[279740] API scrub

codan/org.eclipse.cdt.codan.checkers.ui/.project

@@ -20,9 +20,15 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>

codan/org.eclipse.cdt.codan.checkers.ui/META-INF/MANIFEST.MF

@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: Checkers Ui
 Bundle-SymbolicName: org.eclipse.cdt.codan.checkers.ui;singleton:=true
 Bundle-Version: 1.0.0
-Bundle-Activator: org.eclipse.cdt.codan.checkers.ui.CheckersUiActivator
+Bundle-Activator: org.eclipse.cdt.codan.internal.checkers.ui.CheckersUiActivator
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,
  org.eclipse.ui.ide;bundle-version="3.5.0",

codan/org.eclipse.cdt.codan.checkers.ui/build.properties

@@ -3,7 +3,3 @@ output.. = bin/
 bin.includes = META-INF/,\
                .,\
                plugin.xml
-src.includes = src/,\
-               plugin.xml,\
-               build.properties,\
-               META-INF/

codan/org.eclipse.cdt.codan.checkers.ui/src/org/eclipse/cdt/codan/internal/checkers/ui/CheckersUiActivator.java

@@ -1,4 +1,4 @@
-package org.eclipse.cdt.codan.checkers.ui;
+package org.eclipse.cdt.codan.internal.checkers.ui;
 
 import org.eclipse.ui.plugin.AbstractUIPlugin;
 import org.osgi.framework.BundleContext;

codan/org.eclipse.cdt.codan.checkers/.project

@@ -20,9 +20,15 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>

codan/org.eclipse.cdt.codan.checkers/build.properties

@@ -3,7 +3,3 @@ output.. = bin/
 bin.includes = META-INF/,\
                .,\
                plugin.xml
-src.includes = src/,\
-               plugin.xml,\
-               META-INF/,\
-               build.properties

codan/org.eclipse.cdt.codan.checkers/plugin.xml

@@ -3,74 +3,74 @@
 <plugin>
    <extension
          point="org.eclipse.cdt.codan.core.checkers"
-         id="org.eclipse.cdt.codan.core.checkers.sample">
+         id="org.eclipse.cdt.codan.core.examples.checkers">
 
       <checker
-            class="org.eclipse.cdt.codan.internal.checkers.sample.AssignmentInConditionChecker"
+            class="org.eclipse.cdt.codan.examples.checkers.AssignmentInConditionChecker"
-            id="org.eclipse.cdt.codan.checkers.sample.AssignmentInConditionChecker"
+            id="org.eclipse.cdt.codan.examples.checkers.AssignmentInConditionChecker"
             name="Assignment in condition">
       <problem
             defaultSeverity="Warning"
-            id="org.eclipse.cdt.codan.checkers.sample.AssignmentInConditionProblem"
+            id="org.eclipse.cdt.codan.examples.checkers.AssignmentInConditionProblem"
             name="Assignment in condition">
       </problem>
       
       
       </checker>
             <checker
-            class="org.eclipse.cdt.codan.internal.checkers.sample.StatementHasNoEffectChecker"
+            class="org.eclipse.cdt.codan.examples.checkers.StatementHasNoEffectChecker"
-            id="org.eclipse.cdt.codan.checkers.sample.StatementHasNoEffectChecker"
+            id="org.eclipse.cdt.codan.examples.checkers.StatementHasNoEffectChecker"
             name="StatementHasNoEffectChecker">
       <problem
             category="org.eclipse.cdt.codan.core.categories.ProgrammingProblems"
             defaultSeverity="Warning"
-            id="org.eclipse.cdt.codan.checkers.sample.StatementHasNoEffectProblem"
+            id="org.eclipse.cdt.codan.examples.checkers.StatementHasNoEffectProblem"
             name="Statement has no effect">
       </problem>
       </checker>
       
       <checker
-            class="org.eclipse.cdt.codan.internal.checkers.sample.NonVirtualDestructor"
+            class="org.eclipse.cdt.codan.examples.checkers.NonVirtualDestructor"
-            id="org.eclipse.cdt.codan.checkers.sample.NonVirtualDescructor"
+            id="org.eclipse.cdt.codan.examples.checkers.NonVirtualDescructor"
             name="NonVirtualDescructorChecker">
       <problem
             category="org.eclipse.cdt.codan.core.categories.ProgrammingProblems"
             defaultSeverity="Warning"
-            id="org.eclipse.cdt.codan.checkers.sample.NonVirtualDestructorProblem"
+            id="org.eclipse.cdt.codan.examples.checkers.NonVirtualDestructorProblem"
             name="Class has a virtual method and non-virtual destructor">
       </problem>
       </checker>
 
       <checker
-            class="org.eclipse.cdt.codan.internal.checkers.sample.CatchUsesReference"
+            class="org.eclipse.cdt.codan.examples.checkers.CatchUsesReference"
-            id="org.eclipse.cdt.codan.checkers.sample.CatchUsesReference"
+            id="org.eclipse.cdt.codan.examples.checkers.CatchUsesReference"
             name="CatchUsesReferenceChecker">
       <problem
             category="org.eclipse.cdt.codan.core.categories.ProgrammingProblems"
             defaultSeverity="Warning"
-            id="org.eclipse.cdt.codan.checkers.sample.CatchUsesReference"
+            id="org.eclipse.cdt.codan.examples.checkers.CatchUsesReference"
             name="Catch uses reference to exception">
       </problem>
       </checker>
       <checker
-            class="org.eclipse.cdt.codan.internal.checkers.sample.SuggestedParenthesisChecker"
+            class="org.eclipse.cdt.codan.examples.checkers.SuggestedParenthesisChecker"
-            id="org.eclipse.cdt.codan.checkers.sample.SuggestedParenthesisChecker"
+            id="org.eclipse.cdt.codan.examples.checkers.SuggestedParenthesisChecker"
             name="SuggestedParenthesisChecker">
       <problem
             category="org.eclipse.cdt.codan.core.categories.ProgrammingProblems"
             defaultSeverity="Warning"
-            id="org.eclipse.cdt.codan.checkers.sample.SuggestedParenthesisProblem"
+            id="org.eclipse.cdt.codan.examples.checkers.SuggestedParenthesisProblem"
             name="Suggested parenthesis around expression">
       </problem>
       </checker>
             <checker
-            class="org.eclipse.cdt.codan.internal.checkers.sample.NamingConventionFunctionChecker"
+            class="org.eclipse.cdt.codan.examples.checkers.NamingConventionFunctionChecker"
-            id="org.eclipse.cdt.codan.checkers.sample.NamingConventionFunctionChecker"
+            id="org.eclipse.cdt.codan.examples.checkers.NamingConventionFunctionChecker"
             name="NamingConventionFunctionChecker">
       <problem
             category="org.eclipse.cdt.codan.core.categories.CodeStyle"
             defaultSeverity="Warning"
-            id="org.eclipse.cdt.codan.checkers.sample.NamingConventionFunctionProblem"
+            id="org.eclipse.cdt.codan.examples.checkers.NamingConventionFunctionProblem"
             name="Name convention for function">
       </problem>
       </checker>

codan/org.eclipse.cdt.codan.checkers/src/org/eclipse/cdt/codan/examples/checkers/AssignmentInConditionChecker.java

@@ -8,7 +8,7 @@
  * Contributors:
  *    Alena Laskavaia  - initial API and implementation
  *******************************************************************************/
-package org.eclipse.cdt.codan.internal.checkers.sample;
+package org.eclipse.cdt.codan.examples.checkers;
 
 import org.eclipse.cdt.codan.core.model.AbstractIndexAstChecker;
 import org.eclipse.cdt.core.dom.ast.ASTNodeProperty;
@@ -20,7 +20,7 @@ import org.eclipse.cdt.core.dom.ast.IASTIfStatement;
 import org.eclipse.cdt.core.dom.ast.IASTTranslationUnit;
 
 public class AssignmentInConditionChecker extends AbstractIndexAstChecker {
-	private static final String ER_ID = "org.eclipse.cdt.codan.internal.checkers.sample.AssignmentInConditionProblem";
+	private static final String ER_ID = "org.eclipse.cdt.codan.examples.checkers.AssignmentInConditionProblem";
 
 	public void processAst(IASTTranslationUnit ast) {
 		// traverse the ast using the visitor pattern.

codan/org.eclipse.cdt.codan.checkers/src/org/eclipse/cdt/codan/examples/checkers/CatchUsesReference.java

@@ -9,7 +9,7 @@
  *    Alena Laskavaia  - initial API and implementation
  *******************************************************************************/ 
 
-package org.eclipse.cdt.codan.internal.checkers.sample;
+package org.eclipse.cdt.codan.examples.checkers;
 
 import org.eclipse.cdt.codan.core.model.AbstractIndexAstChecker;
 import org.eclipse.cdt.core.dom.ast.ASTVisitor;
@@ -28,7 +28,7 @@ import org.eclipse.cdt.core.dom.ast.cpp.ICPPASTTryBlockStatement;
  *
  */
 public class CatchUsesReference extends AbstractIndexAstChecker {
-	private static final String ER_ID = "org.eclipse.cdt.codan.internal.checkers.sample.CatchUsesReference";
+	private static final String ER_ID = "org.eclipse.cdt.codan.examples.checkers.CatchUsesReference";
 
 	public void processAst(IASTTranslationUnit ast) {
 		// traverse the ast using the visitor pattern.

codan/org.eclipse.cdt.codan.checkers/src/org/eclipse/cdt/codan/examples/checkers/NamingConventionFunctionChecker.java

