHashTableSize();
-		this.extrapolationOption = newQuery.getExtrapolationOption();
-		this.discreteInclusion = newQuery.discreteInclusion();
-		this.inclusionPlaces = newQuery.inclusionPlaces();
+		name = newQuery.getName();
+		capacity = newQuery.getCapacity();
+		property = newQuery.getProperty();
+		traceOption = newQuery.getTraceOption();
+		searchOption = newQuery.getSearchOption();
+		reductionOption = newQuery.getReductionOption();
+		symmetry = newQuery.useSymmetry();
+		hashTableSize = newQuery.getHashTableSize();
+		extrapolationOption = newQuery.getExtrapolationOption();
+		discreteInclusion = newQuery.discreteInclusion();
+		inclusionPlaces = newQuery.inclusionPlaces();
 	}
 
 	public InclusionPlaces inclusionPlaces() {

=== modified file 'src/pipe/gui/AnimationController.java'
--- src/pipe/gui/AnimationController.java	2011-08-29 22:41:23 +0000
+++ src/pipe/gui/AnimationController.java	2011-10-14 12:17:24 +0000
@@ -26,7 +26,7 @@
 import javax.swing.border.EmptyBorder;
 
 import pipe.dataLayer.NetType;
-import pipe.gui.Pipe.elementType;
+import pipe.gui.Pipe.ElementType;
 import pipe.gui.action.GuiAction;
 import dk.aau.cs.model.tapn.simulation.FiringMode;
 
@@ -64,7 +64,7 @@
 		}
 
 		public void propertyChange(PropertyChangeEvent evt) {
-			if (evt.getPropertyName() == "selected") {
+			if (evt.getPropertyName().equals("selected")) {
 				Boolean b = (Boolean) evt.getNewValue();
 				if (b != null) {
 					setSelected(b.booleanValue());
@@ -87,12 +87,12 @@
 			randomAction, randomAnimateAction, timeAction;
 
 	public AnimationController() {
-		startAction = new AnimateAction("Simulation mode", elementType.START,
+		startAction = new AnimateAction("Simulation mode", ElementType.START,
 				"Toggle simulation mode", "Ctrl A", true);
 
-		stepbackwardAction = new AnimateAction("Back", elementType.STEPBACKWARD,
+		stepbackwardAction = new AnimateAction("Back", ElementType.STEPBACKWARD,
 				"Step backward a firing", "typed 4");
-		stepforwardAction = new AnimateAction("Forward", elementType.STEPFORWARD,
+		stepforwardAction = new AnimateAction("Forward", ElementType.STEPFORWARD,
 				"Step forward a firing", "typed 6");
 
 		stepbackwardAction.setEnabled(false);
@@ -101,9 +101,9 @@
 		// timeAction = new AnimateAction("Time", Pipe.TIMEPASS,
 		// "Let Time pass", "_");
 
-		randomAction = new AnimateAction("Random", elementType.RANDOM,
+		randomAction = new AnimateAction("Random", ElementType.RANDOM,
 				"Randomly fire a transition", "typed 5");
-		randomAnimateAction = new AnimateAction("Simulate", elementType.ANIMATE,
+		randomAnimateAction = new AnimateAction("Simulate", ElementType.ANIMATE,
 				"Randomly fire a number of transitions", "typed 7", true);
 
 		setLayout(new GridBagLayout());
@@ -243,7 +243,7 @@
 			// BigDecimal timeDelayToSet = new
 			// BigDecimal(TimeDelayField.getText(), new
 			// MathContext(Pipe.AGE_PRECISION));
-			if (timeDelayToSet.compareTo(new BigDecimal(0l)) <= 0) {
+			if (timeDelayToSet.compareTo(new BigDecimal(0L)) <= 0) {
 				// Nothing to do, illegal value
 				System.err.println("Illegal value");
 			} else {
@@ -265,21 +265,21 @@
 		 * 
 		 */
 		private static final long serialVersionUID = -4066032248332540289L;
-		private elementType typeID;
+		private ElementType typeID;
 		private AnimationHistoryComponent animBox;
 
-		AnimateAction(String name, elementType typeID, String tooltip, String keystroke) {
+		AnimateAction(String name, ElementType typeID, String tooltip, String keystroke) {
 			super(name, tooltip, keystroke);
 			this.typeID = typeID;
 		}
 
-		AnimateAction(String name, elementType typeID, String tooltip,
+		AnimateAction(String name, ElementType typeID, String tooltip,
 				String keystroke, boolean toggleable) {
 			super(name, tooltip, keystroke, toggleable);
 			this.typeID = typeID;
 		}
 
-		public AnimateAction(String name, elementType typeID, String tooltip,
+		public AnimateAction(String name, ElementType typeID, String tooltip,
 				KeyStroke keyStroke) {
 			super(name, tooltip, keyStroke);
 			this.typeID = typeID;

=== modified file 'src/pipe/gui/Animator.java'
--- src/pipe/gui/Animator.java	2011-08-29 23:00:27 +0000
+++ src/pipe/gui/Animator.java	2011-10-14 12:17:24 +0000
@@ -11,7 +11,7 @@
 
 import pipe.dataLayer.DataLayer;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.Transition;
+import pipe.gui.graphicElements.Transition;
 import pipe.gui.widgets.AnimationSelectmodeDialog;
 import pipe.gui.widgets.EscapableDialog;
 import dk.aau.cs.gui.TabContent;
@@ -109,7 +109,7 @@
 		Iterator<Transition> transitionIterator = current.returnTransitions();
 		while (transitionIterator.hasNext()) {
 			Transition tempTransition = transitionIterator.next();
-			if (tempTransition.isEnabled(true) == true) {
+			if (tempTransition.isEnabled(true)) {
 				current.notifyObservers();
 				tempTransition.repaint();
 			}
@@ -125,7 +125,7 @@
 		Iterator<Transition> transitionIterator = current.returnTransitions();
 		while (transitionIterator.hasNext()) {
 			Transition tempTransition = transitionIterator.next();
-			if (tempTransition.isEnabled(true) == false) {
+			if (!(tempTransition.isEnabled(true))) {
 				current.notifyObservers();
 				tempTransition.repaint();
 			}

=== modified file 'src/pipe/gui/CopyPasteable.java'
--- src/pipe/gui/CopyPasteable.java	2011-08-30 09:50:08 +0000
+++ src/pipe/gui/CopyPasteable.java	2011-10-14 12:17:24 +0000
@@ -1,6 +1,6 @@
 package pipe.gui;
 
-import pipe.dataLayer.PetriNetObject;
+import pipe.gui.graphicElements.PetriNetObject;
 
 /**
  * This is the interface that a component must implement so that it can be
@@ -15,7 +15,7 @@
 	 * 
 	 * @return a copy of the PetriNetObject
 	 */
-	public PetriNetObject copy();
+	PetriNetObject copy();
 
 	/**
 	 * paste()
@@ -26,7 +26,7 @@
 	 * @return a copy of the saved PetriNetObject that can be added to a GuiView
 	 *         instance
 	 */
-	public PetriNetObject paste(double despX, double despY,
+	PetriNetObject paste(double despX, double despY,
 			boolean toAnotherView);
 
 	/**
@@ -34,6 +34,6 @@
 	 * 
 	 * @return true if this object can be copied and pasted
 	 */
-	public boolean isCopyPasteable();
+	boolean isCopyPasteable();
 
 }

=== modified file 'src/pipe/gui/CreateGui.java'
--- src/pipe/gui/CreateGui.java	2011-08-29 23:00:27 +0000
+++ src/pipe/gui/CreateGui.java	2011-10-14 12:17:24 +0000
@@ -58,11 +58,11 @@
 			message.append("\nNew version: ");
 			message.append(versionChecker.getNewVersionNumber());
 			String changelog = versionChecker.getChangelog();
-			if (changelog != ""){
-				message.append("\n");
-				message.append("\n");
+			if (!changelog.equals("")){
+				message.append('\n');
+				message.append('\n');
 				message.append("Changelog:");
-				message.append("\n");
+				message.append('\n');
 				message.append(changelog);
 			}
 

=== modified file 'src/pipe/gui/DrawingSurfaceImpl.java'
--- src/pipe/gui/DrawingSurfaceImpl.java	2011-10-14 11:36:08 +0000
+++ src/pipe/gui/DrawingSurfaceImpl.java	2011-10-14 12:17:24 +0000
@@ -16,28 +16,25 @@
 import java.util.ArrayList;
 import java.util.Observable;
 import java.util.Observer;
-
 import javax.swing.JLayeredPane;
-import javax.swing.JScrollPane;
 import javax.swing.JViewport;
 import javax.swing.SwingUtilities;
 import javax.swing.event.MouseInputAdapter;
-
-import pipe.dataLayer.AnnotationNote;
-import pipe.dataLayer.Arc;
 import pipe.dataLayer.DataLayer;
-import pipe.dataLayer.Note;
-import pipe.dataLayer.PetriNetObject;
-import pipe.dataLayer.Place;
-import pipe.dataLayer.PlaceTransitionObject;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.TimedInputArcComponent;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.dataLayer.TimedTransitionComponent;
-import pipe.dataLayer.TimedTransportArcComponent;
-import pipe.dataLayer.Transition;
 import pipe.gui.GuiFrame.GUIMode;
-import pipe.gui.Pipe.elementType;
+import pipe.gui.Pipe.ElementType;
+import pipe.gui.graphicElements.AnnotationNote;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.Note;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.Place;
+import pipe.gui.graphicElements.PlaceTransitionObject;
+import pipe.gui.graphicElements.Transition;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
 import pipe.gui.handler.AnimationHandler;
 import pipe.gui.handler.AnnotationNoteHandler;
 import pipe.gui.handler.ArcHandler;
@@ -158,12 +155,10 @@
 			add(pnObject);
 		}
 
-		if(CreateGui.getApp().getMode() == elementType.SELECT)
+		if(CreateGui.getApp().getMode() == ElementType.SELECT)
 			this.selection.enableSelection();
 
-		Component component = getParent().getParent();
-		JScrollPane pane = (JScrollPane)component;
-		repaintAll();
+
 	}
 
 	public void addNewPetriNetObject(PetriNetObject newObject) {
@@ -249,9 +244,8 @@
 					((Note) newObject).getNote().addMouseMotionListener(noteHandler);
 				}
 
-				if (newObject instanceof Zoomable) {
-					newObject.zoomUpdate(getZoom());
-				}
+				newObject.zoomUpdate(getZoom());
+				
 			}
 			newObject.setGuiModel(guiModel);
 		}
@@ -261,7 +255,7 @@
 
 	public void update(Observable o, Object diffObj) {
 		if ((diffObj instanceof PetriNetObject) && (diffObj != null)) {
-			if (CreateGui.appGui.getMode() == elementType.CREATING) {
+			if (CreateGui.appGui.getMode() == ElementType.CREATING) {
 
 				addNewPetriNetObject((PetriNetObject) diffObj);
 			}
@@ -631,14 +625,14 @@
 			Point start = e.getPoint();
 			Point p;
 			if (SwingUtilities.isLeftMouseButton(e)) {
-				Pipe.elementType mode = app.getMode();
+				Pipe.ElementType mode = app.getMode();
 				switch (mode) {
 				case PLACE:
 					PlaceTransitionObject pto = newPlace(e.getPoint());
 					getUndoManager().addNewEdit(
 							new AddPetriNetObjectEdit(pto, view, guiModel));
 					if (e.isControlDown()) {
-						app.setFastMode(elementType.FAST_TRANSITION);
+						app.setFastMode(ElementType.FAST_TRANSITION);
 						pnObject.dispatchEvent(e);
 					}
 					break;
@@ -650,19 +644,19 @@
 									(TimedPlaceComponent) pto2, model,
 									guiModel, view));
 					if (e.isControlDown()) {
-						app.setFastMode(elementType.FAST_TRANSITION);
+						app.setFastMode(ElementType.FAST_TRANSITION);
 						pnObject.dispatchEvent(e);
 					}
 					break;
 
 				case IMMTRANS:
 				case TIMEDTRANS:
-					boolean timed = (mode == elementType.TIMEDTRANS ? true : false);
+					boolean timed = (mode == ElementType.TIMEDTRANS ? true : false);
 					pto = newTransition(e.getPoint(), timed);
 					getUndoManager().addNewEdit(
 							new AddPetriNetObjectEdit(pto, view, guiModel));
 					if (e.isControlDown()) {
-						app.setFastMode(elementType.FAST_PLACE);
+						app.setFastMode(ElementType.FAST_PLACE);
 						pnObject.dispatchEvent(e);
 					}
 					break;
@@ -673,7 +667,7 @@
 									(TimedTransitionComponent) pto, model,
 									guiModel, view));
 					if (e.isControlDown()) {
-						app.setFastMode(elementType.FAST_PLACE);
+						app.setFastMode(ElementType.FAST_PLACE);
 						pnObject.dispatchEvent(e);
 					}
 					break;