@@ -8,7 +8,7 @@
  * Contributors:
  *    Alena Laskavaia  - initial API and implementation
  *******************************************************************************/
-package org.eclipse.cdt.codan.internal.checkers.sample;
+package org.eclipse.cdt.codan.examples.checkers;
 
 import java.util.regex.Pattern;
 import org.eclipse.cdt.codan.core.model.AbstractCIndexChecker;
@@ -27,8 +27,8 @@ import org.eclipse.core.runtime.CoreException;
  */
 public class NamingConventionFunctionChecker extends AbstractCIndexChecker
 		implements ICheckerWithParameters {
-	public static final String PARAM_KEY = "pattern";
+	public static final String PARAM_KEY = "pattern"; //$NON-NLS-1$
-	private static final String ER_ID = "org.eclipse.cdt.codan.internal.checkers.sample.NamingConventionFunctionProblem";
+	private static final String ER_ID = "org.eclipse.cdt.codan.examples.checkers.NamingConventionFunctionProblem"; //$NON-NLS-1$
 
 	/*
 	 * (non-Javadoc)

codan/org.eclipse.cdt.codan.checkers/src/org/eclipse/cdt/codan/examples/checkers/NonVirtualDestructor.java

@@ -8,7 +8,7 @@
  * Contributors:
  *    Alena Laskavaia  - initial API and implementation
  *******************************************************************************/
-package org.eclipse.cdt.codan.internal.checkers.sample;
+package org.eclipse.cdt.codan.examples.checkers;
 
 import java.text.MessageFormat;
 
@@ -33,7 +33,7 @@ import org.eclipse.cdt.internal.core.dom.parser.cpp.ICPPInternalBinding;
  * 
  */
 public class NonVirtualDestructor extends AbstractIndexAstChecker {
-	private static final String ER_ID = "org.eclipse.cdt.codan.internal.checkers.sample.NonVirtualDestructorProblem";
+	private static final String ER_ID = "org.eclipse.cdt.codan.examples.checkers.NonVirtualDestructorProblem";
 
 	public void processAst(IASTTranslationUnit ast) {
 		// traverse the ast using the visitor pattern.

codan/org.eclipse.cdt.codan.checkers/src/org/eclipse/cdt/codan/examples/checkers/StatementHasNoEffectChecker.java

@@ -8,7 +8,7 @@
  * Contributors:
  *    Alena Laskavaia  - initial API and implementation
  *******************************************************************************/
-package org.eclipse.cdt.codan.internal.checkers.sample;
+package org.eclipse.cdt.codan.examples.checkers;
 
 import org.eclipse.cdt.codan.core.model.AbstractIndexAstChecker;
 import org.eclipse.cdt.core.dom.ast.ASTVisitor;
@@ -36,7 +36,7 @@ import org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTBinaryExpression;
  * 
  */
 public class StatementHasNoEffectChecker extends AbstractIndexAstChecker {
-	private static final String ER_ID = "org.eclipse.cdt.codan.internal.checkers.sample.StatementHasNoEffectProblem";
+	private static final String ER_ID = "org.eclipse.cdt.codan.examples.checkers.StatementHasNoEffectProblem";
 
 	public void processAst(IASTTranslationUnit ast) {
 		// traverse the ast using the visitor pattern.

codan/org.eclipse.cdt.codan.checkers/src/org/eclipse/cdt/codan/examples/checkers/SuggestedParenthesisChecker.java

@@ -8,7 +8,7 @@
  * Contributors:
  *    Alena Laskavaia  - initial API and implementation
  *******************************************************************************/
-package org.eclipse.cdt.codan.internal.checkers.sample;
+package org.eclipse.cdt.codan.examples.checkers;
 
 import org.eclipse.cdt.codan.core.model.AbstractIndexAstChecker;
 import org.eclipse.cdt.core.dom.ast.ASTNodeProperty;
@@ -29,7 +29,7 @@ import org.eclipse.cdt.core.dom.ast.IASTUnaryExpression;
  * 
  */
 public class SuggestedParenthesisChecker extends AbstractIndexAstChecker {
-	private static final String ER_ID = "org.eclipse.cdt.codan.internal.checkers.sample.SuggestedParenthesisProblem";
+	private static final String ER_ID = "org.eclipse.cdt.codan.examples.checkers.SuggestedParenthesisProblem";
 
 	public void processAst(IASTTranslationUnit ast) {
 		// traverse the ast using the visitor pattern.

codan/org.eclipse.cdt.codan.core.test/build.properties

@@ -3,3 +3,4 @@ output.. = bin/
 bin.includes = META-INF/,\
                .,\
                src/org/eclipse/cdt/codan/core/checkers/
+jre.compilation.profile = J2SE-1.5

codan/org.eclipse.cdt.codan.core/.project

@@ -20,9 +20,15 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>

codan/org.eclipse.cdt.codan.core/build.properties

@@ -4,8 +4,4 @@ bin.includes = META-INF/,\
                .,\
                plugin.xml,\
                schema/
-src.includes = src/,\
+src.includes = schema/
-               schema/,\
-               plugin.xml,\
-               build.properties,\
-               META-INF/

codan/org.eclipse.cdt.codan.core/plugin.xml

@@ -65,7 +65,7 @@
                thread="main"
               visible="true">
            <run
-                 class="org.eclipse.cdt.codan.core.CodanApplication">
+                 class="org.eclipse.cdt.codan.internal.core.CodanApplication">
            </run>
         </application>
      </extension>

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/CodanCorePlugin.java

@@ -13,7 +13,7 @@ import org.osgi.framework.BundleContext;
  */
 public class CodanCorePlugin extends Plugin {
 	// The plug-in ID
-	public static final String PLUGIN_ID = "org.eclipse.cdt.codan.core";
+	public static final String PLUGIN_ID = "org.eclipse.cdt.codan.core"; //$NON-NLS-1$
 	public static final String NATURE_ID = CodeAnlysisNature.NATURE_ID;
 	// The shared instance
 	private static CodanCorePlugin plugin;
@@ -34,6 +34,7 @@ public class CodanCorePlugin extends Plugin {
 	 * @see
 	 * org.eclipse.core.runtime.Plugins#start(org.osgi.framework.BundleContext)
 	 */
+	@Override
 	public void start(BundleContext context) throws Exception {
 		super.start(context);
 		plugin = this;
@@ -45,6 +46,7 @@ public class CodanCorePlugin extends Plugin {
 	 * @see
 	 * org.eclipse.core.runtime.Plugin#stop(org.osgi.framework.BundleContext)
 	 */
+	@Override
 	public void stop(BundleContext context) throws Exception {
 		plugin = null;
 		super.stop(context);

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/CodanRuntime.java

@@ -13,42 +13,94 @@ package org.eclipse.cdt.codan.core;
 import org.eclipse.cdt.codan.core.model.ICheckersRegistry;
 import org.eclipse.cdt.codan.core.model.ICodanAstReconciler;
 import org.eclipse.cdt.codan.core.model.ICodanBuilder;
+import org.eclipse.cdt.codan.core.model.IProblemLocationFactory;
 import org.eclipse.cdt.codan.core.model.IProblemReporter;
 import org.eclipse.cdt.codan.internal.core.CheckersRegisry;
 import org.eclipse.cdt.codan.internal.core.CodanBuilder;
 import org.eclipse.cdt.codan.internal.core.model.CodanMarkerProblemReporter;
+import org.eclipse.cdt.codan.internal.core.model.ProblemLocationFactory;
 
 /**
  * Runtime singleton class to get access to Codan framework parts
  * 
+ * Clients may extend this class to override default framework parts.
  */
 public class CodanRuntime {
 	private static CodanRuntime instance = new CodanRuntime();
 	private IProblemReporter problemReporter = new CodanMarkerProblemReporter();
 	private CodanBuilder builder = new CodanBuilder();
 	private CheckersRegisry checkers = CheckersRegisry.getInstance();
+	private IProblemLocationFactory locFactory = new ProblemLocationFactory();
 
+	/**
+	 * CodanRuntime - only can be called by subclasses to override default constructor
+	 */
+	protected CodanRuntime() {
+		// nothing here
+	}
+
+	/**
+	 * Get runtime problem reporter. Default reported generated problem markers.
+	 * @return
+	 */
 	public IProblemReporter getProblemReporter() {
 		return problemReporter;
 	}
 
+	/**
+	 * Set different problem reporter.
+	 * @param reporter
+	 */
 	public void setProblemReporter(IProblemReporter reporter) {
 		problemReporter = reporter;
 	}
 
+	/**
+	 * Get instance of of Codan Runtime
+	 * @return
+	 */
 	public static CodanRuntime getInstance() {
 		return instance;
 	}
 
+	/**
+	 * Get builder. Builder can used to run code analysis on given resource using API.
+	 * @return
+	 */
 	public ICodanBuilder getBuilder() {
 		return builder;
 	}
 
+	/**
+	 * Get quick builder. Can be used to run code analysis on given ast.
+	 * @return
+	 */
 	public ICodanAstReconciler getAstQuickBuilder() {
 		return builder;
 	}
 
+	/**
+	 * Get checkers registry. 
+	 * @return
+	 */
 	public ICheckersRegistry getChechersRegistry() {
 		return checkers;
 	}
+
+	/**
+	 * Get problem location factory.
+	 * @return
+	 */
+	public IProblemLocationFactory getProblemLocationFactory() {
+		return locFactory;
+	}
+
+	/**
+	 * Set another problem location factory - only need if default is not sufficient, i.e
+	 * IProblemLocation is implemented differently
+	 * @param factory
+	 */
+	public void setProblemLocationFactory(IProblemLocationFactory factory) {
+		locFactory = factory;
+	}
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/PreferenceConstants.java

@@ -14,7 +14,7 @@ package org.eclipse.cdt.codan.core;
  * Constant definitions for plug-in preferences
  */
 public class PreferenceConstants {
-	public static final String P_RUN_ON_BUILD = "booleanPreference";
+	public static final String P_RUN_ON_BUILD = "booleanPreference"; //$NON-NLS-1$
-	public static final String P_PROBLEMS = "problems";
+	public static final String P_PROBLEMS = "problems"; //$NON-NLS-1$
-	public static final String P_USE_PARENT = "useParentScope";
+	public static final String P_USE_PARENT = "useParentScope"; //$NON-NLS-1$
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/AbstractCIndexChecker.java

@@ -21,11 +21,11 @@ import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.CoreException;
 
 /**
- * Checker that works with C-Index of a file (but not AST)
+ * Implementation of IChecker that works with C-Index of a file (but not AST)
  * 
+ * Clients may extend this class.
  */
-public abstract class AbstractCIndexChecker extends AbstractChecker implements
+public abstract class AbstractCIndexChecker extends AbstractChecker implements ICIndexChecker {
-		ICIndexChecker {
 	private IFile file;
 	protected IIndex index;
 
@@ -36,11 +36,8 @@ public abstract class AbstractCIndexChecker extends AbstractChecker implements
 	void processFile(IFile file) throws CoreException, InterruptedException {
 		// create translation unit and access index
 		ICElement model = CoreModel.getDefault().create(file);
-		if (!(model instanceof ITranslationUnit))
+		if (!(model instanceof ITranslationUnit)) return; // not a C/C++ file
-			return;
 		ITranslationUnit tu = (ITranslationUnit) model;
-		if (tu == null)
-			return; // not a C/C++ file
 		index = CCorePlugin.getIndexManager().getIndex(tu.getCProject());
 		// lock the index for read access
 		index.acquireReadLock();

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/AbstractChecker.java

@@ -15,6 +15,12 @@ import org.eclipse.cdt.codan.internal.core.CheckersRegisry;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IResource;
 
+/**
+ * Convenience implementation of IChecker interface.
+ * Has a default implementation for common methods.
+ *
+ * Clients may extend this class.
+ */
 public abstract class AbstractChecker implements IChecker {
 	protected String name;
 
@@ -44,15 +50,18 @@ public abstract class AbstractChecker implements IChecker {
 	 *            internationalization)
 	 */
 	public void reportProblem(String id, IFile file, int lineNumber, String arg) {
-		getProblemReporter().reportProblem(id,
+		getProblemReporter().reportProblem(id, createProblemLocation(file, lineNumber), arg);
-				new ProblemLocation(file, lineNumber), arg);
 	}
 
+	/**
+	 * Finds an instance of problem by given id, in user profile registered for specific file
+	 * @param id - problem id
+	 * @param file - file in scope
+	 * @return problem instance
+	 */
 	public IProblem getProblemById(String id, IFile file) {
-		IProblem problem = CheckersRegisry.getInstance().getResourceProfile(
+		IProblem problem = CheckersRegisry.getInstance().getResourceProfile(file).findProblem(id);
-				file).findProblem(id);
+		if (problem == null) throw new IllegalArgumentException("Id is not registered"); //$NON-NLS-1$
-		if (problem == null)
-			throw new IllegalArgumentException("Id is not registered");
 		return problem;
 	}
 
@@ -68,8 +77,7 @@ public abstract class AbstractChecker implements IChecker {
 	 *            - line
 	 */
 	public void reportProblem(String id, IFile file, int lineNumber) {
-		getProblemReporter().reportProblem(id,
+		getProblemReporter().reportProblem(id, createProblemLocation(file, lineNumber), new Object[] {});
-				new ProblemLocation(file, lineNumber), new Object[] {});
 	}
 
 	/**
@@ -79,6 +87,35 @@ public abstract class AbstractChecker implements IChecker {
 		return CodanRuntime.getInstance().getProblemReporter();
 	}
 
+	/**
+	 * Convenience method to return codan runtime
+	 * @return
+	 */
+	protected CodanRuntime getRuntime() {
+		return CodanRuntime.getInstance();
+	}
+
+	/**
+	 * Convenience method to create and return instance of IProblemLocation
+	 * @param file - file where problem is found
+	 * @param line - line number 1-relative
+	 * @return instance of IProblemLocation
+	 */
+	protected IProblemLocation createProblemLocation(IFile file, int line) {
+		return getRuntime().getProblemLocationFactory().createProblemLocation(file, line);
+	}
+
+	/**
+	 * Convenience method to create and return instance of IProblemLocation
+	 * @param file - file where problem is found
+	 * @param startChar - start char of the problem in the file, is zero-relative
+	 * @param endChar - end char of the problem in the file, is zero-relative and exclusive.
+	 * @return instance of IProblemLocation
+	 */
+	protected IProblemLocation createProblemLocation(IFile file, int startChar, int endChar) {
+		return getRuntime().getProblemLocationFactory().createProblemLocation(file, startChar, endChar);
+	}
+
 	public boolean runInEditor() {
 		return false;
 	}

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/AbstractIndexAstChecker.java

@@ -27,11 +27,11 @@ import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.Path;
 
 /**
- * @author Alena
+ * Convenience implementation of checker that work on index based ast of a c/c++ program.
  * 
+ * Clients may extend this class.
  */
-public abstract class AbstractIndexAstChecker extends AbstractChecker implements
+public abstract class AbstractIndexAstChecker extends AbstractChecker implements ICAstChecker {
-		ICAstChecker {
 	private IFile file;
 
 	protected IFile getFile() {
@@ -41,18 +41,14 @@ public abstract class AbstractIndexAstChecker extends AbstractChecker implements
 	void processFile(IFile file) throws CoreException, InterruptedException {
 		// create translation unit and access index
 		ICElement model = CoreModel.getDefault().create(file);
-		if (!(model instanceof ITranslationUnit))
+		if (!(model instanceof ITranslationUnit)) return; // not a C/C++ file
-			return;
 		ITranslationUnit tu = (ITranslationUnit) model;
-		if (tu == null)
-			return; // not a C/C++ file
 		IIndex index = CCorePlugin.getIndexManager().getIndex(tu.getCProject());
 		// lock the index for read access
 		index.acquireReadLock();
 		try {
 			// create index based ast
-			IASTTranslationUnit ast = tu.getAST(index,
+			IASTTranslationUnit ast = tu.getAST(index, ITranslationUnit.AST_SKIP_INDEXED_HEADERS);
-					ITranslationUnit.AST_SKIP_INDEXED_HEADERS);
 			// traverse the ast using the visitor pattern.
 			this.file = file;
 			processAst(ast);
@@ -80,19 +76,16 @@ public abstract class AbstractIndexAstChecker extends AbstractChecker implements
 	public void reportProblem(String id, IASTNode astNode, String message) {
 		IASTFileLocation astLocation = astNode.getFileLocation();
 		IPath location = new Path(astLocation.getFileName());
-		IFile astFile = ResourcesPlugin.getWorkspace().getRoot()
+		IFile astFile = ResourcesPlugin.getWorkspace().getRoot().getFileForLocation(location);
-				.getFileForLocation(location);
 		if (astFile == null) {
 			astFile = file;
 		}
-		ProblemLocation loc;
+		IProblemLocation loc;
-		if (astLocation.getStartingLineNumber() == astLocation
+		if (astLocation.getStartingLineNumber() == astLocation.getEndingLineNumber()) loc = getRuntime()
-				.getEndingLineNumber())
+				.getProblemLocationFactory().createProblemLocation(astFile, astLocation.getNodeOffset(),
-			loc = new ProblemLocation(astFile, astLocation.getNodeOffset(),
+						astLocation.getNodeOffset() + astLocation.getNodeLength());
-					astLocation.getNodeOffset() + astLocation.getNodeLength());
+		else loc = getRuntime().getProblemLocationFactory().createProblemLocation(astFile,
-		else
+				astLocation.getStartingLineNumber());
-			loc = new ProblemLocation(astFile, astLocation
-					.getStartingLineNumber());
 		getProblemReporter().reportProblem(id, loc, message);
 	}
 

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/CodanSeverity.java

@@ -12,9 +12,17 @@ package org.eclipse.cdt.codan.core.model;
 
 import org.eclipse.core.resources.IMarker;
 
+/**
+ * 
+ * Represents Severity of the codan problem. It is directly mapped to markers severity,
+ * therefore not intended to be extended.
+ * 
+ * @noextend This class is not intended to be extended by clients.
+ * @noinstantiate This class is not intended to be instantiated by clients.
+ *
+ */
 public enum CodanSeverity {
-	Info(IMarker.SEVERITY_INFO), Warning(IMarker.SEVERITY_WARNING), Error(
+	Info(IMarker.SEVERITY_INFO), Warning(IMarker.SEVERITY_WARNING), Error(IMarker.SEVERITY_ERROR);
-			IMarker.SEVERITY_ERROR);
 	private int value;
 
 	private CodanSeverity(int value) {
@@ -26,7 +34,7 @@ public enum CodanSeverity {
 	}
 
 	/**
-	 * @return
+	 * @return array of string value for all severities
 	 */
 	public static String[] stringValues() {
 		CodanSeverity[] values = values();

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ICAstChecker.java

@@ -13,9 +13,16 @@ package org.eclipse.cdt.codan.core.model;
 import org.eclipse.cdt.core.dom.ast.IASTTranslationUnit;
 
 /**
- * @author Alena
+ * Checker that can/want to process C/C++ AST (Abstract Syntax Tree) of a program
+ * Default implementation {@link AbstractIndexAstChecker}
  * 
+ * Clients may implement and extend this interface.
  */
 public interface ICAstChecker extends IChecker {
+	/**
+	 * Run this checker on a given ast.
+	 * Ast locks would be obtained by the framework before calling this method. 
+	 * @param ast 
+	 */
 	void processAst(IASTTranslationUnit ast);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ICIndexChecker.java

@@ -13,9 +13,15 @@ package org.eclipse.cdt.codan.core.model;
 import org.eclipse.cdt.core.model.ITranslationUnit;
 
 /**
- * @author Alena
+ * Extension of IChecker that works with C-Index of a file (but not AST)
+ * Default implementation {@link AbstractCIndexChecker}
  * 
+ * Client may implement this interface.
  */
 public interface ICIndexChecker extends IChecker {
+	/**
+	 * Run checker on translation unit
+	 * @param unit - translation unit
+	 */
 	void processUnit(ITranslationUnit unit);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IChecker.java