=== modified file 'src/pipe/gui/Export.java'
--- src/pipe/gui/Export.java	2011-03-30 17:05:37 +0000
+++ src/pipe/gui/Export.java	2011-10-14 12:17:24 +0000
@@ -31,7 +31,7 @@
 import javax.swing.JOptionPane;
 
 import pipe.dataLayer.DataLayer;
-import pipe.dataLayer.PetriNetObject;
+import pipe.gui.graphicElements.PetriNetObject;
 import pipe.gui.widgets.FileBrowser;
 
 /**
@@ -85,7 +85,7 @@
 		// /* The Swing way
 		PrintRequestAttributeSet pras = new HashPrintRequestAttributeSet();
 		DocFlavor flavour = DocFlavor.SERVICE_FORMATTED.PRINTABLE;
-		PrintService printService[] = PrintServiceLookup.lookupPrintServices(
+		PrintService[] printService = PrintServiceLookup.lookupPrintServices(
 				flavour, pras);
 
 		if (printService.length == 0) {

=== modified file 'src/pipe/gui/GuiFrame.java'
--- src/pipe/gui/GuiFrame.java	2011-10-14 11:36:08 +0000
+++ src/pipe/gui/GuiFrame.java	2011-10-14 12:17:24 +0000
@@ -60,12 +60,12 @@
 import pipe.dataLayer.DataLayer;
 import pipe.dataLayer.NetType;
 import pipe.dataLayer.PNMLWriter;
-import pipe.dataLayer.PetriNetObject;
 import pipe.dataLayer.TAPNQuery;
 import pipe.dataLayer.Template;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.gui.Pipe.elementType;
+import pipe.gui.Pipe.ElementType;
 import pipe.gui.action.GuiAction;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
 import pipe.gui.handler.SpecialMacHandler;
 import pipe.gui.widgets.EscapableDialog;
 import pipe.gui.widgets.FileBrowser;
@@ -94,7 +94,7 @@
 	private String frameTitle; // Frame title
 	private GuiFrame appGui;
 	private DrawingSurfaceImpl appView;
-	private Pipe.elementType mode, prev_mode, old_mode; // *** mode WAS STATIC ***
+	private Pipe.ElementType mode, prev_mode, old_mode; // *** mode WAS STATIC ***
 	private int newNameCounter = 1;
 	private JTabbedPane appTab;
 	private StatusBar statusBar;
@@ -305,7 +305,7 @@
 		      
 		      if (dirURL.getProtocol().equals("jar")) {
 		        /* A JAR path */
-		        String jarPath = dirURL.getPath().substring(5, dirURL.getPath().indexOf("!")); //strip out only the JAR file
+		        String jarPath = dirURL.getPath().substring(5, dirURL.getPath().indexOf('!')); //strip out only the JAR file
 		        JarFile jar = new JarFile(URLDecoder.decode(jarPath, "UTF-8"));
 		        Enumeration<JarEntry> entries = jar.entries(); //gives ALL entries in jar
 		        Set<String> result = new HashSet<String>(); //avoid duplicates in case it is a subdirectory
@@ -313,7 +313,7 @@
 		          String name = entries.nextElement().getName();
 		          if (name.startsWith("resources/Example nets/")) { //filter according to the path
 		            String entry = name.substring("resources/Example nets/".length());
-		            int checkSubdir = entry.indexOf("/");
+		            int checkSubdir = entry.indexOf('/');
 		            if (checkSubdir >= 0) {
 		              // if it is a subdirectory, we just return the directory name
 		              entry = entry.substring(0, checkSubdir);
@@ -327,8 +327,7 @@
 			Arrays.sort(nets, new Comparator<String>() {
 				public int compare(String one, String two) {
 
-					int toReturn = ((String) one).compareTo(
-							((String) two));
+					int toReturn = one.compareTo(two);
 					// Special hack to get intro-example first
 					if (one.equals("intro-example.xml")) {
 						toReturn = -1;
@@ -388,34 +387,35 @@
 		 JMenu drawMenu = new JMenu("Draw");
 		 drawMenu.setMnemonic('D');
 		 addMenuItem(drawMenu, selectAction = new TypeAction("Select",
-				 elementType.SELECT, "Select components (S)", "S", true));
+				 ElementType.SELECT, "Select components (S)", "S", true));
 		 drawMenu.addSeparator();
 
 		 addMenuItem(drawMenu, timedPlaceAction = new TypeAction("Place",
-				 elementType.TAPNPLACE, "Add a place (P)", "P", true));
+				 ElementType.TAPNPLACE, "Add a place (P)", "P", true));
 
 		 addMenuItem(drawMenu, transAction = new TypeAction("Transition",
-				 elementType.TAPNTRANS, "Add a transition (T)", "T", true));
+				 ElementType.TAPNTRANS, "Add a transition (T)", "T", true));
 
 		 addMenuItem(drawMenu, timedArcAction = new TypeAction("Arc",
-				 elementType.TAPNARC, "Add an arc (A)", "A", true));
+				 ElementType.TAPNARC, "Add an arc (A)", "A", true));
 
 		 addMenuItem(drawMenu, transportArcAction = new TypeAction(
-				 "Transport Arc", elementType.TRANSPORTARC, "Add a transport arc (R)", "R",
+				 "Transport Arc", ElementType.TRANSPORTARC, "Add a transport arc (R)", "R",
 				 true));
 
 		 addMenuItem(drawMenu, inhibarcAction = new TypeAction("Inhibitor Arc",
-				 elementType.TAPNINHIBITOR_ARC, "Add an inhibitor arc (I)", "I", true));
+				 ElementType.TAPNINHIBITOR_ARC, "Add an inhibitor arc (I)", "I", true));
 
 		 addMenuItem(drawMenu, annotationAction = new TypeAction("Annotation",
-				 elementType.ANNOTATION, "Add an annotation (N)", "N", true));
+				 ElementType.ANNOTATION, "Add an annotation (N)", "N", true));
 		 
 		 drawMenu.addSeparator();
 		 
 		 addMenuItem(drawMenu, tokenAction = new TypeAction("Add token",
-				 elementType.ADDTOKEN, "Add a token (+)", "typed +", true));
+				 ElementType.ADDTOKEN, "Add a token (+)", "typed +", true));
+
 		 addMenuItem(drawMenu, deleteTokenAction = new TypeAction(
-				 "Delete token", elementType.DELTOKEN, "Delete a token (-)", "typed -",
+				 "Delete token", ElementType.DELTOKEN, "Delete a token (-)", "typed -",
 				 true));
 
 		 /* ViewMenu */
@@ -437,7 +437,7 @@
 		 viewMenu.addSeparator();
 		 addMenuItem(viewMenu, toggleGrid = new GridAction("Cycle grid",
 				 "Change the grid size", "G"));
-		 addMenuItem(viewMenu, dragAction = new TypeAction("Drag", elementType.DRAG,
+		 addMenuItem(viewMenu, dragAction = new TypeAction("Drag", ElementType.DRAG,
 				 "Drag the drawing", "D", true));
 		 
 		 viewMenu.addSeparator();
@@ -453,17 +453,17 @@
 		 JMenu animateMenu = new JMenu("Simulator");
 		 animateMenu.setMnemonic('A');
 		 addMenuItem(animateMenu, startAction = new AnimateAction(
-				 "Simulation mode", elementType.START, "Toggle simulation mode (M)",
+				 "Simulation mode", ElementType.START, "Toggle simulation mode (M)",
 				 "M", true));
 		 animateMenu.addSeparator();
 		 addMenuItem(animateMenu, stepbackwardAction = new AnimateAction("Back",
-				 elementType.STEPBACKWARD, "Step backward a firing", "typed 4"));
+				 ElementType.STEPBACKWARD, "Step backward a firing", "typed 4"));
 		 addMenuItem(animateMenu,
 				 stepforwardAction = new AnimateAction("Forward",
-						 elementType.STEPFORWARD, "Step forward a firing", "typed 6"));
+						 ElementType.STEPFORWARD, "Step forward a firing", "typed 6"));
 
 		 addMenuItem(animateMenu, timeAction = new AnimateAction("Delay 1",
-				 elementType.TIMEPASS, "Let time pass 1 time unit", "typed 1"));
+				 ElementType.TIMEPASS, "Let time pass 1 time unit", "typed 1"));
 
 		 /*
 		  * addMenuItem(animateMenu, randomAction = new AnimateAction("Random",
@@ -472,9 +472,9 @@
 		  * AnimateAction("Simulate", Pipe.ANIMATE,
 		  * "Randomly fire a number of transitions", "typed 7",true));
 		  */
-		 randomAction = new AnimateAction("Random", elementType.RANDOM,
+		 randomAction = new AnimateAction("Random", ElementType.RANDOM,
 				 "Randomly fire a transition", "typed 5");
-		 randomAnimateAction = new AnimateAction("Simulate", elementType.ANIMATE,
+		 randomAnimateAction = new AnimateAction("Simulate", ElementType.ANIMATE,
 				 "Randomly fire a number of transitions", "typed 7", true);
 
 		 
@@ -866,7 +866,7 @@
 					setGUIMode(GUIMode.draw);
 
 					// TODO: change this code... it's ugly :)
-					if (appGui.getMode() == elementType.SELECT) {
+					if (appGui.getMode() == ElementType.SELECT) {
 						appGui.activateSelectAction();
 					}
 
@@ -886,7 +886,7 @@
 
 	// HAK Method called by netModel object when it changes
 	public void update(Observable o, Object obj) {
-		if ((mode != elementType.CREATING) && (!appView.isInAnimationMode())) {
+		if ((mode != ElementType.CREATING) && (!appView.isInAnimationMode())) {
 			appView.setNetChanged(true);
 		}
 	}
@@ -1030,7 +1030,7 @@
 		int currentlySelected = appTab.getSelectedIndex();
 
 		
-		if (namePrefix == null || namePrefix == "") {
+		if (namePrefix == null || namePrefix.equals("")) {
 			name = "New Petri net " + (newNameCounter++) + ".xml";
 		} else {
 			name = namePrefix + ".xml";
@@ -1046,7 +1046,7 @@
 				TabContent currentTab = (TabContent) appTab.getSelectedComponent();
 				if (CreateGui.getApp() != null) {
 					// Notifies used to indicate new instances.
-					CreateGui.getApp().setMode(elementType.CREATING);
+					CreateGui.getApp().setMode(ElementType.CREATING);
 				}
 
 				ModelLoader loader = new ModelLoader(currentTab.drawingSurface());
@@ -1111,7 +1111,7 @@
 				TabContent currentTab = (TabContent) appTab.getSelectedComponent();
 				if (CreateGui.getApp() != null) {
 					// Notifies used to indicate new instances.
-					CreateGui.getApp().setMode(elementType.CREATING);
+					CreateGui.getApp().setMode(ElementType.CREATING);
 				}
 
 				ModelLoader loader = new ModelLoader(currentTab.drawingSurface());
@@ -1199,7 +1199,7 @@
 		// Loop through all tabs and check if they have been saved
 		for (int counter = 0; counter < appTab.getTabCount(); counter++) {
 			appTab.setSelectedIndex(counter);
-			if (checkForSave() == false) {
+			if (!(checkForSave())) {
 				return false;
 			}
 		}
@@ -1208,7 +1208,7 @@
 
 	public void setRandomAnimationMode(boolean on) {
 
-		if (on == false) {
+		if (!(on)) {
 			stepforwardAction.setEnabled(CreateGui.getAnimationHistory().isStepForwardAllowed());
 			stepbackwardAction.setEnabled(CreateGui.getAnimationHistory().isStepBackAllowed());
 
@@ -1314,12 +1314,12 @@
 		setMode(old_mode);
 	}
 
-	public void setFastMode(Pipe.elementType _mode) {
+	public void setFastMode(Pipe.ElementType _mode) {
 		old_mode = mode;
 		setMode(_mode);
 	}
 