@@ -14,6 +14,8 @@ import org.eclipse.core.resources.IResource;
 
 /**
  * Interface that checker must implement. CDT Checker must be able to process a resource.
+ * 
+ * Clients may implement and extend this interface.
  */
 public interface IChecker {
 	/**
@@ -26,7 +28,7 @@ public interface IChecker {
 	/**
 	 * Implement this method to trim down type of resource you are interested in,
 	 * usually it will be c/c++ files only
-	 * @param resource
+	 * @param resource - resource to run on
 	 * @return
 	 */
 	boolean enabledInContext(IResource resource);

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ICheckerWithParameters.java

@@ -11,9 +11,15 @@
 package org.eclipse.cdt.codan.core.model;
 
 /**
- * @author Alena
+ * Interface for checker with parameters, if checker implements this
+ * interface method would be called on initialization so checker has
+ * a chance to set default values for its parameters
  * 
  */
 public interface ICheckerWithParameters {
+	/**
+	 * Implement this method to set default parameters for checkers with parameters. 
+	 * @param problem - instance of problem working copy
+	 */
 	void initParameters(IProblemWorkingCopy problem);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ICheckersRegistry.java

@@ -15,52 +15,82 @@ import java.util.Iterator;
 import org.eclipse.core.resources.IResource;
 
 /**
- * @author Alena
+ * This interface an API to add/remove checker and problems programmatically,
+ * get problem profiles and change problem default settings
  * 
  */
-public interface ICheckersRegistry {
+public interface ICheckersRegistry extends Iterable<IChecker> {
+	/**
+	 * Iterator for registered checkers
+	 * @return
+	 */
 	public abstract Iterator<IChecker> iterator();
 
+	/**
+	 * Add another checker
+	 * @param checker
+	 */
 	public abstract void addChecker(IChecker checker);
 
-	public abstract void addProblem(IProblem p, String category);
+	/**
+	 * Add problem p with default category by category id into default profile, category must exists in default profile
+	 * @param p - problem
+	 * @param categoryId - category id
+	 */
+	public abstract void addProblem(IProblem p, String categoryId);
 
-	public abstract void addCategory(IProblemCategory p, String category);
+	/**
+	 * Add subcategory with id categoryId into parent category, 
+	 * if parent does not exist in default, profile - if not will be added to the root
+	 * @param category - new category
+	 * @param parentCategoryId - parent category id
+	 */
+	public abstract void addCategory(IProblemCategory category, String parentCategoryId);
 
+	/**
+	 * Add problem reference to a checker, i.e. claim that checker can produce this problem.
+	 * If checker does not claim any problems it cannot be enabled.
+	 * @param c - checker
+	 * @param p - problem
+	 */
 	public abstract void addRefProblem(IChecker c, IProblem p);
 
 	/**
+	 * Get default profile, default profile is kind of "Installation Default". Always the same, comes from default in checker extensions
 	 * @return
 	 */
 	public abstract IProblemProfile getDefaultProfile();
 
 	/**
-	 * @return
+	 * Get workspace profile. User can change setting for workspace profile.
+	 * @return profile
 	 */
 	public abstract IProblemProfile getWorkspaceProfile();
 
 	/**
-	 * @param element
+	 * Get resource profile. For example given directory can have different profile
-	 * @return
+	 * than parent project.
+	 * 
+	 * @param element - resource
+	 * @return profile
 	 */
 	public abstract IProblemProfile getResourceProfile(IResource element);
 
 	/**
+	 * Returns profile working copy for given resource element. (If profile is not
+	 * specified for given element it will search for parent resource and so on).
 	 * @param element
 	 * @return
 	 */
-	public abstract IProblemProfile getResourceProfileWorkingCopy(
+	public abstract IProblemProfile getResourceProfileWorkingCopy(IResource element);
-			IResource element);
 
 	/**
-	 * Set profile for resource. This method is called by UI, and should not be
+	 * Set profile for resource. 
-	 * called by clients directly
+	 * @noreference This method is not intended to be referenced by clients.
-	 * 
 	 * @param resource
 	 *            - resource
 	 * @param profile
 	 *            - problems profile
 	 */
-	public abstract void updateProfile(IResource resource,
+	public abstract void updateProfile(IResource resource, IProblemProfile profile);
-			IProblemProfile profile);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ICodanAstReconciler.java

@@ -14,9 +14,17 @@ import org.eclipse.cdt.core.dom.ast.IASTTranslationUnit;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 /**
- * @author Alena
+ * Allows to run all checkers that can run on ast via editing using API
+ * 
+ * @noextend This interface is not intended to be extended by clients.
+ * @noimplement This interface is not intended to be implemented by clients.
  * 
  */
 public interface ICodanAstReconciler {
+	/**
+	 * Run code analysis on ast
+	 * @param ast - ast to be reconciled 
+	 * @param monitor - progress monitor
+	 */
 	public void reconcileAst(IASTTranslationUnit ast, IProgressMonitor monitor);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ICodanBuilder.java

@@ -14,9 +14,19 @@ import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 /**
- * @author Alena
+ * Interface for "Codan Builder". Clients can cann processResource method to
+ * traverse the resource tree, calling all the checker (this interface allows
+ * to call framework without using UI). You can obtain instance of this
+ * class as CodanRuntime.getInstance().getBuilder()
  * 
+ * @noextend This interface is not intended to be extended by clients.
+ * @noimplement This interface is not intended to be implemented by clients.
  */
 public interface ICodanBuilder {
+	/**
+	 * Run code analysis on given resource
+	 * @param resource - resource to process
+	 * @param monitor - progress monitor
+	 */
 	public void processResource(IResource resource, IProgressMonitor monitor);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblem.java

@@ -10,9 +10,14 @@
  *******************************************************************************/
 package org.eclipse.cdt.codan.core.model;
 
-
 /**
- * Interface representing code analysis problem
+ * Interface representing code analysis problem type. For example "Null Pointer Dereference"
+ * is a problem. It has user visible Name and Message (translatable), as well as some other
+ * parameters, changeable by user such as enablement, severity and so on. Same problem
+ * cannot have two severities determined by runtime. If it is the case - two Problem should
+ * be created (i.e. one for error and one for warning).
+ *   
+ * Clients may implement and extend this interface.
  * 
  */
 public interface IProblem extends IProblemElement {
@@ -53,8 +58,9 @@ public interface IProblem extends IProblemElement {
 	public Object getParameter(Object key);
 
 	/**
-	 * Get root paramterInfo - contains description of types of all the
+	 * Get parameter info root - contains description of types of all the
-	 * parameters or null if not defined
+	 * parameters or null if not defined (used by ui to generate user controls
+	 * for changing parameters)
 	 * 
 	 * @return
 	 */

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemCategory.java

@@ -11,8 +11,9 @@
 package org.eclipse.cdt.codan.core.model;
 
 /**
- * Problem category
+ * Problem category.
- *
+ * 
+ * Clients may extend and implement this interface.
  */
 public interface IProblemCategory extends IProblemElement {
 	/**
@@ -32,17 +33,4 @@ public interface IProblemCategory extends IProblemElement {
 	 */
 	IProblemElement[] getChildren();
 
-	/**
-	 * Find problem by id within children recursively
-	 * @param id
-	 * @return
-	 */
-	IProblem findProblem(String id);
-
-	/**
-	 * Find category by id within children recursively
-	 * @param id
-	 * @return
-	 */
-	IProblemCategory findCategory(String id);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemElement.java

@@ -11,9 +11,17 @@
 package org.eclipse.cdt.codan.core.model;
 
 /**
- * Problem category or problem 
+ * Problem category {@link IProblemCategory} or problem {@link IProblem} 
  * 
+ * @noextend This interface is not intended to be extended by clients.
+ * @noimplement This interface is not intended to be implemented by clients.
  */
 public interface IProblemElement extends Cloneable {
+	/**
+	 * clone method should be implemented to support problem cloning
+	 * @see {@link Object#clone}
+	 * @return new object which is copy of this one
+	 * @throws CloneNotSupportedException - it is declared with this exception but it should NOT throw it
+	 */
 	Object clone() throws CloneNotSupportedException;
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemLocation.java

@@ -16,6 +16,8 @@ import org.eclipse.core.resources.IFile;
  * Interface to describe problem location. Usually contains file and linenumber,
  * also supports character positions for sophisticated errors.
  * 
+ * @noextend This interface is not intended to be extended by clients.
+ * @noimplement This interface is not intended to be implemented by clients.
  */
 public interface IProblemLocation {
 	/**

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemLocationFactory.java

@@ -0,0 +1,39 @@
+/*******************************************************************************
+ * Copyright (c) 2009 Alena Laskavaia 
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *    Alena Laskavaia  - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.cdt.codan.core.model;
+
+import org.eclipse.core.resources.IFile;
+
+/**
+ * Factory interface that allows to create problem locations.
+ *
+ * Clients may implement and extend this interface.
+ */
+public interface IProblemLocationFactory {
+
+	/**
+	 * Create and return instance of IProblemLocation
+	 * @param file - file where problem is found
+	 * @param line - line number where problem is found, starts with 1
+	 * @return instance of IProblemLocation
+	 */
+	public IProblemLocation createProblemLocation(IFile file, int line);
+
+	/**
+	 * Create and return instance of IProblemLocation
+	 * @param file - file where problem is found
+	 * @param startChar - start char of the problem in the file, is zero-relative
+	 * @param endChar - end char of the problem in the file, is zero-relative and exclusive.
+	 * @return instance of IProblemLocation
+	 */
+	public IProblemLocation createProblemLocation(IFile file, int startChar, int endChar);
+
+}

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemParameterInfo.java

@@ -11,15 +11,15 @@
 package org.eclipse.cdt.codan.core.model;
 
 /**
- * Problem parameter usually key=value settings that allow to alter checker
+ * Problem parameter usually key=value settings that allows to alter checker
  * behaviour for given problem. For example if checker finds violation of naming
  * conventions for function, parameter would be the pattern of allowed names.
  * ProblemParameterInfo represent parameter meta-info for the ui.
  * If more that one parameter required ParameterInfo should describe hash or array of parameters.
  * This is only needed for auto-generated ui for parameter editing. For complex case custom ui control should be used
  * 
- * @author Alena
+ * @noextend This interface is not intended to be extended by clients.
- * 
+ * @noimplement This interface is not intended to be implemented by clients.
  */
 public interface IProblemParameterInfo {
 	String getKey();
@@ -42,13 +42,14 @@ public interface IProblemParameterInfo {
 	String getUiInfo();
 
 	/**
-	 * User visible label for the control in UI
+	 * User visible label for the parameter control in UI
+	 * @return the label
 	 */
 	String getLabel();
 
 	/**
 	 * Available if type is list or hash. Returns value of subparamer with the
-	 * name of key. For the "list" key must be "#".
+	 * name of key. For the "list" type key is the number (index).
 	 * 
 	 * @param key
 	 *            - name of the subparameter.

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemProfile.java

@@ -11,15 +11,21 @@
 package org.eclipse.cdt.codan.core.model;
 
 /**
- * Problem Profile contains tree of categories and problems. For user profile is quick way
+ * Problem Profile contains tree of categories and problems. For the user 
- * to switch between problems sets depends on task he is doing (i.e. find real bugs, vs doing code style report)
+ * the profile is quick way to switch between problem sets depending on the 
- * User can set different profiles in different projects. 
+ * task he is doing (i.e. find real bugs, vs doing code style report)
- * Profiles can have different categories and different problems set, problems with the same id
+ * User can set different profiles for different projects. 
- * can have different severities/enablement in different profiles. To obtain
+ * Profiles can have different categories and different problem sets, 
- * profile use class {@link CheckersRegisry#getResourceProfile,
+ * problems with the same id can have different severities/enablement in different profiles.
+ * Category tree can have few reference to a same problem, but only instance of Problem
+ * with the same id can exist in the same profile (i.e. two category can have same problem listed in both, 
+ * but they both should point to the same problem instance). 
+ *  
+ * To obtain read-only profile use method {@link CheckersRegisry#getResourceProfile,
  * CheckersRegisry#getDefaultProfile() or CheckersRegisry#getWorkspaceProfile()}
- * .
  * 
+ * @noextend This interface is not intended to be extended by clients.
+ * @noimplement This interface is not intended to be implemented by clients.
  */
 public interface IProblemProfile extends IProblemElement {
 	/**
@@ -28,7 +34,7 @@ public interface IProblemProfile extends IProblemElement {
 	IProblemCategory getRoot();
 
 	/**
-	 * Find and return problem by id
+	 * Find and return problem by id if it contained in this profile
 	 * 
 	 * @param id
 	 *            - problem id
@@ -37,7 +43,7 @@ public interface IProblemProfile extends IProblemElement {
 	IProblem findProblem(String id);
 
 	/**
-	 * Find and return category by id
+	 * Find and return category by id if it is contained in this profile
 	 * 
 	 * @param id
 	 *            - category id
@@ -46,7 +52,7 @@ public interface IProblemProfile extends IProblemElement {
 	IProblemCategory findCategory(String id);
 
 	/**
-	 * Get all defined problems
+	 * Get all problems defined in this profile (if problem duplicated in a category tree, it returns only one instance of each)
 	 * 
 	 * @return array of problems defined in profile
 	 */

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemReporter.java

@@ -10,20 +10,20 @@
  *******************************************************************************/
 package org.eclipse.cdt.codan.core.model;
 
-
 /**
  * IProblemReporter - interface to report problems
- *
+ * 
+ * Clients may implement and extend this interface
  */
 public interface IProblemReporter {
-	public static final String GENERIC_CODE_ANALYSIS_MARKER_TYPE = "org.eclipse.cdt.codan.core.codanProblem";
+	public static final String GENERIC_CODE_ANALYSIS_MARKER_TYPE = "org.eclipse.cdt.codan.core.codanProblem"; //$NON-NLS-1$
+
 	/**
-	 * Report a problem with "problemId" id on location determined by "loc", 
+	 * Report a problem with "problemId" id on the location determined by "loc", 
-	 * using problem specific error message customised by args.
+	 * using problem specific error message customized by args.
-	 * @param problemId - id of the problem registers with checker
+	 * @param problemId - id of the problem registered with a checker
 	 * @param loc - location object
-	 * @param args - custom args, can be null, in this case default message is reported
+	 * @param args - custom arguments, can be null, in this case default message is reported
 	 */
-	public void reportProblem(String problemId,  IProblemLocation loc,
+	public void reportProblem(String problemId, IProblemLocation loc, Object... args);
-			Object ... args);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/IProblemWorkingCopy.java

@@ -10,22 +10,43 @@
  *******************************************************************************/
 package org.eclipse.cdt.codan.core.model;
 
-
 /**
  * Modifiable problem
- * @author Alena
  * 
+ * Clients may extend and implement this interface
  */
 public interface IProblemWorkingCopy extends IProblem {
+	/**
+	 * Set severity for this this problem instance. Severity can only be changed in profile
+	 * not by checker when printing problems.
+	 * @param sev - codan severity
+	 */
 	void setSeverity(CodanSeverity sev);
 
-	void setEnabled(boolean checked);
+	/**
+	 * Set checker enablement.
+	 * @param enabled - true if problem is enabled in profile
+	 */
+	void setEnabled(boolean enabled);
 
-	void setMessagePattern(String message);
+	/**
+	 * Set default message pattern. UI would call this method if user does not like default
+	 * settings, checker should not use method, default message pattern should be set in 
+	 * checker extension
+	 * @param messagePattern - java style message patter i.e. "Variable {0} is never used"
+	 */
+	void setMessagePattern(String messagePattern);
 
+	/**
+	 * Set value for the checker parameter, checker may set value during initialization only
+	 * @param key - key of the parameter
+	 * @param value - parameter value
+	 */
 	public void setParameter(Object key, Object value);
 
-	public IProblemCategory getCategory();
+	/**
-
+	 * Set parameter info object for the given problem, see {@link IProblemParameterInfo}
+	 * @param info
+	 */
 	public void setParameterInfo(IProblemParameterInfo info);
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/core/model/ProblemLocation.java

@@ -13,36 +13,25 @@ package org.eclipse.cdt.codan.core.model;
 import org.eclipse.core.resources.IFile;
 
 /**
- * Implementation of IProblemLocation
+ * Abstract Implementation of IProblemLocation
  * 
+ * Clients may extend this class.
  */
-public class ProblemLocation implements IProblemLocation {
+public abstract class ProblemLocation implements IProblemLocation {
 	protected IFile file;
 	protected int line;
 	protected int posStart;
 	protected int posEnd;
 	protected Object extra;
 
-	/**
+	protected ProblemLocation(IFile file, int line) {
-	 * @param file
-	 * @param line
-	 * @param lineEnd
-	 * @param posStart
-	 * @param posEnd
-	 */
-	public ProblemLocation(IFile file, int line) {
 		this.file = file;
 		this.line = line;
 		this.posStart = -1;
 		this.posEnd = -1;
 	}
 
-	/**
+	protected ProblemLocation(IFile file, int startChar, int endChar) {
-	 * @param file
-	 * @param startingLineNumber
-	 * @param endingLineNumber
-	 */
-	public ProblemLocation(IFile file, int startChar, int endChar) {
 		this.file = file;
 		this.line = -1;
 		this.posStart = startChar;

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/CheckersRegisry.java

@@ -38,11 +38,13 @@ import org.eclipse.core.runtime.Platform;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 
 public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
-	private static final String EXTENSION_POINT_NAME = "checkers";
+	private static final String NAME_ATTR = "name"; //$NON-NLS-1$
-	private static final String CHECKER_ELEMENT = "checker";
+	private static final String ID_ATTR = "id"; //$NON-NLS-1$
-	private static final String PROBLEM_ELEMENT = "problem";
+	private static final String EXTENSION_POINT_NAME = "checkers"; //$NON-NLS-1$
-	private static final String CATEGORY_ELEMENT = "category";
+	private static final String CHECKER_ELEMENT = "checker"; //$NON-NLS-1$
-	private static final Object DEFAULT = "DEFAULT";
+	private static final String PROBLEM_ELEMENT = "problem"; //$NON-NLS-1$
+	private static final String CATEGORY_ELEMENT = "category"; //$NON-NLS-1$
+	private static final Object DEFAULT = "DEFAULT"; //$NON-NLS-1$
 	private Collection<IChecker> checkers = new ArrayList<IChecker>();
 	private static CheckersRegisry instance;
 	private HashMap<Object, IProblemProfile> profiles = new HashMap<Object, IProblemProfile>();
@@ -55,10 +57,9 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	}
 