-	public void setMode(Pipe.elementType _mode) {
+	public void setMode(Pipe.ElementType _mode) {
 		// Don't bother unless new mode is different.
 		if (mode != _mode) {
 			prev_mode = mode;
@@ -1327,7 +1327,7 @@
 		}
 	}
 
-	public Pipe.elementType getMode() {
+	public Pipe.ElementType getMode() {
 		return mode;
 	}
 
@@ -1337,40 +1337,40 @@
 		mode = prev_mode;
 
 		if (placeAction != null) {
-			placeAction.setSelected(mode == elementType.PLACE);
+			placeAction.setSelected(mode == ElementType.PLACE);
 		}
 		if (transAction != null) {
-			transAction.setSelected(mode == elementType.IMMTRANS);
+			transAction.setSelected(mode == ElementType.IMMTRANS);
 		}
 
 		if (timedtransAction != null) {
-			timedtransAction.setSelected(mode == elementType.TIMEDTRANS);
+			timedtransAction.setSelected(mode == ElementType.TIMEDTRANS);
 		}
 
 		if (arcAction != null) {
-			arcAction.setSelected(mode == elementType.ARC);
+			arcAction.setSelected(mode == ElementType.ARC);
 		}
 
 		if (timedArcAction != null)
-			timedArcAction.setSelected(mode == elementType.TAPNARC);
+			timedArcAction.setSelected(mode == ElementType.TAPNARC);
 
 		if (transportArcAction != null)
-			transportArcAction.setSelected(mode == elementType.TRANSPORTARC);
+			transportArcAction.setSelected(mode == ElementType.TRANSPORTARC);
 
 		if (timedPlaceAction != null)
-			timedPlaceAction.setSelected(mode == elementType.TAPNPLACE);
+			timedPlaceAction.setSelected(mode == ElementType.TAPNPLACE);
 
 		if (tokenAction != null)
-			tokenAction.setSelected(mode == elementType.ADDTOKEN);
+			tokenAction.setSelected(mode == ElementType.ADDTOKEN);
 
 		if (deleteTokenAction != null)
-			deleteTokenAction.setSelected(mode == elementType.DELTOKEN);
+			deleteTokenAction.setSelected(mode == ElementType.DELTOKEN);
 
 		if (selectAction != null)
-			selectAction.setSelected(mode == elementType.SELECT);
+			selectAction.setSelected(mode == ElementType.SELECT);
 
 		if (annotationAction != null)
-			annotationAction.setSelected(mode == elementType.ANNOTATION);
+			annotationAction.setSelected(mode == ElementType.ANNOTATION);
 
 	}
 
@@ -1398,7 +1398,7 @@
 
 	public void activateSelectAction() {
 		// Set selection mode at startup
-		setMode(elementType.SELECT);
+		setMode(ElementType.SELECT);
 		selectAction.actionPerformed(null);
 	}
 
@@ -1441,21 +1441,21 @@
 		 * 
 		 */
 		private static final long serialVersionUID = 8582324286370859664L;
-		private elementType typeID;
+		private ElementType typeID;
 		private AnimationHistoryComponent animBox;
 
-		AnimateAction(String name, elementType typeID, String tooltip, String keystroke) {
+		AnimateAction(String name, ElementType typeID, String tooltip, String keystroke) {
 			super(name, tooltip, keystroke);
 			this.typeID = typeID;
 		}
 
-		AnimateAction(String name, elementType typeID, String tooltip,
+		AnimateAction(String name, ElementType typeID, String tooltip,
 				String keystroke, boolean toggleable) {
 			super(name, tooltip, keystroke, toggleable);
 			this.typeID = typeID;
 		}
 
-		public AnimateAction(String name, elementType typeID, String tooltip,
+		public AnimateAction(String name, ElementType typeID, String tooltip,
 				KeyStroke keyStroke) {
 			super(name, tooltip, keyStroke);
 			this.typeID = typeID;
@@ -1527,7 +1527,7 @@
 				animBox.stepForward();
 				CreateGui.getAnimator().stepForward();
 				// update mouseOverView
-				for (pipe.dataLayer.Place p : CreateGui.getModel().getPlaces()) {
+				for (pipe.gui.graphicElements.Place p : CreateGui.getModel().getPlaces()) {
 					if (((TimedPlaceComponent) p).isAgeOfTokensShown()) {
 						((TimedPlaceComponent) p).showAgeOfTokens(true);
 					}
@@ -1539,7 +1539,7 @@
 				animBox.stepBackwards();
 				CreateGui.getAnimator().stepBack();
 				// update mouseOverView
-				for (pipe.dataLayer.Place p : CreateGui.getModel().getPlaces()) {
+				for (pipe.gui.graphicElements.Place p : CreateGui.getModel().getPlaces()) {
 					if (((TimedPlaceComponent) p).isAgeOfTokensShown()) {
 						((TimedPlaceComponent) p).showAgeOfTokens(true);
 					}
@@ -1608,7 +1608,7 @@
 			s.append("The following queries are associated with the currently selected objects:\n\n");
 			for (TAPNQuery q : queriesToDelete) {
 				s.append(q.getName());
-				s.append("\n");
+				s.append('\n');
 			}
 			s.append("\nAre you sure you want to remove the current selection and all associated queries?");
 
@@ -1651,14 +1651,14 @@
 		 * 
 		 */
 		private static final long serialVersionUID = 1333311291148756241L;
-		private Pipe.elementType typeID;
+		private Pipe.ElementType typeID;
 
-		TypeAction(String name, Pipe.elementType typeID, String tooltip, String keystroke) {
+		TypeAction(String name, Pipe.ElementType typeID, String tooltip, String keystroke) {
 			super(name, tooltip, keystroke);
 			this.typeID = typeID;
 		}
 
-		TypeAction(String name, Pipe.elementType typeID, String tooltip, String keystroke,
+		TypeAction(String name, Pipe.ElementType typeID, String tooltip, String keystroke,
 				boolean toggleable) {
 			super(name, tooltip, keystroke, toggleable);
 			this.typeID = typeID;
@@ -1714,7 +1714,7 @@
 			setMode(typeID);
 			statusBar.changeText(typeID);
 
-			if ((typeID != elementType.ARC) && (appView.createArc != null)) {
+			if ((typeID != ElementType.ARC) && (appView.createArc != null)) {
 
 				appView.createArc.delete();
 				appView.createArc = null;
@@ -1722,13 +1722,13 @@
 
 			}
 
-			if (typeID == elementType.SELECT) {
+			if (typeID == ElementType.SELECT) {
 				// disable drawing to eliminate possiblity of connecting arc to
 				// old coord of moved component
 				statusBar.changeText(typeID);
 				appView.getSelectionObject().enableSelection();
 				appView.setCursorType("arrow");
-			} else if (typeID == elementType.DRAG) {
+			} else if (typeID == ElementType.DRAG) {
 				appView.setCursorType("move");
 			} else {
 				appView.setCursorType("crosshair");
@@ -1810,7 +1810,7 @@
 						return;
 					}
 				}
-				if (doZoom == true) {
+				if (doZoom) {
 					updateZoomCombo();
 					appView.zoomTo(new java.awt.Point((int) midpointX,
 							(int) midpointY));
@@ -1924,7 +1924,7 @@
 		buffer.append("TAPAAL Engine (verifytapn) Information:\n");
 		buffer.append("   Located: ");
 		buffer.append(verifytapnPath);
-		buffer.append("\n");
+		buffer.append('\n');
 		buffer.append("   Version: ");
 		buffer.append(verifytapnversion);
 		buffer.append("\n\n");
@@ -1932,7 +1932,7 @@
 		buffer.append("UPPAAL Engine (verifyta) Information:\n");
 		buffer.append("   Located: ");
 		buffer.append(verifytaPath);
-		buffer.append("\n");
+		buffer.append('\n');
 		buffer.append("   Version: ");
 		buffer.append(verifytaversion);
 
@@ -2159,7 +2159,7 @@
 		}
 
 		public void propertyChange(PropertyChangeEvent evt) {
-			if (evt.getPropertyName() == "selected") {
+			if (evt.getPropertyName().equals("selected")) {
 				Boolean b = (Boolean) evt.getNewValue();
 				if (b != null) {
 					setSelected(b.booleanValue());

=== modified file 'src/pipe/gui/KBoundAnalyzer.java'
--- src/pipe/gui/KBoundAnalyzer.java	2011-05-21 13:59:16 +0000
+++ src/pipe/gui/KBoundAnalyzer.java	2011-10-14 12:17:24 +0000
@@ -28,7 +28,7 @@
 		this.tapnNetwork = tapnNetwork;
 		this.modelChecker = modelChecker;
 		this.messenger = messenger;
-		this.spinner = tokensControl;
+		spinner = tokensControl;
 	}
 
 	public void analyze() {

=== modified file 'src/pipe/gui/Pipe.java'
--- src/pipe/gui/Pipe.java	2011-10-14 11:36:08 +0000
+++ src/pipe/gui/Pipe.java	2011-10-14 12:17:24 +0000
@@ -11,7 +11,7 @@
 	public static final String CLASS_FILE_DESC = "Java Class File";
 
 	//Enum for all actions and types of elements
-	public static enum elementType {
+	public static enum ElementType {
 		PLACE, IMMTRANS, TIMEDTRANS, ANNOTATION, ARC, INHIBARC, 
 		//TAPN Elements
 		TAPNPLACE, TAPNTRANS, TAPNARC, TRANSPORTARC, TAPNINHIBITOR_ARC,
@@ -24,7 +24,7 @@
 		
 	}
 
-	public static final elementType DEFAULT_ELEMENT_TYPE = elementType.SELECT;
+	public static final ElementType DEFAULT_ELEMENT_TYPE = ElementType.SELECT;
 
 	public static final int PLACE_TRANSITION_HEIGHT = 30;
 	public static final int DASHED_PADDING = 8;

=== modified file 'src/pipe/gui/RunVerification.java'
--- src/pipe/gui/RunVerification.java	2011-06-18 15:14:39 +0000
+++ src/pipe/gui/RunVerification.java	2011-10-14 12:17:24 +0000
@@ -25,7 +25,7 @@
 	private IconSelector iconSelector;
 	public RunVerification(ModelChecker modelChecker, IconSelector selector, Messenger messenger) {
 		super(modelChecker, messenger);
-		this.iconSelector = selector;
+		iconSelector = selector;
 	}
 
 	@Override
@@ -69,7 +69,7 @@
 			System.getProperty("line.separator") + 	
 			System.getProperty("line.separator");
 			
-			if (extraInformation != ""){
+			if (!extraInformation.equals("")){
 				message += extraInformation +			
 				System.getProperty("line.separator") + 	
 				System.getProperty("line.separator");
@@ -100,7 +100,7 @@
 		gbc.anchor = GridBagConstraints.WEST;		
 		panel.add(new JLabel(toHTML(result.getResultString())), gbc);
 		
-		if(this.modelChecker.supportsStats()){
+		if(modelChecker.supportsStats()){
 			gbc = new GridBagConstraints();
 			gbc.gridx = 0;
 			gbc.gridy = 1;

=== modified file 'src/pipe/gui/SelectionManager.java'
--- src/pipe/gui/SelectionManager.java	2011-10-09 14:30:45 +0000
+++ src/pipe/gui/SelectionManager.java	2011-10-14 12:17:24 +0000
@@ -13,11 +13,12 @@
 import java.awt.event.MouseWheelEvent;
 import java.util.ArrayList;
 
-import pipe.dataLayer.Arc;
-import pipe.dataLayer.ArcPath;
-import pipe.dataLayer.PetriNetObject;
-import pipe.dataLayer.PlaceTransitionObject;
 import pipe.gui.GuiFrame.GUIMode;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.ArcPath;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.PlaceTransitionObject;
+
 
 /**
  * @author Peter Kyme, Michael Camacho Class to handle selection rectangle
@@ -34,8 +35,8 @@
 	private Point startPoint;
 	private Rectangle selectionRectangle = new Rectangle(-1, -1);
 	private boolean isSelecting;
-	private static final Color selectionColor = new Color(000, 000, 255, 030);
-	private static final Color selectionColorOutline = new Color(000, 000, 100);
+	private static final Color selectionColor = new Color(0, 0, 255, 30);
+	private static final Color selectionColorOutline = new Color(0, 0, 100);
 	private DrawingSurfaceImpl drawingSurface;
 	private boolean enabled = true;
 