 	private void readCheckersRegistry() {
-		IExtensionPoint ep = Platform.getExtensionRegistry().getExtensionPoint(
+		IExtensionPoint ep = Platform.getExtensionRegistry().getExtensionPoint(CodanCorePlugin.PLUGIN_ID,
-				CodanCorePlugin.PLUGIN_ID, EXTENSION_POINT_NAME);
+				EXTENSION_POINT_NAME);
-		if (ep == null)
+		if (ep == null) return;
-			return;
 		IConfigurationElement[] elements = ep.getConfigurationElements();
 		// process categories
 		for (int i = 0; i < elements.length; i++) {
@@ -76,16 +77,14 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 			processChecker(configurationElement);
 		}
 		// init parameters for checkers with parameters
-		for (Iterator iterator = problemList.keySet().iterator(); iterator
+		for (Iterator<IChecker> iterator = problemList.keySet().iterator(); iterator.hasNext();) {
-				.hasNext();) {
+			IChecker c = iterator.next();
-			IChecker c = (IChecker) iterator.next();
 			if (c instanceof ICheckerWithParameters) {
 				Collection<IProblem> list = problemList.get(c);
-				for (Iterator iterator2 = list.iterator(); iterator2.hasNext();) {
+				for (Iterator<IProblem> iterator2 = list.iterator(); iterator2.hasNext();) {
-					IProblem p = (IProblem) iterator2.next();
+					IProblem p = iterator2.next();
 					if (p instanceof IProblemWorkingCopy) {
-						((ICheckerWithParameters) c)
+						((ICheckerWithParameters) c).initParameters((IProblemWorkingCopy) p);
-								.initParameters((IProblemWorkingCopy) p);
 					}
 				}
 			}
@@ -97,15 +96,12 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	 */
 	private void processCategories(IConfigurationElement configurationElement) {
 		if (configurationElement.getName().equals(CATEGORY_ELEMENT)) {
-			String id = getAtt(configurationElement, "id");
+			String id = getAtt(configurationElement, ID_ATTR);
-			if (id == null)
+			if (id == null) return;
-				return;
+			String name = getAtt(configurationElement, NAME_ATTR);
-			String name = getAtt(configurationElement, "name");
+			if (name == null) return;
-			if (name == null)
-				return;
 			CodanProblemCategory cat = new CodanProblemCategory(id, name);
-			String category = getAtt(configurationElement, "parentCategory",
+			String category = getAtt(configurationElement, "parentCategory", false); //$NON-NLS-1$
-					false);
 			addCategory(cat, category);
 		}
 	}
@@ -116,27 +112,22 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	private void processChecker(IConfigurationElement configurationElement) {
 		try {
 			if (configurationElement.getName().equals(CHECKER_ELEMENT)) {
-				String id = getAtt(configurationElement, "id");
+				String id = getAtt(configurationElement, ID_ATTR);
-				if (id == null)
+				if (id == null) return;
-					return;
+				String name = getAtt(configurationElement, NAME_ATTR, false);
-				String name = getAtt(configurationElement, "name", false);
+				if (name == null) name = id;
-				if (name == null)
-					name = id;
 				IChecker checkerObj = null;
 				try {
-					Object checker = configurationElement
+					Object checker = configurationElement.createExecutableExtension("class"); //$NON-NLS-1$
-							.createExecutableExtension("class");
 					checkerObj = (IChecker) checker;
 					addChecker(checkerObj);
 				} catch (CoreException e) {
 					CodanCorePlugin.log(e);
 					return;
 				}
-				IConfigurationElement[] children1 = configurationElement
+				IConfigurationElement[] children1 = configurationElement.getChildren("problemRef"); //$NON-NLS-1$
-						.getChildren("problemRef");
 				boolean hasRef = false;
-				IConfigurationElement[] children2 = configurationElement
+				IConfigurationElement[] children2 = configurationElement.getChildren(PROBLEM_ELEMENT);
-						.getChildren(PROBLEM_ELEMENT);
 				if (children2 != null) {
 					for (IConfigurationElement ref : children2) {
 						IProblem p = processProblem(ref);
@@ -147,8 +138,7 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 				if (children1 != null) {
 					for (IConfigurationElement ref : children1) {
 						hasRef = true;
-						IProblem p = getDefaultProfile().findProblem(
+						IProblem p = getDefaultProfile().findProblem(ref.getAttribute("refId")); //$NON-NLS-1$
-								ref.getAttribute("refId"));
 						addRefProblem(checkerObj, p);
 					}
 				}
@@ -167,39 +157,30 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	 * @param configurationElement
 	 * @return
 	 */
-	private CodanProblem processProblem(
+	private CodanProblem processProblem(IConfigurationElement configurationElement) {
-			IConfigurationElement configurationElement) {
 		if (configurationElement.getName().equals(PROBLEM_ELEMENT)) {
-			String id = getAtt(configurationElement, "id");
+			String id = getAtt(configurationElement, ID_ATTR);
-			if (id == null)
+			if (id == null) return null;
-				return null;
+			String name = getAtt(configurationElement, NAME_ATTR);
-			String name = getAtt(configurationElement, "name");
+			if (name == null) name = id;
-			if (name == null)
-				name = id;
 			CodanProblem p = new CodanProblem(id, name);
-			String category = getAtt(configurationElement, "category", false);
+			String category = getAtt(configurationElement, "category", false); //$NON-NLS-1$
-			if (category == null)
+			if (category == null) category = "org.eclipse.cdt.codan.core.categories.ProgrammingProblems"; //$NON-NLS-1$
-				category = "org.eclipse.cdt.codan.core.categories.ProgrammingProblems";
 			addProblem(p, category);
 			return p;
 		}
 		return null;
 	}
 
-	private static String getAtt(IConfigurationElement configurationElement,
+	private static String getAtt(IConfigurationElement configurationElement, String name) {
-			String name) {
 		return getAtt(configurationElement, name, true);
 	}
 
-	private static String getAtt(IConfigurationElement configurationElement,
+	private static String getAtt(IConfigurationElement configurationElement, String name, boolean req) {
-			String name, boolean req) {
 		String elementValue = configurationElement.getAttribute(name);
 		if (elementValue == null && req)
-			CodanCorePlugin.log("Extension "
+			CodanCorePlugin.log("Extension " + configurationElement.getDeclaringExtension().getUniqueIdentifier() //$NON-NLS-1$
-					+ configurationElement.getDeclaringExtension()
+					+ " missing required attribute: " + configurationElement.getName() + "." + name); //$NON-NLS-1$ //$NON-NLS-2$
-							.getUniqueIdentifier()
-					+ " missing required attribute: "
-					+ configurationElement.getName() + "." + name);
 		return elementValue;
 	}
 
@@ -213,8 +194,7 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	}
 
 	public static CheckersRegisry getInstance() {
-		if (instance == null)
+		if (instance == null) return new CheckersRegisry();
-			new CheckersRegisry();
 		return instance;
 	}
 
@@ -238,8 +218,7 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	 */
 	public void addProblem(IProblem p, String category) {
 		IProblemCategory cat = getDefaultProfile().findCategory(category);
-		if (cat == null)
+		if (cat == null) cat = getDefaultProfile().getRoot();
-			cat = getDefaultProfile().getRoot();
 		((ProblemProfile) getDefaultProfile()).addProblem(p, cat);
 	}
 
@@ -252,8 +231,7 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	 */
 	public void addCategory(IProblemCategory p, String category) {
 		IProblemCategory cat = getDefaultProfile().findCategory(category);
-		if (cat == null)
+		if (cat == null) cat = getDefaultProfile().getRoot();
-			cat = getDefaultProfile().getRoot();
 		((ProblemProfile) getDefaultProfile()).addCategory(p, cat);
 	}
 
@@ -310,15 +288,17 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 			} catch (CloneNotSupportedException e) {
 				wp = getDefaultProfile();
 			}
+			profiles.put(ResourcesPlugin.getWorkspace(), wp);
 		}
 		return wp;
 	}
 
 	public void updateProfile(IResource element, IProblemProfile profile) {
-		if (profile == null)
+		// updating profile can invalidate all cached profiles
-			profiles.remove(element);
+		IProblemProfile defaultProfile = getDefaultProfile();
-		else
+		profiles.clear();
-			profiles.put(element, profile);
+		profiles.put(DEFAULT, defaultProfile);
+		if (profile != null && element != null) profiles.put(element, profile);
 	}
 
 	/*
@@ -335,17 +315,13 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 				try {
 					prof = (IProblemProfile) getWorkspaceProfile().clone();
 					// load default values
-					CodanPreferencesLoader loader = new CodanPreferencesLoader(
+					CodanPreferencesLoader loader = new CodanPreferencesLoader(prof);
-							prof);
+					IEclipsePreferences node = new ProjectScope((IProject) element).getNode(CodanCorePlugin.PLUGIN_ID);
-					IEclipsePreferences node = new ProjectScope(
+					boolean useWorkspace = node.getBoolean(PreferenceConstants.P_USE_PARENT, false);
-							(IProject) element)
-							.getNode(CodanCorePlugin.PLUGIN_ID);
-					boolean useWorkspace = node.getBoolean(
-							PreferenceConstants.P_USE_PARENT, false);
 					if (!useWorkspace) {
 						loader.load(node);
 					}
-					updateProfile(element, prof);
+					profiles.put(element, prof);
 				} catch (CloneNotSupportedException e) {
 					// cant
 				}
@@ -366,20 +342,13 @@ public class CheckersRegisry implements Iterable<IChecker>, ICheckersRegistry {
 	 * getResourceProfileWorkingCopy(org.eclipse.core.resources.IResource)
 	 */
 	public IProblemProfile getResourceProfileWorkingCopy(IResource element) {
-		if (element instanceof IProject) {
+
-			try {
+		try {
-				IProblemProfile prof = (IProblemProfile) getWorkspaceProfile()
+			IProblemProfile prof = (IProblemProfile) getResourceProfile(element).clone();
-						.clone();
+			return prof;
-				// load default values
+		} catch (CloneNotSupportedException e) {
-				CodanPreferencesLoader loader = new CodanPreferencesLoader(prof);
+			// cant
-				IEclipsePreferences node = new ProjectScope((IProject) element)
+			return null;
-						.getNode(CodanCorePlugin.PLUGIN_ID);
-				loader.load(node);
-				return prof;
-			} catch (CloneNotSupportedException e) {
-				// cant
-			}
 		}
-		return null;
 	}
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/CodanApplication.java

@@ -1,9 +1,9 @@
-package org.eclipse.cdt.codan.core;
+package org.eclipse.cdt.codan.internal.core;
 
 import java.util.ArrayList;
 import java.util.Collection;
 
-import org.eclipse.cdt.codan.internal.core.CodanBuilder;
+import org.eclipse.cdt.codan.core.CodanRuntime;
 import org.eclipse.cdt.codan.internal.core.model.CodanMarkerProblemReporter;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IProject;
@@ -12,14 +12,20 @@ import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.equinox.app.IApplication;
 import org.eclipse.equinox.app.IApplicationContext;
 
+/**
+ * 
+ * Application to support headless build
+ * 
+ * @noextend This class is not intended to be extended by clients.
+ * @noinstantiate This class is not intended to be instantiated by clients.
+ */
 public class CodanApplication implements IApplication {
 	private Collection<String> projects = new ArrayList<String>();
 	private boolean verbose = false;
 	private boolean all = false;
 
 	public Object start(IApplicationContext context) throws Exception {
-		String[] args = (String[]) context.getArguments().get(
+		String[] args = (String[]) context.getArguments().get("application.args"); //$NON-NLS-1$
-				"application.args");
 		if (args == null || args.length == 0) {
 			help();
 			return EXIT_OK;
@@ -29,10 +35,9 @@ public class CodanApplication implements IApplication {
 		CodanRuntime runtime = CodanRuntime.getInstance();
 		runtime.setProblemReporter(new CodanMarkerProblemReporter() {
 			@Override
-			public void reportProblem(String id, int severity, IFile file,
+			public void reportProblem(String id, int severity, IFile file, int lineNumber, int startChar, int endChar,
-					int lineNumber, int startChar, int endChar, String message) {
+					String message) {
-				System.out.println(file.getLocation() + ":" + lineNumber + ": "
+				System.out.println(file.getLocation() + ":" + lineNumber + ": " + message);
-						+ message);
 			}
 		});
 		IWorkspaceRoot root = ResourcesPlugin.getWorkspace().getRoot();
@@ -44,8 +49,7 @@ public class CodanApplication implements IApplication {
 				log("Launching analysis on project " + project);
 				IProject wProject = root.getProject(project);
 				if (!wProject.exists()) {
-					System.err.println("Error: project " + project
+					System.err.println("Error: project " + project + " does not exist");
-							+ " does not exist");
 					continue;
 				}
 				wProject.accept(codanBuilder.new CodanResourceVisitor());
@@ -58,8 +62,7 @@ public class CodanApplication implements IApplication {
 	 * @param string
 	 */
 	private void log(String string) {
-		if (verbose)
+		if (verbose) System.err.println(string);
-			System.err.println(string);
 	}
 
 	/**

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/CodanBuilder.java

@@ -41,9 +41,8 @@ import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.NullProgressMonitor;
 
-public class CodanBuilder extends IncrementalProjectBuilder implements
+public class CodanBuilder extends IncrementalProjectBuilder implements ICodanBuilder, ICodanAstReconciler {
-		ICodanBuilder, ICodanAstReconciler {
+	public static final String BUILDER_ID = "org.eclipse.cdt.codan.core.codanBuilder"; //$NON-NLS-1$
-	public static final String BUILDER_ID = "org.eclipse.cdt.codan.core.codanBuilder";
 
 	public class CodanDeltaVisitor implements IResourceDeltaVisitor {
 		/*
@@ -63,17 +62,17 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 		public boolean visit(IResourceDelta delta) throws CoreException {
 			IResource resource = delta.getResource();
 			switch (delta.getKind()) {
-			case IResourceDelta.ADDED:
+				case IResourceDelta.ADDED:
-				// handle added resource
+					// handle added resource
-				processResource(resource, new NullProgressMonitor());
+					processResource(resource, new NullProgressMonitor());
-				break;
+					break;
-			case IResourceDelta.REMOVED:
+				case IResourceDelta.REMOVED:
-				// handle removed resource
+					// handle removed resource
-				break;
+					break;
-			case IResourceDelta.CHANGED:
+				case IResourceDelta.CHANGED:
-				// handle changed resource
+					// handle changed resource
-				processResource(resource, new NullProgressMonitor());
+					processResource(resource, new NullProgressMonitor());
-				break;
+					break;
 			}
 			// return true to continue visiting children.
 			return true;
@@ -82,8 +81,7 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 
 	public class CodanResourceVisitor implements IResourceVisitor {
 		public boolean visit(IResource resource) {
-			if (!(resource instanceof IProject))
+			if (!(resource instanceof IProject)) processResource(resource, new NullProgressMonitor());
-				processResource(resource, new NullProgressMonitor());
 			// return true to continue visiting children.
 			return true;
 		}
@@ -95,8 +93,9 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 	 * @see org.eclipse.core.internal.events.InternalBuilder#build(int,
 	 * java.util.Map, org.eclipse.core.runtime.IProgressMonitor)
 	 */
-	protected IProject[] build(int kind, Map args, IProgressMonitor monitor)
+	@SuppressWarnings("rawtypes")
-			throws CoreException {
+	@Override
+	protected IProject[] build(int kind, Map args, IProgressMonitor monitor) throws CoreException {
 		if (kind == FULL_BUILD) {
 			fullBuild(monitor);
 		} else {
@@ -115,21 +114,16 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 		// CodanCorePlugin.PLUGIN_ID, "problems", "", null);
 		// System.err.println("set = " + string);
 		// delete general markers
-		IProblemReporter problemReporter = CodanRuntime.getInstance()
+		IProblemReporter problemReporter = CodanRuntime.getInstance().getProblemReporter();
-				.getProblemReporter();
 		if (problemReporter instanceof CodanMarkerProblemReporter) {
-			((CodanMarkerProblemReporter) problemReporter)
+			((CodanMarkerProblemReporter) problemReporter).deleteMarkers(resource);
-					.deleteMarkers(resource);
 		}
 		for (IChecker checker : CheckersRegisry.getInstance()) {
 			try {
 				boolean run = false;
-				if (checker.enabledInContext(resource))
+				if (checker.enabledInContext(resource)) run = true;
-					run = true;
+				if (areProblemsForCheckerEnabled(checker, resource)) run = true;
-				if (areProblemsForCheckerEnabled(checker, resource))
+				if (run) checker.processResource(resource);
-					run = true;
-				if (run)
-					checker.processResource(resource);
 			} catch (Throwable e) {
 				CodanCorePlugin.log(e);
 			}
@@ -144,8 +138,7 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 	}
 
 	public void reconcileAst(IASTTranslationUnit ast, IProgressMonitor monitor) {
-		if (ast == null)
+		if (ast == null) return;
-			return;
 		String filePath = ast.getFilePath();
 		IWorkspace workspace = ResourcesPlugin.getWorkspace();
 		IWorkspaceRoot root = workspace.getRoot();
@@ -154,24 +147,20 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 		resources = root.findFilesForLocationURI(uri);
 		if (resources != null && resources.length > 0) {
 			IFile resource = resources[0];
-			IProblemReporter problemReporter = CodanRuntime.getInstance()
+			IProblemReporter problemReporter = CodanRuntime.getInstance().getProblemReporter();
-					.getProblemReporter();
 			// TODO: this is wrong - should not delete all markers -
 			// only those that contributed by the checker that we run now
 			if (problemReporter instanceof CodanMarkerProblemReporter) {
-				((CodanMarkerProblemReporter) problemReporter)
+				((CodanMarkerProblemReporter) problemReporter).deleteMarkers(resource);
-						.deleteMarkers(resource);
 			}
 			for (IChecker checker : CheckersRegisry.getInstance()) {
 				try {
 					boolean run = false;
-					if (checker.enabledInContext(resource))
+					if (checker.enabledInContext(resource)) run = true;
-						run = true;
 					if (areProblemsForCheckerEnabled(checker, resource)) {
 						run = true;
 					}
-					if (run && checker instanceof ICAstChecker
+					if (run && checker instanceof ICAstChecker && checker.runInEditor())
-							&& checker.runInEditor())
 						((ICAstChecker) checker).processAst(ast);
 				} catch (Throwable e) {
 					CodanCorePlugin.log(e);
@@ -185,35 +174,28 @@ public class CodanBuilder extends IncrementalProjectBuilder implements
 	 * @param resource
 	 * @return
 	 */
-	private boolean areProblemsForCheckerEnabled(IChecker checker,
+	private boolean areProblemsForCheckerEnabled(IChecker checker, IResource resource) {
-			IResource resource) {
+		IProblemProfile resourceProfile = CheckersRegisry.getInstance().getResourceProfile(resource);
-		IProblemProfile resourceProfile = CheckersRegisry.getInstance()
+		Collection<IProblem> refProblems = CheckersRegisry.getInstance().getRefProblems(checker);
-				.getResourceProfile(resource);
+		for (Iterator<IProblem> iterator = refProblems.iterator(); iterator.hasNext();) {
-		Collection<IProblem> refProblems = CheckersRegisry.getInstance()
+			IProblem p = iterator.next();
-				.getRefProblems(checker);
-		for (Iterator iterator = refProblems.iterator(); iterator.hasNext();) {
-			IProblem p = (IProblem) iterator.next();
 			// we need to check problem enablement in particular profile
 			IProblem problem = resourceProfile.findProblem(p.getId());
-			if (problem == null)
+			if (problem == null) throw new IllegalArgumentException("Id is not registered"); //$NON-NLS-1$
-				throw new IllegalArgumentException("Id is not registered");
+			if (problem.isEnabled()) return true;
-			if (problem.isEnabled())
-				return true;
 		}
 		// no problem is enabled for this checker, skip the checker
 		return false;
 	}
 
-	protected void fullBuild(final IProgressMonitor monitor)
+	protected void fullBuild(final IProgressMonitor monitor) throws CoreException {
-			throws CoreException {
 		try {
 			getProject().accept(new CodanResourceVisitor());
 		} catch (CoreException e) {
 		}
 	}
 