@@ -43,17 +44,17 @@
 		addMouseListener(this);
 		addMouseMotionListener(this);
 		//addMouseWheelListener(this);
-		this.drawingSurface = _view;
+		drawingSurface = _view;
 	}
 
 	public void updateBounds() {
-		if (enabled == true) {
+		if (enabled) {
 			setBounds(0, 0, drawingSurface.getWidth(), drawingSurface.getHeight());
 		}
 	}
 
 	public void enableSelection() {
-		if (enabled == false) {
+		if (!(enabled)) {
 			drawingSurface.add(this);
 			enabled = true;
 			updateBounds();
@@ -61,7 +62,7 @@
 	}
 
 	public void disableSelection() {
-		if (enabled == true) {
+		if (enabled) {
 			this.clearSelection();
 			drawingSurface.remove(this);
 			enabled = false;
@@ -200,7 +201,7 @@
 	 * java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent)
 	 */
 	public void mouseReleased(MouseEvent e) {
-		if (isSelecting == true) {
+		if (isSelecting) {
 			// Select anything that intersects with the rectangle.
 			processSelection(e);
 			isSelecting = false;
@@ -245,15 +246,12 @@
 	}
 
 	public void mouseClicked(MouseEvent e) {
-		;// Not needed
 	}
 
 	public void mouseEntered(MouseEvent e) {
-		; // Not needed
 	}
 
 	public void mouseExited(MouseEvent e) {
-		; // Not needed
 	}
 
 	/*
@@ -263,11 +261,10 @@
 	 * java.awt.event.MouseMotionListener#mouseMoved(java.awt.event.MouseEvent)
 	 */
 	public void mouseMoved(MouseEvent e) {
-		; // Not needed
 	}
 
 	public int getSelectionCount() {
-		Component netObj[] = drawingSurface.getComponents();
+		Component[] netObj = drawingSurface.getComponents();
 		int selectionCount = 0;
 		// Get all the objects in the current window
 		for (int i = 0; i < netObj.length; i++) {

=== modified file 'src/pipe/gui/StatusBar.java'
--- src/pipe/gui/StatusBar.java	2011-10-14 11:36:08 +0000
+++ src/pipe/gui/StatusBar.java	2011-10-14 12:17:24 +0000
@@ -58,7 +58,7 @@
 		label.setText(newText);
 	}
 
-	public void changeText(Pipe.elementType type) {
+	public void changeText(Pipe.ElementType type) {
 		switch (type) {
 		case PLACE:
 			changeText(textforPlace);

=== modified file 'src/pipe/gui/TikZExporter.java'
--- src/pipe/gui/TikZExporter.java	2011-08-30 08:42:12 +0000
+++ src/pipe/gui/TikZExporter.java	2011-10-14 12:17:24 +0000
@@ -3,20 +3,21 @@
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintWriter;
-import java.math.BigDecimal;
-import java.util.ArrayList;
-
-import pipe.dataLayer.Arc;
-import pipe.dataLayer.ArcPathPoint;
+import java.util.List;
+
+import dk.aau.cs.model.tapn.TimedToken;
+
 import pipe.dataLayer.DataLayer;
 import pipe.dataLayer.NetType;
-import pipe.dataLayer.Place;
-import pipe.dataLayer.TimedInhibitorArcComponent;
-import pipe.dataLayer.TimedInputArcComponent;
-import pipe.dataLayer.TimedPlaceComponent;
-import pipe.dataLayer.TimedTransitionComponent;
-import pipe.dataLayer.Transition;
-import pipe.dataLayer.TimedTransportArcComponent;
+import pipe.gui.graphicElements.Arc;
+import pipe.gui.graphicElements.ArcPathPoint;
+import pipe.gui.graphicElements.Place;
+import pipe.gui.graphicElements.Transition;
+import pipe.gui.graphicElements.tapn.TimedInhibitorArcComponent;
+import pipe.gui.graphicElements.tapn.TimedInputArcComponent;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
+import pipe.gui.graphicElements.tapn.TimedTransitionComponent;
+import pipe.gui.graphicElements.tapn.TimedTransportArcComponent;
 
 public class TikZExporter {
 
@@ -156,7 +157,7 @@
 			out.append(exportMathName(trans.getName()));
 			out.append("] at (");
 			out.append(trans.getPositionX() * scale);
-			out.append(",");
+			out.append(',');
 			out.append(trans.getPositionY() * scale * (-1));
 			out.append(") (");
 			out.append(trans.getId());
@@ -181,12 +182,12 @@
 
 			out.append("\\node[place,label=above:");
 			out.append(exportMathName(place.getName()));
-			out.append(",");
+			out.append(',');
 			out.append(invariant);
 			out.append(tokensInPlace);
 			out.append("] at (");
 			out.append(place.getPositionX() * scale);
-			out.append(",");
+			out.append(',');
 			out.append(place.getPositionY() * scale * (-1));
 			out.append(") (");
 			out.append(place.getId());
@@ -203,11 +204,13 @@
 	}
 
 	protected String getTokenListStringFor(Place place) {
-		ArrayList<BigDecimal> tokens = ((TimedPlaceComponent) place).getTokens();
+		
+		List<TimedToken> tokens = ((TimedPlaceComponent) place).underlyingPlace().tokens();
+		
 		String tokensInPlace = "";
 		if (tokens.size() > 0) {
 			if (tokens.size() == 1 && !net.netType().equals(NetType.UNTIMED)) {
-				tokensInPlace = "structured tokens={" + tokens.get(0).setScale(1) + "},";
+				tokensInPlace = "structured tokens={" + tokens.get(0).age().setScale(1) + "},";
 			} else {
 				tokensInPlace = exportMultipleTokens(tokens);
 			}
@@ -224,7 +227,7 @@
 		return invariant;
 	}
 
-	private String exportMultipleTokens(ArrayList<BigDecimal> tokens) {
+	private String exportMultipleTokens(List<TimedToken> tokens) {
 		StringBuffer out = new StringBuffer();
 
 		out.append("structured tokens={\\#");
@@ -233,10 +236,10 @@
 		if (!net.netType().equals(NetType.UNTIMED)) {
 			out.append("pin=above:{\\{");
 			for (int i = 0; i < tokens.size() - 1; i++) {
-				out.append(tokens.get(i).setScale(1));
-				out.append(",");
+				out.append(tokens.get(i).age().setScale(1));
+				out.append(',');
 			}
-			out.append(tokens.get(tokens.size() - 1).setScale(1));
+			out.append(tokens.get(tokens.size() - 1).age().setScale(1));
 			out.append("\\}},");
 		}
 		return out.toString();
@@ -283,9 +286,9 @@
 			out.append(last);
 
 		for (int i = 0; i < subscripts; i++) {
-			out.append("}");
+			out.append('}');
 		}
-		out.append("$");
+		out.append('$');
 		return out.toString();
 	}
 

=== modified file 'src/pipe/gui/Translatable.java'
--- src/pipe/gui/Translatable.java	2011-02-03 19:03:15 +0000
+++ src/pipe/gui/Translatable.java	2011-10-14 12:17:24 +0000
@@ -10,6 +10,6 @@
  */
 public interface Translatable {
 
-	public void translate(int x, int y);
+	void translate(int x, int y);
 
 }

=== modified file 'src/pipe/gui/VersionChecker.java'
--- src/pipe/gui/VersionChecker.java	2011-08-29 23:00:27 +0000
+++ src/pipe/gui/VersionChecker.java	2011-10-14 12:17:24 +0000
@@ -11,7 +11,7 @@
 import dk.aau.cs.debug.Logger;
 
 public class VersionChecker {
-	private final static String versionURL = "http://www.tapaal.net/fileadmin/version.txt";
+	private static final String versionURL = "http://www.tapaal.net/fileadmin/version.txt";
 	private static final int timeoutMs = 6000;
 	private URL url;
 	private String newestVersion;

=== modified file 'src/pipe/gui/Zoomable.java'
--- src/pipe/gui/Zoomable.java	2011-02-03 19:03:15 +0000
+++ src/pipe/gui/Zoomable.java	2011-10-14 12:17:24 +0000
@@ -10,6 +10,6 @@
  */
 public interface Zoomable {
 
-	public void zoomUpdate(int zoom);
+	void zoomUpdate(int zoom);
 
 }

=== modified file 'src/pipe/gui/Zoomer.java'
--- src/pipe/gui/Zoomer.java	2011-07-16 11:42:34 +0000
+++ src/pipe/gui/Zoomer.java	2011-10-14 12:17:24 +0000
@@ -61,7 +61,7 @@
 	}
 
 	public static double getZoomedValue(double x, int zoom) {
-		return (x * zoom * 0.01);
+		return x * zoom * 0.01;
 	}
 
 	public static AffineTransform getTransform(int zoom) {
@@ -77,7 +77,7 @@
 	}
 
 	public static double getUnzoomedValue(double x, int zoom) {
-		return (x / (zoom * 0.01));
+		return x / (zoom * 0.01);
 	}
 
 }

=== modified file 'src/pipe/gui/action/DeletePetriNetObjectAction.java'
--- src/pipe/gui/action/DeletePetriNetObjectAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/DeletePetriNetObjectAction.java	2011-10-14 12:17:24 +0000
@@ -12,10 +12,10 @@
 import javax.swing.AbstractAction;
 import javax.swing.JOptionPane;
 
-import pipe.dataLayer.PetriNetObject;
 import pipe.dataLayer.TAPNQuery;
-import pipe.dataLayer.TimedPlaceComponent;
 import pipe.gui.CreateGui;
+import pipe.gui.graphicElements.PetriNetObject;
+import pipe.gui.graphicElements.tapn.TimedPlaceComponent;
 import dk.aau.cs.gui.TabContent;
 import dk.aau.cs.model.tapn.TimedPlace;
 
@@ -51,7 +51,7 @@
 		s.append("The following queries are associated with the currently selected objects:\n\n");
 		for (TAPNQuery q : queriesToDelete) {
 			s.append(q.getName());
-			s.append("\n");
+			s.append('\n');
 		}
 		s.append("\nAre you sure you want to remove the current selection and all associated queries?");
 

=== modified file 'src/pipe/gui/action/EditAnnotationBackgroundAction.java'
--- src/pipe/gui/action/EditAnnotationBackgroundAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/EditAnnotationBackgroundAction.java	2011-10-14 12:17:24 +0000
@@ -4,7 +4,7 @@
 
 import javax.swing.AbstractAction;
 
-import pipe.dataLayer.AnnotationNote;
+import pipe.gui.graphicElements.AnnotationNote;
 
 /**
  * Action to toggle the background of a note between white and transparent

=== modified file 'src/pipe/gui/action/EditAnnotationBorderAction.java'
--- src/pipe/gui/action/EditAnnotationBorderAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/EditAnnotationBorderAction.java	2011-10-14 12:17:24 +0000
@@ -8,8 +8,8 @@
 
 import javax.swing.AbstractAction;
 
-import pipe.dataLayer.AnnotationNote;
 import pipe.gui.CreateGui;
+import pipe.gui.graphicElements.AnnotationNote;
 
 public class EditAnnotationBorderAction extends AbstractAction {
 

=== modified file 'src/pipe/gui/action/EditNoteAction.java'
--- src/pipe/gui/action/EditNoteAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/EditNoteAction.java	2011-10-14 12:17:24 +0000
@@ -7,7 +7,7 @@
 
 import javax.swing.AbstractAction;
 
-import pipe.dataLayer.Note;
+import pipe.gui.graphicElements.Note;
 
 public class EditNoteAction extends AbstractAction {
 

=== removed file 'src/pipe/gui/action/EditWeightAction.java'
--- src/pipe/gui/action/EditWeightAction.java	2011-10-04 18:07:57 +0000
+++ src/pipe/gui/action/EditWeightAction.java	1970-01-01 00:00:00 +0000
@@ -1,62 +0,0 @@
-package pipe.gui.action;
-
-import java.awt.Container;
-import java.awt.event.ActionEvent;
-
-import javax.swing.AbstractAction;
-import javax.swing.JOptionPane;
-
-import pipe.dataLayer.Arc;
-import pipe.gui.CreateGui;
-
-/**
- * This class allows the user to change the weight on an arc.
- * 
- * @author unknown
- * 
- * @author Dave Patterson May 4, 2007: Handle cancel choice without an
- *         exception. Change error messages to ask for a positive integer.
- */
-public class EditWeightAction extends AbstractAction {
-
-	private static final long serialVersionUID = 2003;
-	private Container contentPane;
-	private Arc myArc;
-
-	public EditWeightAction(Container contentPane, Arc a) {
-		this.contentPane = contentPane;
-		myArc = a;
-	}
-
-	public void actionPerformed(ActionEvent e) {
-		int currentWeighting = myArc.getWeight();
-
-		String input = JOptionPane.showInputDialog("Weighting:", String
-				.valueOf(currentWeighting));
-
-		if (input == null) {
-			return; // do nothing if the user clicks "Cancel"
-		}
-
-		try {
-			int newWeighting = Integer.parseInt(input);
-			if (newWeighting < 1) {
-				JOptionPane.showMessageDialog(contentPane,
-						"Weighting cannot be less than 1. Please re-enter");
-			} else if (newWeighting != currentWeighting) {
-				CreateGui.getView().getUndoManager().addNewEdit(
-						myArc.setWeight(newWeighting));
-			}
-		} catch (NumberFormatException nfe) {
-			JOptionPane.showMessageDialog(contentPane,
-					"Enter a positive integer greater than 0.",
-					"Invalid entry", JOptionPane.ERROR_MESSAGE);
-		} catch (Exception exc) {
-			exc.printStackTrace();
-			JOptionPane.showMessageDialog(contentPane,
-					"Enter a positive integer greater than 0.",
-					"Invalid entry", JOptionPane.ERROR_MESSAGE);
-		}
-	}
-
-}

=== modified file 'src/pipe/gui/action/InsertPointAction.java'
--- src/pipe/gui/action/InsertPointAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/InsertPointAction.java	2011-10-14 12:17:24 +0000
@@ -7,8 +7,8 @@
 import java.awt.event.ActionEvent;
 import java.awt.geom.Point2D;
 
-import pipe.dataLayer.Arc;
 import pipe.gui.CreateGui;
+import pipe.gui.graphicElements.Arc;
 
 /**
  * This class is used to split an arc in two at the point the user clicks the

=== modified file 'src/pipe/gui/action/ShowHideInfoAction.java'
--- src/pipe/gui/action/ShowHideInfoAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/ShowHideInfoAction.java	2011-10-14 12:17:24 +0000
@@ -2,7 +2,7 @@
 
 import java.awt.event.ActionEvent;
 
-import pipe.dataLayer.PlaceTransitionObject;
+import pipe.gui.graphicElements.PlaceTransitionObject;
 
 
 public class ShowHideInfoAction extends javax.swing.AbstractAction {

=== modified file 'src/pipe/gui/action/SplitArcAction.java'
--- src/pipe/gui/action/SplitArcAction.java	2011-08-30 10:07:54 +0000
+++ src/pipe/gui/action/SplitArcAction.java	2011-10-14 12:17:24 +0000
@@ -4,8 +4,8 @@
 import java.awt.event.ActionEvent;
 import java.awt.geom.Point2D;
 
-import pipe.dataLayer.Arc;
 import pipe.gui.CreateGui;
+import pipe.gui.graphicElements.Arc;
 
 /**
  * This class is used to split an arc in two at the point the user clicks the

=== modified file 'src/pipe/gui/action/SplitArcPointAction.java'
--- src/pipe/gui/action/SplitArcPointAction.java	2011-02-03 19:03:15 +0000
+++ src/pipe/gui/action/SplitArcPointAction.java	2011-10-14 12:17:24 +0000
@@ -7,8 +7,8 @@
 
 import java.awt.event.ActionEvent;
 
-import pipe.dataLayer.ArcPathPoint;
 import pipe.gui.CreateGui;
+import pipe.gui.graphicElements.ArcPathPoint;
 
 /**
  * @author Nadeem

=== modified file 'src/pipe/gui/action/ToggleArcPointAction.java'
--- src/pipe/gui/action/ToggleArcPointAction.java	2011-02-03 19:03:15 +0000
+++ src/pipe/gui/action/ToggleArcPointAction.java	2011-10-14 12:17:24 +0000
@@ -7,8 +7,8 @@
 
 import java.awt.event.ActionEvent;
 
-import pipe.dataLayer.ArcPathPoint;
 import pipe.gui.CreateGui;
+import pipe.gui.graphicElements.ArcPathPoint;
 
 public class ToggleArcPointAction extends javax.swing.AbstractAction {
 

=== added directory 'src/pipe/gui/graphicElements'
=== renamed file 'src/pipe/dataLayer/AnnotationNote.java' => 'src/pipe/gui/graphicElements/AnnotationNote.java'
--- src/pipe/dataLayer/AnnotationNote.java	2011-10-14 11:36:08 +0000
+++ src/pipe/gui/graphicElements/AnnotationNote.java	2011-10-14 12:17:24 +0000
@@ -1,8 +1,4 @@
-/*
- * Created on 04-Mar-2004
- * Author is Michael Camacho
- */
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.BasicStroke;
 import java.awt.Dimension;
@@ -29,9 +25,6 @@
 
 public class AnnotationNote extends Note {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 3503959956765396720L;
 
 	private boolean fillNote = true;
@@ -65,7 +58,6 @@
 		dragPoints[3] = new ResizePoint(this, ResizePoint.RIGHT);
 		dragPoints[4] = new ResizePoint(this, ResizePoint.BOTTOM
 				| ResizePoint.RIGHT);
-		;
 		dragPoints[5] = new ResizePoint(this, ResizePoint.BOTTOM);
 		dragPoints[6] = new ResizePoint(this, ResizePoint.BOTTOM
 				| ResizePoint.LEFT);
@@ -162,23 +154,6 @@
 		}
 	}
 
-	public AnnotationNote paste(double x, double y, boolean toAnotherView) {
-		return new AnnotationNote(this.note.getText(), Grid.getModifiedX(x
-				+ this.getX()), Grid.getModifiedY(y + this.getY()), this.note
-				.getWidth(), this.note.getHeight(), this.isShowingBorder());
-	}
-
-	public AnnotationNote copy() {
-		AnnotationNote annotation = new AnnotationNote(this.note.getText(), Zoomer.getUnzoomedValue(this.getX(), zoom), Zoomer.getUnzoomedValue(this.getY(), zoom),	this.note.getWidth(), this.note.getHeight(), this.isShowingBorder());
-		AnnotationNoteHandler noteHandler = new AnnotationNoteHandler((DrawingSurfaceImpl)getParent(), annotation);
-		annotation.addMouseListener(noteHandler);
-		annotation.addMouseMotionListener(noteHandler);
-		annotation.getNote().addMouseListener(noteHandler);
-		annotation.getNote().addMouseMotionListener(noteHandler);
-		
-		return annotation;
-	}
-
 	@Override
 	public void paintComponent(Graphics g) {
 		super.paintComponent(g);
@@ -274,9 +249,6 @@
 
 	public class ResizePoint extends javax.swing.JComponent {
 
-		/**
-	 * 
-	 */
 		private static final long serialVersionUID = -1615544376708838434L;
 		private int SIZE = 3;
 		private static final int TOP = 1;
@@ -341,7 +313,7 @@
 			}
 		}
 
-		// change ResizePoint's size a little bit acording to the zoom percent
+		// Change ResizePoint's size a little bit acording to the zoom percent
 		private void setZoom(int percent) {
 			if (zoom >= 220) {
 				SIZE = 5;
@@ -352,5 +324,16 @@
 			}
 		}
 	}
+	
+	public AnnotationNote copy() {
+		AnnotationNote annotation = new AnnotationNote(note.getText(), Zoomer.getUnzoomedValue(this.getX(), zoom), Zoomer.getUnzoomedValue(this.getY(), zoom),	note.getWidth(), note.getHeight(), this.isShowingBorder());
+		AnnotationNoteHandler noteHandler = new AnnotationNoteHandler((DrawingSurfaceImpl)getParent(), annotation);
+		annotation.addMouseListener(noteHandler);
+		annotation.addMouseMotionListener(noteHandler);
+		annotation.getNote().addMouseListener(noteHandler);
+		annotation.getNote().addMouseMotionListener(noteHandler);
+		
+		return annotation;
+	}
 
 }

=== renamed file 'src/pipe/dataLayer/Arc.java' => 'src/pipe/gui/graphicElements/Arc.java'
--- src/pipe/dataLayer/Arc.java	2011-09-18 15:10:09 +0000
+++ src/pipe/gui/graphicElements/Arc.java	2011-10-14 12:17:24 +0000
@@ -1,4 +1,4 @@
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.Rectangle;
 import java.awt.geom.Point2D;
@@ -9,82 +9,37 @@
 import pipe.gui.DrawingSurfaceImpl;
 import pipe.gui.Pipe;
 import pipe.gui.undo.AddArcPathPointEdit;
-import pipe.gui.undo.ArcWeightEdit;
 import dk.aau.cs.gui.undo.Command;
 
 /**
- * <b>Arc</b> - Petri-Net Arc Class
- * 
- * @see <p>
- *      <a href="..\PNMLSchema\index.html">PNML - Petri-Net XMLSchema
- *      (stNet.xsd)</a>
- * @see </p>
- *      <p>
- *      <a href="..\..\..\UML\dataLayer.html">UML - PNML Package </a>
- *      </p>
- * @version 1.0
- * @author James D Bloom
- * 
- * @author Pere Bonet modifed the delete method so that the weight label of an
- *         arc is deleted when the associated arc is deleted
- * 
- * @author Edwin Chung 16 Mar 2007: modified the constructor and several other
- *         functions so that DataLayer objects can be created outside the GUI
- * 
- * @author Nick Dingle 18 Oct 2007: added the ability for an arc to be "tagged"
- *         (permit the passage of tagged tokens).
+   Implementation of Element for drawing an arc
  */
 public abstract class Arc extends PetriNetObject implements Cloneable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 6527845538091358791L;
-	// public final static String TYPE = "arc";
-	/** Current Marking */
-	protected int weight = 1;
-	protected NameLabel weightLabel;
+
+	protected NameLabel label;
 
 	private static Point2D.Double point;
 
-	/** references to the objects this arc connects */
+	/** References to the objects this arc connects */
 	private PlaceTransitionObject source = null;
 	private PlaceTransitionObject target = null;
-	// private boolean deleted = false; // Used for cleanup purposes
 
 	protected ArcPath myPath = new ArcPath(this);
 
-	// true if arc is not hidden when a bidirectional arc is used
-	protected boolean inView = true;
-
-	// bounds of arc need to be grown in order to avoid clipping problems
+	// Bounds of arc need to be grown in order to avoid clipping problems
 	protected int zoomGrow = 10;
 
 	/**
 	 * Create Petri-Net Arc object
 	 * 
-	 * @param startPositionXInput
-	 *            Start X-axis Position
-	 * @param startPositionYInput
-	 *            Start Y-axis Position
-	 * @param endPositionXInput
-	 *            End X-axis Position
-	 * @param endPositionYInput
-	 *            End Y-axis Position
-	 * @param sourceInput
-	 *            Arc source
-	 * @param targetInput
-	 *            Arc target
-	 * @param idInput
-	 *            Arc id
-	 * @param inputTagged
-	 *            TODO
 	 */
 	public Arc(double startPositionXInput, double startPositionYInput,
 			double endPositionXInput, double endPositionYInput,
 			PlaceTransitionObject sourceInput,
 			PlaceTransitionObject targetInput, int weightInput, String idInput) {
-		weightLabel = new NameLabel(zoom);
+		label = new NameLabel(zoom);
 		myPath.addPoint((float) startPositionXInput,
 				(float) startPositionYInput, ArcPathPoint.STRAIGHT);
 		myPath.addPoint((float) endPositionXInput, (float) endPositionYInput,
@@ -94,14 +49,13 @@
 		id = idInput;
 		setSource(sourceInput);
 		setTarget(targetInput);
-		setWeight(weightInput);
 	}
 
 	/**
 	 * Create Petri-Net Arc object
 	 */
 	public Arc(PlaceTransitionObject newSource) {
-		weightLabel = new NameLabel(zoom);
+		label = new NameLabel(zoom);
 		source = newSource;
 		myPath.addPoint();
 		myPath.addPoint();
@@ -130,45 +84,33 @@
 	 */
 	public void setTarget(PlaceTransitionObject targetInput) {
 		target = targetInput;
-		// if (CreateGui.getApp() != null) {
-		// updateArcPosition();
-		// }
+	}
+
+	public void setLabelPosition() {
+		label.setPosition((int) (myPath.midPoint.x)
+				+ label.getWidth() / 2 - 4, (int) (myPath.midPoint.y));
 	}
 
 	/**
-	 * Set weight
+	 * Get id
 	 * 
-	 * @param weightInput
-	 *            String value for Arc weight;
+	 * @return String value for Arc id;
 	 */
-	public Command setWeight(int weightInput) {
-		int oldWeight = weight;
-
-		weight = weightInput;
-		if (weight == 1) {
-			weightLabel.setText("");
+	@Override
+	public String getId() {
+		if (id != null) {
+			return id;
 		} else {
-			weightLabel.setText(Integer.toString(weight));
+			if (source != null && target != null) {
+				return source.getId() + " to " + target.getId();
+			}
 		}
-		weightLabel.updateSize();
-		setWeightLabelPosition();
-		repaint();
-		return new ArcWeightEdit(this, oldWeight, weight);
-	}
-
-	public void setWeightLabelPosition() {
-		weightLabel.setPosition(
-				(int) (myPath.midPoint.x) + weightLabel.getWidth() / 2 - 4,
-				(int) (myPath.midPoint.y));
+		return "";
 	}
 
 	@Override
 	public String getName() {
-		if (source != null && target != null) {
-			return source.getId() + " to " + target.getId();
-		} else {
-			return "";
-		}
+		return getId();
 	}
 
 	/**
@@ -208,15 +150,6 @@
 	}
 
 	/**
-	 * Get weight
-	 * 
-	 * @return Integer value for Arc weight;
-	 */
-	public int getWeight() {
-		return weight;
-	}
-
-	/**
 	 * Updates the start position of the arc, resets the arrowhead and updates
 	 * the bounds
 	 */
@@ -250,8 +183,8 @@
 		repaint();
 	}
 
-	public void updateWeightLabel(boolean displayConstantNames) {
-
+	public void updateLabel(boolean displayConstantNames) {
+		//No label to update for this type
 	}
 
 	/** Updates the bounding box of the arc component based on the arcs bounds */
@@ -294,8 +227,8 @@
 			myPath.addPointsToGui((JLayeredPane) getParent());
 		}
 		updateArcPosition();
-		if (getParent() != null && weightLabel.getParent() == null) {
-			getParent().add(weightLabel);
+		if (getParent() != null && label.getParent() == null) {
+			getParent().add(label);
 		}
 	}
 
@@ -303,12 +236,10 @@
 	public void delete() {
 		if (!deleted) {
 			if (getParent() != null) {
-				getParent().remove(weightLabel);
+				getParent().remove(label);
 			}
-			if (source != null)
-				source.removeFromArc(this);
-			if (target != null)
-				target.removeToArc(this);
+			if(source != null) source.removeFromArc(this);
+			if(target != null) target.removeToArc(this);
 			myPath.forceHidePoints();
 			super.delete();
 			deleted = true;
@@ -324,14 +255,6 @@
 		return new AddArcPathPointEdit(this, newPoint);
 	}
 
-	/*
-	 * CB Joakim Byg - probably not needed public abstract String getType(); EOC
-	 */
-
-	public boolean inView() {
-		return inView;
-	}
-
 	public Transition getTransition() {
 		if (getTarget() instanceof Transition) {
 			return (Transition) getTarget();
@@ -342,7 +265,7 @@
 
 	public void removeFromView() {
 		if (getParent() != null) {
-			getParent().remove(weightLabel);
+			getParent().remove(label);
 		}
 		myPath.forceHidePoints();
 		removeFromContainer();
@@ -376,8 +299,8 @@
 	public void zoomUpdate(int percent) {
 		zoom = percent;
 		this.updateArcPosition();
-		weightLabel.zoomUpdate(percent);
-		weightLabel.updateSize();
+		label.zoomUpdate(percent);
+		label.updateSize();
 	}
 
 	public void setZoom(int percent) {

=== renamed file 'src/pipe/dataLayer/ArcPath.java' => 'src/pipe/gui/graphicElements/ArcPath.java'
--- src/pipe/dataLayer/ArcPath.java	2011-06-24 14:48:28 +0000
+++ src/pipe/gui/graphicElements/ArcPath.java	2011-10-14 12:17:24 +0000
@@ -1,7 +1,4 @@
-/**
- * Created on 12-Feb-2004
- */
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.BasicStroke;
 import java.awt.Rectangle;
@@ -40,10 +37,7 @@
 	protected ArcPathPoint currentPoint;
 	private boolean pointLock = false;
 	private static Stroke proximityStroke = new BasicStroke(
-			Pipe.ARC_PATH_PROXIMITY_WIDTH/*
-										 * , BasicStroke.CAP_BUTT,
-										 * BasicStroke.JOIN_MITER
-										 */);
+			Pipe.ARC_PATH_PROXIMITY_WIDTH);
 	private static Stroke stroke = new BasicStroke(
 			Pipe.ARC_PATH_SELECTION_WIDTH);
 	private Shape shape, proximityShape;
@@ -133,7 +127,7 @@
 		}
 
 		shape = stroke.createStrokedShape(this);
-		getArc().setWeightLabelPosition();
+		getArc().setLabelPosition();
 		proximityShape = proximityStroke.createStrokedShape(this);
 	}
 
@@ -189,18 +183,18 @@
 			int curveEndIndex = 0;
 			myCurrentPoint = pathPoints.get(c);
 
-			if (myCurrentPoint.getPointType() == true) {
+			if (myCurrentPoint.getPointType()) {
 				curveStartIndex = c - 1;
 
-				for (; c <= endIndex && myCurrentPoint.getPointType() == true; c++) {
+				for (; c <= endIndex && myCurrentPoint.getPointType(); c++) {
 					myCurrentPoint = pathPoints.get(c);
 					curveEndIndex = c;
 				}
 				/* calculate a cubic for each section of the curve */
 				int lengthOfCurve = curveEndIndex - curveStartIndex;
 				int k1;
-				int x[] = new int[lengthOfCurve + 2];
-				int y[] = new int[lengthOfCurve + 2];
+				int[] x = new int[lengthOfCurve + 2];
+				int[] y = new int[lengthOfCurve + 2];
 				X = new Cubic[lengthOfCurve + 2];
 				Y = new Cubic[lengthOfCurve + 2];
 
@@ -244,7 +238,7 @@
 			myPreviousPoint = pathPoints.get(c - 1);
 			myCurrentPoint = pathPoints.get(c);
 
-			if (myCurrentPoint.getPointType() == false) {
+			if (!(myCurrentPoint.getPointType())) {
 				myCurrentPoint.setControl1(getControlPoint(myPreviousPoint
 						.getPoint(), myCurrentPoint.getPoint(), myPreviousPoint
 						.getPoint(), myCurrentPoint.getPoint()));
@@ -252,7 +246,7 @@
 						.getPoint(), myPreviousPoint.getPoint(), myCurrentPoint
 						.getPoint(), myPreviousPoint.getPoint()));
 			} else {
-				if (c > 1 && myPreviousPoint.getPointType() == false) {
+				if (c > 1 && !(myPreviousPoint.getPointType())) {
 					myPreviousButOnePoint = pathPoints.get(c - 2);
 					myCurrentPoint.setControl1(getControlPoint(
 							myPreviousButOnePoint.getPoint(), myPreviousPoint
@@ -261,7 +255,7 @@
 				}
 				if (c < getEndIndex()) {
 					myNextPoint = pathPoints.get(c + 1);
-					if (myNextPoint.getPointType() == false) {
+					if (!(myNextPoint.getPointType())) {
 						myCurrentPoint.setControl2(getControlPoint(myNextPoint
 								.getPoint(), myCurrentPoint.getPoint(),
 								myCurrentPoint.getPoint(), myPreviousPoint
@@ -280,7 +274,7 @@
 		if (!(getEndIndex() > 0)) {
 			return;
 		} else if (source != null && source instanceof Transition
-				&& (pathPoints.get(1)).getPointType() == true) {
+				&& (pathPoints.get(1)).getPointType()) {
 			ArcPathPoint myPoint = pathPoints.get(1);
 			ArcPathPoint myLastPoint = pathPoints.get(0);
 			float distance = (float) getMod(myPoint.getPoint(), myLastPoint
@@ -296,7 +290,7 @@
 			myPoint.setControl2(getControlPoint(myPoint.getPoint(), myPoint
 					.getControl1(), myPoint.getPoint(), myPoint.getControl1()));
 		} else if (target != null && source instanceof Place
-				&& (pathPoints.get(getEndIndex())).getPointType() == true) {
+				&& (pathPoints.get(getEndIndex())).getPointType()) {
 			ArcPathPoint myPoint = pathPoints.get(getEndIndex());
 			ArcPathPoint myLastPoint = pathPoints.get(getEndIndex() - 1);
 			float distance = (float) getMod(myPoint.getPoint(), myLastPoint

=== renamed file 'src/pipe/dataLayer/ArcPathPoint.java' => 'src/pipe/gui/graphicElements/ArcPathPoint.java'
--- src/pipe/dataLayer/ArcPathPoint.java	2011-02-03 19:03:15 +0000
+++ src/pipe/gui/graphicElements/ArcPathPoint.java	2011-10-14 12:17:24 +0000
@@ -4,7 +4,7 @@
  * @author Edwin Chung 16 Mar 2007: modified the constructor and several other
  * functions so that DataLayer objects can be created outside the GUI
  */
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.Graphics;
 import java.awt.Graphics2D;
@@ -23,9 +23,6 @@
 
 public class ArcPathPoint extends PetriNetObject {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 7584441718171173604L;
 	public static final boolean STRAIGHT = false;
 	public static final boolean CURVED = true;
@@ -74,7 +71,6 @@
 		return point;
 	}
 
-	//
 	public void setPointLocation(float x, float y) {
 		double realX = Zoomer.getUnzoomedValue(x, zoom);
 		double realY = Zoomer.getUnzoomedValue(y, zoom);
@@ -195,8 +191,7 @@
 	}
 
 	@Override
-	public void delete() {// Won't delete if only two points left. General
-							// delete.
+	public void delete() {// Won't delete if only two points left. General delete.
 		if (isDeleteable()) {
 			if (getArcPath().getArc().isSelected()) {
 				return;
@@ -246,7 +241,6 @@
 
 	@Override
 	public void addedToGui() {
-		;
 	}
 
 	void hidePoint() {
@@ -274,7 +268,6 @@
 
 	@Override
 	public void undelete(DrawingSurfaceImpl view) {
-		;
 	}
 
 	@Override
@@ -285,8 +278,7 @@
 
 	public void zoomUpdate(int zoom) {
 		this.zoom = zoom;
-		// change ArcPathPoint's size a little bit when it's zoomed in or zoomed
-		// out
+		// change ArcPathPoint's size a little bit when it's zoomed in or zoomed out
 		if (zoom > 213) {
 			SIZE = 5;
 		} else if (zoom > 126) {

=== renamed file 'src/pipe/dataLayer/NameLabel.java' => 'src/pipe/gui/graphicElements/NameLabel.java'
--- src/pipe/dataLayer/NameLabel.java	2011-08-30 08:56:51 +0000
+++ src/pipe/gui/graphicElements/NameLabel.java	2011-10-14 12:17:24 +0000
@@ -1,4 +1,4 @@
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.Font;
 
@@ -11,21 +11,14 @@
 import pipe.gui.Zoomer;
 
 /**
- * <b>NameLabel</b> - This class is for the labels of PN Objects
+ * This class is for the labels of PN Objects
  * 
- * @see </p>
- *      <p>
- *      <a href="uml\NameLabel.png">NameLabel UML</a>
- *      </p>
  * @version 1.0
  * @author Camilla Clifford
  */
 public class NameLabel extends JTextArea implements Cloneable, Translatable,
 		Zoomable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 5167510420195429773L;
 	private int positionX;
 	private int positionY;
@@ -51,7 +44,7 @@
 		setCursor(new java.awt.Cursor(java.awt.Cursor.CROSSHAIR_CURSOR));
 		setEditable(false);
 		setFocusable(false);
-		setOpaque(false); // added by OP
+		setOpaque(false);
 		setBorder(BorderFactory.createEmptyBorder());
 		setBackground(Pipe.BACKGROUND_COLOR);
 

=== renamed file 'src/pipe/dataLayer/Note.java' => 'src/pipe/gui/graphicElements/Note.java'
--- src/pipe/dataLayer/Note.java	2011-02-12 12:15:54 +0000
+++ src/pipe/gui/graphicElements/Note.java	2011-10-14 12:17:24 +0000
@@ -1,7 +1,7 @@
 /*
  * Note.java
  */
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.Component;
 import java.awt.Dimension;
@@ -26,9 +26,6 @@
  */
 public abstract class Note extends PetriNetObject implements Translatable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 8965208519103066242L;
 	protected JTextArea note = new JTextArea();
 	protected boolean drawBorder = true;

=== renamed file 'src/pipe/dataLayer/PetriNetObject.java' => 'src/pipe/gui/graphicElements/PetriNetObject.java'
--- src/pipe/dataLayer/PetriNetObject.java	2011-09-18 15:10:09 +0000
+++ src/pipe/gui/graphicElements/PetriNetObject.java	2011-10-14 12:17:24 +0000
@@ -1,4 +1,4 @@
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -10,44 +10,30 @@
 
 import javax.swing.JComponent;
 
-import pipe.gui.CopyPasteable;
+import pipe.dataLayer.DataLayer;
 import pipe.gui.DrawingSurfaceImpl;
 import pipe.gui.Pipe;
 import pipe.gui.Translatable;
 import pipe.gui.Zoomable;
 
 /**
- * <b>PetriNetObject</b> - Petri-Net Object Class<b> - <i>Abstract</i></b>
- * 
- * @see <p>
- *      <a href="..\PNMLSchema\index.html">PNML - Petri-Net XMLSchema
- *      (stNet.xsd)</a>
- * @see </p>
- *      <p>
- *      <a href="..\..\..\UML\dataLayer.html">UML - PNML Package </a>
- *      </p>
- * @version 1.0
- * @author James D Bloom
+ * Petri-Net Object Class 
+ * Implements things in common between all types of objects
  */
 public abstract class PetriNetObject extends JComponent implements Zoomable,
-		CopyPasteable, Cloneable, Translatable {
+		Cloneable, Translatable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 2693171860021066729L;
 
-	protected final static int COMPONENT_DRAW_OFFSET = 5;
+	protected static final int COMPONENT_DRAW_OFFSET = 5;
 
-	/** Id */
 	protected String id = null;
 
-	/** Name Label for displaying name */
+	/* Name Label for displaying name */
 	protected NameLabel pnName;
 	protected Color objectColour = Pipe.ELEMENT_LINE_COLOUR;
 	protected Color selectionBorderColour = Pipe.SELECTION_LINE_COLOUR;
-	protected boolean selected = false; // True if part of the current
-										// selection.
+	protected boolean selected = false; // True if part of the current selection.
 	protected boolean selectable = true; // True if object can be selected.
 	protected boolean draggable = true; // True if object can be dragged.
 	protected boolean copyPasteable = true; // True if object can be cloned.
@@ -61,9 +47,6 @@
 	protected int zoom = 100;
 	private DataLayer guiModel;
 
-	/**
-	 * Create PetriNetObject
-	 */
 	public PetriNetObject() {
 	}
 
@@ -75,12 +58,6 @@
 		return guiModel;
 	}
 
-	/**
-	 * Set id
-	 * 
-	 * @param idInput
-	 *            String value for id;
-	 */
 	public void setId(String idInput) {
 		id = idInput;
 		setName(idInput);
@@ -200,10 +177,6 @@
 		super.paintComponent(g);
 	}
 
-	public boolean isCopyPasteable() {
-		return copyPasteable;
-	}
-
 	public abstract int getLayerOffset();
 
 	public int getZoom() {
@@ -228,12 +201,6 @@
 				pnObjectCopy.removeMouseMotionListener((MouseMotionListener) mouseListeners[i]);
 			}
 
-//			mouseListeners = pnObjectCopy.getListeners(MouseWheelListener.class);
-//
-//			for (int i = 0; i < mouseListeners.length; i++) {
-//				pnObjectCopy.removeMouseWheelListener((MouseWheelListener) mouseListeners[i]);
-//			}
-
 			return pnObjectCopy;
 		} catch (CloneNotSupportedException e) {
 			throw new Error(e);

=== renamed file 'src/pipe/dataLayer/Place.java' => 'src/pipe/gui/graphicElements/Place.java'
--- src/pipe/dataLayer/Place.java	2011-08-30 09:36:10 +0000
+++ src/pipe/gui/graphicElements/Place.java	2011-10-14 12:17:24 +0000
@@ -1,4 +1,4 @@
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.BasicStroke;
 import java.awt.Graphics;
@@ -13,54 +13,28 @@
 import pipe.gui.Zoomer;
 
 /**
- * <b>Place</b> - Petri-Net Place Class
- * 
- * @see <p>
- *      <a href="..\PNMLSchema\index.html">PNML - Petri-Net XMLSchema
- *      (stNet.xsd)</a>
- * @see </p>
- *      <p>
- *      <a href="..\..\..\UML\dataLayer.html">UML - PNML Package </a>
- *      </p>
- * @version 1.0
- * @author James D Bloom
- * 
- * @author Edwin Chung corresponding states of matrixes has been set to change
- *         when markings are altered. Users will be prompted to save their work
- *         when the markings of places are altered. (6th Feb 2007)
- * 
- * @author Edwin Chung 16 Mar 2007: modified the constructor and several other
- *         functions so that DataLayer objects can be created outside the GUI
+  * Class for drawing a Place
  */
 public class Place extends PlaceTransitionObject {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = -5155964364065651381L;
-	public final static String type = "Place";
-	/** Initial Marking */
-	protected Integer initialMarking = 0;
-
-	/** Current Marking */
-	protected Integer currentMarking = 0;
-
-	/** Initial Marking X-axis Offset */
+
+	// Initial Marking X-axis Offset 
 	protected Double markingOffsetX = 0d;
 
-	/** Initial Marking Y-axis Offset */
+	// Initial Marking Y-axis Offset 
 	protected Double markingOffsetY = 0d;
 
-	/** Value of the capacity restriction; 0 means no capacity restriction */
+	// Value of the capacity restriction; 0 means no capacity restriction 
 	protected Integer capacity = 0;
 
 	public static final int DIAMETER = Pipe.PLACE_TRANSITION_HEIGHT;
 
-	/** Token Width and Height */
+	// Token Width and Height
 	public static int tWidth = 4;
 	public static int tHeight = 4;
 
-	/** Ellipse2D.Double place */
+	// Ellipse2D.Double place
 	protected static Ellipse2D.Double placeEllipse = new Ellipse2D.Double(0, 0,	DIAMETER, DIAMETER);
 	protected static Shape proximityPlace = (new BasicStroke(Pipe.PLACE_TRANSITION_PROXIMITY_RADIUS)).createStrokedShape(placeEllipse);
 
@@ -70,8 +44,6 @@
 			double markingOffsetYInput, int capacityInput) {
 		super(positionXInput, positionYInput, idInput, nameInput,
 				nameOffsetXInput, nameOffsetYInput);
-		initialMarking = new Integer(initialMarkingInput);
-		currentMarking = new Integer(initialMarkingInput);
 		markingOffsetX = new Double(markingOffsetXInput);
 		markingOffsetY = new Double(markingOffsetYInput);
 		componentWidth = DIAMETER;
@@ -92,16 +64,14 @@
 		this.incrementCopyNumber();
 		Place copy = new Place(Grid.getModifiedX(x + this.getX()+ Pipe.PLACE_TRANSITION_HEIGHT / 2), 
 				Grid.getModifiedY(y	+ this.getY() + Pipe.PLACE_TRANSITION_HEIGHT / 2));
-		copy.pnName.setName(this.pnName.getName() + "(" + this.getCopyNumber()	+ ")");
+		copy.pnName.setName(pnName.getName() + "(" + this.getCopyNumber()	+ ")");
 		this.newCopy(copy);
-		copy.nameOffsetX = this.nameOffsetX;
-		copy.nameOffsetY = this.nameOffsetY;
-		copy.capacity = this.capacity;
-		copy.attributesVisible = this.attributesVisible;
-		copy.initialMarking = this.initialMarking;
-		copy.currentMarking = this.currentMarking;
-		copy.markingOffsetX = this.markingOffsetX;
-		copy.markingOffsetY = this.markingOffsetY;
+		copy.nameOffsetX = nameOffsetX;
+		copy.nameOffsetY = nameOffsetY;
+		copy.capacity = capacity;
+		copy.attributesVisible = attributesVisible;
+		copy.markingOffsetX = markingOffsetX;
+		copy.markingOffsetY = markingOffsetY;
 		copy.update(true);
 		return copy;
 	}
@@ -109,14 +79,12 @@
 	public Place copy() {
 		Place copy = new Place(Zoomer.getUnzoomedValue(this.getX(), zoom), Zoomer.getUnzoomedValue(this.getY(), zoom));
 		copy.pnName.setName(this.getName());
-		copy.nameOffsetX = this.nameOffsetX;
-		copy.nameOffsetY = this.nameOffsetY;
-		copy.capacity = this.capacity;
-		copy.attributesVisible = this.attributesVisible;
-		copy.initialMarking = this.initialMarking;
-		copy.currentMarking = this.currentMarking;
-		copy.markingOffsetX = this.markingOffsetX;
-		copy.markingOffsetY = this.markingOffsetY;
+		copy.nameOffsetX = nameOffsetX;
+		copy.nameOffsetY = nameOffsetY;
+		copy.capacity = capacity;
+		copy.attributesVisible = attributesVisible;
+		copy.markingOffsetX = markingOffsetX;
+		copy.markingOffsetY = markingOffsetY;
 		copy.setOriginal(this);
 		return copy;
 	}
@@ -148,25 +116,6 @@
 	}
 
 	/**
-	 * Set initial marking
-	 * 
-	 * @param initialMarkingInput
-	 *            Integer value for initial marking
-	 */
-	public void setInitialMarking(int initialMarkingInput) {
-		initialMarking = initialMarkingInput;
-	}
-
-	/**
-	 * Get current marking
-	 * 
-	 * @return Integer value for current marking
-	 */
-	public int getCurrentMarking() {
-		return ((currentMarking == null) ? 0 : currentMarking.intValue());
-	}
-
-	/**
 	 * Get X-axis offset for initial marking
 	 * 
 	 * @return Double value for X-axis offset of initial marking
@@ -263,7 +212,7 @@
 
 	@Override
 	public void update(boolean displayConstantNames) {
-		if (attributesVisible == true) {
+		if (attributesVisible) {
 			pnName.setText("\nk=" + (capacity > 0 ? capacity : "\u221E"));
 		} else {
 			pnName.setText("");
@@ -278,10 +227,8 @@
 
 		Place toReturn = (Place) super.clone();
 
-		toReturn.initialMarking = this.initialMarking;
-		toReturn.currentMarking = this.currentMarking;
-		toReturn.markingOffsetX = this.markingOffsetX;
-		toReturn.markingOffsetY = this.markingOffsetY;
+		toReturn.markingOffsetX = markingOffsetX;
+		toReturn.markingOffsetY = markingOffsetY;
 		toReturn.componentWidth = componentWidth;
 		toReturn.componentHeight = componentHeight;
 		toReturn.setCentre((int) positionX, (int) positionY);

=== renamed file 'src/pipe/dataLayer/PlaceTransitionObject.java' => 'src/pipe/gui/graphicElements/PlaceTransitionObject.java'
--- src/pipe/dataLayer/PlaceTransitionObject.java	2011-09-18 15:10:09 +0000
+++ src/pipe/gui/graphicElements/PlaceTransitionObject.java	2011-10-14 12:17:24 +0000
@@ -1,4 +1,4 @@
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.Graphics;
 import java.awt.Graphics2D;
@@ -11,28 +11,12 @@
 import pipe.gui.Zoomer;
 
 /**
- * <b>PlaceTransitionObject</b> - Petri-Net PLace or Transition SuperClass<b> -
- * <i>Abstract</i></b>
- * 
- * @see <p>
- *      <a href="..\PNMLSchema\index.html">PNML - Petri-Net XMLSchema
- *      (stNet.xsd)</a>
- * @see </p>
- *      <p>
- *      <a href="..\..\..\UML\dataLayer.html">UML - PNML Package </a>
- *      </p>
- * @version 1.0
- * @author James D Bloom
- * 
- * @author Edwin Chung 16 Mar 2007: modified the constructor and several other
- *         functions so that DataLayer objects can be created outside the GUI
+ * Petri-Net Place or Transition SuperClass
+ * 
  */
 public abstract class PlaceTransitionObject extends PetriNetObject implements
 Cloneable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = -6629006415467929184L;
 	/** X-axis Position on screen */
 	protected double positionX;
@@ -187,6 +171,18 @@
 	}
 
 	/**
+	 * Set id
+	 * 
+	 * @param idInput
+	 *            String value for Place id;
+	 */
+	@Override
+	public void setId(String idInput) {
+		id = idInput;
+		setName(id);
+	}
+
+	/**
 	 * Get id
 	 * 
 	 * @return String value for Place id;
@@ -220,7 +216,7 @@
 	 * @return Double value for X-axis offset of ...
 	 */
 	public Double getNameOffsetXObject() {
-		return this.nameOffsetX;
+		return nameOffsetX;
 	}
 
 	/**
@@ -229,7 +225,7 @@
 	 * @return Double value for Y-axis offset of ...
 	 */
 	public Double getNameOffsetYObject() {
-		return this.nameOffsetY;
+		return nameOffsetY;
 	}
 
 	/**
@@ -308,32 +304,20 @@
 
 	/** Adds outwards arc to place/transition */
 	public void addConnectTo(Arc newArc) {
-		// System.out.println("DEBUG: added arc (to)!:" + newArc + " de " +
-		// this);
 		connectTo.add(newArc);
 	}
 
 	/** Adds inwards arc to place/transition */
 	public void addConnectFrom(Arc newArc) {
-		// System.out.println("DEBUG: added arc (from)!:" + newArc + " de " +
-		// this);
 		connectFrom.add(newArc);
 	}
 
 	public void removeFromArc(Arc oldArc) {
-		if (connectFrom.remove(oldArc)) {
-			// System.out.println("DEBUG: removeFromArc_ok");
-		} else {
-			// System.out.println("DEBUG: removeFromArc_ko");
-		}
+		connectFrom.remove(oldArc);
 	}
 
 	public void removeToArc(Arc oldArc) {
-		if (connectTo.remove(oldArc)) {
-			// System.out.println("DEBUG: removeToArc_ok");
-		} else {
-			// System.out.println("DEBUG: removeToArc_ko");
-		}
+		connectTo.remove(oldArc);
 	}
 
 	/** Updates location of any attached arcs */
@@ -517,8 +501,8 @@
 		PlaceTransitionObject toReturn = (PlaceTransitionObject) super.clone();
 		toReturn.pnName = (NameLabel) pnName.clone();
 
-		toReturn.connectFrom = this.connectFrom;
-		toReturn.connectTo = this.connectTo;
+		toReturn.connectFrom = connectFrom;
+		toReturn.connectTo = connectTo;
 
 		return toReturn;
 	}

=== renamed file 'src/pipe/dataLayer/Transition.java' => 'src/pipe/gui/graphicElements/Transition.java'
--- src/pipe/dataLayer/Transition.java	2011-08-30 09:20:01 +0000
+++ src/pipe/gui/graphicElements/Transition.java	2011-10-14 12:17:24 +0000
@@ -1,4 +1,4 @@
-package pipe.dataLayer;
+package pipe.gui.graphicElements;
 
 import java.awt.BasicStroke;
 import java.awt.Graphics;
@@ -14,100 +14,38 @@
 import java.util.Iterator;
 
 import pipe.gui.CreateGui;
-import pipe.gui.Grid;
 import pipe.gui.Pipe;
 import pipe.gui.Zoomer;
 import pipe.gui.undo.TransitionRotationEdit;
 import dk.aau.cs.gui.undo.Command;
 
 /**
- * <b>Transition</b> - Petri-Net Transition Class
- * 
- * @see <p>
- *      <a href="..\PNMLSchema\index.html">PNML - Petri-Net XMLSchema
- *      (stNet.xsd)</a>
- * @see </p>
- *      <p>
- *      <a href="..\..\..\UML\dataLayer.html">UML - PNML Package </a>
- *      </p>
- * @version 1.0
- * @author James D Bloom *
- * @author Dave Patterson Add fields and methods to handle delay time for
- *         exponentially distributed timed transitions.
- * 
- *         Note: The exponential distribution is based on a single parameter,
- *         which can either be specified as a delay or a rate. The two values
- *         are inverses of each other, so no matter how the parameter is
- *         specified, the code after the constructor is the same. When a timed
- *         transition is found to be enabled, a projected delay is calculated
- *         based on its exponential distribution. As long as the transition does
- *         not get disabled before it can be fired, that delay governs the
- *         timing of the transition's firing. If other timed transitions are
- *         fired, the delay before they fire (that is, the progress of the
- *         virtual clock) is decremented from this transition's delay time to
- *         simulate the progress of time in the virtual space. Thus, at any
- *         time, the next timed transition to fire is the one with the lowest
- *         delay remaining. If a timed transition gets an expected delay and
- *         then later becomes disabled, its delay is no longer valid. When it
- *         next becomes enabled, it will get a new expected delay (an offset
- *         from the current virtual time). This explaination was included to
- *         clarify any confusion about fields and methods with "delay" in their
- *         names. They have nothing to do with whether the parameter of the
- *         exponential distribution is specified as a rate, or an expected
- *         delay. to the
+ * Petri-Net Transition Class for Drawing Transitions
  */
 public class Transition extends PlaceTransitionObject {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 942116302162925121L;
-	/** Transition is of Rectangle2D.Double */
+	
+	//Transition is of Rectangle2D.Double
 	private GeneralPath transition;
 	private Shape proximityTransition;
-	/** Place Width */
+
+	// Transition Size
 	public static final int TRANSITION_HEIGHT = Pipe.PLACE_TRANSITION_HEIGHT;
-	/** Place Width */
 	public static final int TRANSITION_WIDTH = TRANSITION_HEIGHT / 3;
-
+	
 	protected int angle;
+	
+	// Animation Suff
 	protected boolean enabled = false;
-	// private boolean enabledBackwards = false;
 	public boolean highlighted = false;
 
-	private boolean infiniteServer = false;
-
 	private static final double rootThreeOverTwo = 0.5 * Math.sqrt(3);
 
 	private ArrayList<ArcAngleCompare> arcAngleList = new ArrayList<ArcAngleCompare>();
 
-	/** The transition priority */
-	private Integer priority = 1;
-
-	public Transition(Transition t) {
-
-		this(t.positionX, t.positionY, t.id, t.getName(), t.nameOffsetX,
-				t.nameOffsetY, t.infiniteServer, t.angle, t.priority);
-
-	}
-
 	/**
 	 * Create Petri-Net Transition object
-	 * 
-	 * @param positionXInput
-	 *            X-axis Position
-	 * @param positionYInput
-	 *            Y-axis Position
-	 * @param idInput
-	 *            Transition id
-	 * @param nameInput
-	 *            Name
-	 * @param nameOffsetXInput
-	 *            Name X-axis Position
-	 * @param nameOffsetYInput
-	 *            Name Y-axis Position
-	 * @param infServer
-	 *            TODO
 	 */
 	public Transition(double positionXInput, double positionYInput,
 			String idInput, String nameInput, double nameOffsetXInput,
@@ -117,14 +55,11 @@
 				nameOffsetXInput, nameOffsetYInput);
 		componentWidth = TRANSITION_HEIGHT; // sets width
 		componentHeight = TRANSITION_HEIGHT;// sets height
-		infiniteServer = infServer;
 		constructTransition();
 		angle = 0;
 		setCentre((int) positionX, (int) positionY);
 		rotate(angleInput);
 		updateBounds();
-		// this.updateEndPoints();
-		this.priority = priority;
 	}
 
 	/**
@@ -145,41 +80,6 @@
 		this.updateEndPoints();
 	}
 
-	public Transition paste(double x, double y, boolean fromAnotherView) {
-		this.incrementCopyNumber();
-		Transition copy = new Transition(Grid.getModifiedX(x + this.getX()
-				+ Pipe.PLACE_TRANSITION_HEIGHT / 2), Grid.getModifiedY(y
-				+ this.getY() + Pipe.PLACE_TRANSITION_HEIGHT / 2));
-		copy.pnName.setName(this.pnName.getName() + "(" + this.getCopyNumber()
-				+ ")");
-
-		this.newCopy(copy);
-		copy.nameOffsetX = this.nameOffsetX;
-		copy.nameOffsetY = this.nameOffsetY;
-
-		copy.angle = this.angle;
-
-		copy.attributesVisible = this.attributesVisible;
-		copy.priority = this.priority;
-		copy.transition.transform(AffineTransform.getRotateInstance(Math
-				.toRadians(copy.angle), Transition.TRANSITION_HEIGHT / 2,
-				Transition.TRANSITION_HEIGHT / 2));
-		return copy;
-	}
-
-	public Transition copy() {
-		Transition copy = new Transition(Zoomer.getUnzoomedValue(this.getX(),
-				zoom), Zoomer.getUnzoomedValue(this.getY(), zoom));
-		copy.pnName.setName(this.getName());
-		copy.nameOffsetX = this.nameOffsetX;
-		copy.nameOffsetY = this.nameOffsetY;
-		copy.angle = this.angle;
-		copy.attributesVisible = this.attributesVisible;
-		copy.priority = this.priority;
-		copy.setOriginal(this);
-		return copy;
-	}
-
 	@Override
 	public void paintComponent(Graphics g) {
 		super.paintComponent(g);
@@ -242,7 +142,7 @@
 	 * @return True if enabled
 	 */
 	public boolean isEnabled(boolean animationStatus) {
-		if (animationStatus == true) {
+		if (animationStatus) {
 			if (isEnabled()) {
 				highlighted = true;
 				return true;
@@ -254,15 +154,6 @@
 	}
 
 	/**
-	 * Determines whether Transition is enabled backwards
-	 * 
-	 * @return True if enabled
-	 */
-	// public boolean isEnabledBackwards(){
-	// return enabledBackwards;
-	// }
-
-	/**
 	 * Determines whether Transition is enabled
 	 * 
 	 * @return True if enabled
@@ -272,14 +163,6 @@
 		return enabled;
 	}
 
-	// public void setHighlighted(boolean status) {
-	// highlighted = status;
-	// }
-
-	public boolean isInfiniteServer() {
-		return infiniteServer;
-	}
-
 	/**
 	 * Sets whether Transition is enabled
 	 * 
@@ -287,20 +170,9 @@
 	 */
 	@Override
 	public void setEnabled(boolean status) {
-		if (enabled && !status) {
-		}
 		enabled = status;
 	}
 
-	/**
-	 * Sets whether Transition is enabled
-	 * 
-	 * @return enabled if True
-	 */
-	// public void setEnabledBackwards(boolean status){
-	// enabledBackwards = status;
-	// }
-
 	/* Called at the end of animation to reset Transitions to false */
 	public void setEnabledFalse() {
 		enabled = false;
@@ -311,10 +183,6 @@
 		return angle;
 	}
 
-	public int getPriority() {
-		return priority;
-	}
-
 	protected void constructTransition() {
 		transition = new GeneralPath();
 		transition.append(new Rectangle2D.Double(
@@ -366,12 +234,6 @@
 		}
 	}
 
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see
-	 * pipe.dataLayer.PlaceTransitionObject#updateEndPoint(pipe.dataLayer.Arc)
-	 */
 	@Override
 	public void updateEndPoint(Arc arc) {
 		boolean match = false;
@@ -379,7 +241,7 @@
 		Iterator<ArcAngleCompare> arcIterator = arcAngleList.iterator();
 		while (arcIterator.hasNext()) {
 			ArcAngleCompare thisArc = arcIterator.next();
-			if (thisArc.arc == arc || !arc.inView()) {
+			if (thisArc.arc == arc) {
 				thisArc.calcAngle();
 				match = true;
 				break;
@@ -459,12 +321,11 @@
 
 		arcIterator = left.iterator();
 		double inc = TRANSITION_HEIGHT / (left.size() + 1);
-		double current = TRANSITION_HEIGHT / 2 - inc;
+		double current = TRANSITION_HEIGHT / 2d - inc;
 		while (arcIterator.hasNext()) {
 			ArcAngleCompare thisArc = arcIterator.next();
 			transform.transform(new Point2D.Double(-0.5 * TRANSITION_WIDTH,
-					current + 1), transformed); // +1 due to rounding making it
-												// off by 1
+					current + 1), transformed); // +1 due to rounding making it off by 1
 			if (thisArc.sourceOrTarget()) {
 				thisArc.arc.setTargetLocation(positionX + centreOffsetLeft()
 						+ transformed.x, positionY + centreOffsetTop()
@@ -534,8 +395,8 @@
 
 	class ArcAngleCompare implements Comparable<ArcAngleCompare> {
 
-		private final static boolean SOURCE = false;
-		private final static boolean TARGET = true;
+		private static final boolean SOURCE = false;
+		private static final boolean TARGET = true;
 		private Arc arc;
 		private Transition transition;