-	protected void incrementalBuild(IResourceDelta delta,
+	protected void incrementalBuild(IResourceDelta delta, IProgressMonitor monitor) throws CoreException {
-			IProgressMonitor monitor) throws CoreException {
 		// the visitor does the work.
 		delta.accept(new CodanDeltaVisitor());
 	}

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/CodanPreferencesLoader.java

@@ -54,11 +54,10 @@ public class CodanPreferencesLoader {
 	 */
 	public void setProperty(String id, String s) {
 		IProblem prob = baseModel.findProblem(id);
-		if (!(prob instanceof CodanProblem))
+		if (!(prob instanceof CodanProblem)) return;
-			return;
 		String sevs = s;
 		boolean enabled = true;
-		if (sevs.startsWith("-")) {
+		if (sevs.startsWith("-")) { //$NON-NLS-1$
 			sevs = sevs.substring(1);
 			enabled = false;
 		}
@@ -95,8 +94,7 @@ public class CodanPreferencesLoader {
 	 */
 	public String getProperty(String id) {
 		IProblem prob = baseModel.findProblem(id);
-		if (!(prob instanceof CodanProblem))
+		if (!(prob instanceof CodanProblem)) return null;
-			return null;
 		String enabled = prob.isEnabled() ? "" : "-";
 		String severity = prob.getSeverity().toString();
 		String res = enabled + severity;

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/CodeAnlysisNature.java

@@ -20,7 +20,7 @@ public class CodeAnlysisNature implements IProjectNature {
 	/**
 	 * ID of this project nature
 	 */
-	public static final String NATURE_ID = "org.eclipse.cdt.codan.core.codanNature";
+	public static final String NATURE_ID = "org.eclipse.cdt.codan.core.codanNature"; //$NON-NLS-1$
 	private IProject project;
 
 	/*
@@ -32,9 +32,7 @@ public class CodeAnlysisNature implements IProjectNature {
 		IProjectDescription desc = project.getDescription();
 		ICommand[] commands = desc.getBuildSpec();
 		for (int i = 0; i < commands.length; ++i) {
-			if (commands[i].getBuilderName().equals(CodanBuilder.BUILDER_ID)) {
+			if (commands[i].getBuilderName().equals(CodanBuilder.BUILDER_ID)) { return; }
-				return;
-			}
 		}
 		ICommand[] newCommands = new ICommand[commands.length + 1];
 		System.arraycopy(commands, 0, newCommands, 0, commands.length);
@@ -57,8 +55,7 @@ public class CodeAnlysisNature implements IProjectNature {
 			if (commands[i].getBuilderName().equals(CodanBuilder.BUILDER_ID)) {
 				ICommand[] newCommands = new ICommand[commands.length - 1];
 				System.arraycopy(commands, 0, newCommands, 0, i);
-				System.arraycopy(commands, i + 1, newCommands, i,
+				System.arraycopy(commands, i + 1, newCommands, i, commands.length - i - 1);
-						commands.length - i - 1);
 				description.setBuildSpec(newCommands);
 				project.setDescription(description, null);
 				return;

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/model/CodanMarkerProblemReporter.java

@@ -24,7 +24,6 @@ import org.eclipse.core.runtime.CoreException;
 
 public class CodanMarkerProblemReporter implements IProblemReporter {
 
-
 	/*
 	 * (non-Javadoc)
 	 * 
@@ -36,27 +35,20 @@ public class CodanMarkerProblemReporter implements IProblemReporter {
 	public void reportProblem(String id, IProblemLocation loc, Object... args) {
 		IFile file = loc.getFile();
 		int lineNumber = loc.getLineNumber();
-		if (file == null)
+		if (file == null) throw new NullPointerException("file"); //$NON-NLS-1$
-			throw new NullPointerException("file");
+		if (id == null) throw new NullPointerException("id"); //$NON-NLS-1$
-		if (id == null)
+		IProblem problem = CheckersRegisry.getInstance().getResourceProfile(file).findProblem(id);
-			throw new NullPointerException("id");
+		if (problem == null) throw new IllegalArgumentException("Id is not registered"); //$NON-NLS-1$
-		IProblem problem = CheckersRegisry.getInstance().getResourceProfile(
+		if (problem.isEnabled() == false) return; // skip
-				file).findProblem(id);
-		if (problem == null)
-			throw new IllegalArgumentException("Id is not registered");
-		if (problem.isEnabled() == false)
-			return; // skip
 		int severity = problem.getSeverity().intValue();
 		String messagePattern = problem.getMessagePattern();
 		String message = id;
 		if (messagePattern == null) {
-			if (args != null && args.length > 0 && args[0] instanceof String)
+			if (args != null && args.length > 0 && args[0] instanceof String) message = (String) args[0];
-				message = (String) args[0];
 		} else {
 			MessageFormat.format(messagePattern, args);
 		}
-		reportProblem(id, severity, file, lineNumber, loc.getStartingChar(),
+		reportProblem(id, severity, file, lineNumber, loc.getStartingChar(), loc.getEndingChar(), message);
-				loc.getEndingChar(), message);
 	}
 
 	/*
@@ -66,28 +58,22 @@ public class CodanMarkerProblemReporter implements IProblemReporter {
 	 * org.eclipse.cdt.codan.core.model.IProblemReporter#reportProblem(java.
 	 * lang.String, org.eclipse.core.resources.IFile, int, java.lang.String)
 	 */
-	public void reportProblem(String id, int severity, IFile file,
+	public void reportProblem(String id, int severity, IFile file, int lineNumber, int startChar, int endChar,
-			int lineNumber, int startChar, int endChar, String message) {
+			String message) {
 		try {
 			// Do not put in duplicates
-			IMarker[] cur = file.findMarkers(GENERIC_CODE_ANALYSIS_MARKER_TYPE,
+			IMarker[] cur = file.findMarkers(GENERIC_CODE_ANALYSIS_MARKER_TYPE, false, IResource.DEPTH_ZERO);
-					false, IResource.DEPTH_ZERO);
 			if (cur != null) {
 				for (IMarker element : cur) {
-					int line = ((Integer) element
+					int line = ((Integer) element.getAttribute(IMarker.LINE_NUMBER)).intValue();
-							.getAttribute(IMarker.LINE_NUMBER)).intValue();
 					if (line == lineNumber) {
-						String mesg = (String) element
+						String mesg = (String) element.getAttribute(IMarker.MESSAGE);
-								.getAttribute(IMarker.MESSAGE);
+						int sev = ((Integer) element.getAttribute(IMarker.SEVERITY)).intValue();
-						int sev = ((Integer) element
+						if (sev == severity && mesg.equals(message)) return;
-								.getAttribute(IMarker.SEVERITY)).intValue();
-						if (sev == severity && mesg.equals(message))
-							return;
 					}
 				}
 			}
-			IMarker marker = file
+			IMarker marker = file.createMarker(GENERIC_CODE_ANALYSIS_MARKER_TYPE);
-					.createMarker(GENERIC_CODE_ANALYSIS_MARKER_TYPE);
 			marker.setAttribute(IMarker.MESSAGE, message);
 			marker.setAttribute(IMarker.SEVERITY, severity);
 			marker.setAttribute(IMarker.LINE_NUMBER, lineNumber);
@@ -101,8 +87,7 @@ public class CodanMarkerProblemReporter implements IProblemReporter {
 
 	public void deleteMarkers(IResource file) {
 		try {
-			file.deleteMarkers(GENERIC_CODE_ANALYSIS_MARKER_TYPE, false,
+			file.deleteMarkers(GENERIC_CODE_ANALYSIS_MARKER_TYPE, false, IResource.DEPTH_ZERO);
-					IResource.DEPTH_ZERO);
 		} catch (CoreException ce) {
 			ce.printStackTrace();
 		}
@@ -111,8 +96,7 @@ public class CodanMarkerProblemReporter implements IProblemReporter {
 	public void deleteAllMarkers() {
 		try {
 			// TODO delete contributed markers too
-			ResourcesPlugin.getWorkspace().getRoot().deleteMarkers(
+			ResourcesPlugin.getWorkspace().getRoot().deleteMarkers(GENERIC_CODE_ANALYSIS_MARKER_TYPE, false,
-					GENERIC_CODE_ANALYSIS_MARKER_TYPE, false,
 					IResource.DEPTH_INFINITE);
 		} catch (CoreException e) {
 			// TODO Auto-generated catch block

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/model/CodanProblem.java

@@ -11,6 +11,7 @@
 package org.eclipse.cdt.codan.internal.core.model;
 
 import java.util.HashMap;
+
 import org.eclipse.cdt.codan.core.model.CodanSeverity;
 import org.eclipse.cdt.codan.core.model.IProblemCategory;
 import org.eclipse.cdt.codan.core.model.IProblemParameterInfo;
@@ -24,6 +25,7 @@ public class CodanProblem implements IProblemWorkingCopy {
 	private boolean enabled = true;
 	private HashMap<Object, Object> parameters = new HashMap<Object, Object>(0);
 	private IProblemParameterInfo parameterInfo;
+	private boolean frozen;
 
 	public CodanSeverity getSeverity() {
 		return severity;
@@ -32,6 +34,7 @@ public class CodanProblem implements IProblemWorkingCopy {
 	public CodanProblem(String problemId, String name) {
 		this.id = problemId;
 		this.name = name;
+		this.frozen = false;
 	}
 
 	public String getName() {
@@ -57,8 +60,7 @@ public class CodanProblem implements IProblemWorkingCopy {
 	}
 
 	public void setSeverity(CodanSeverity sev) {
-		if (sev == null)
+		if (sev == null) throw new NullPointerException();
-			throw new NullPointerException();
 		this.severity = sev;
 	}
 
@@ -101,11 +103,20 @@ public class CodanProblem implements IProblemWorkingCopy {
 		return message;
 	}
 
+	protected void freeze() {
+		frozen = true;
+	}
+
 	/**
 	 * @param message
 	 *            the message to set
 	 */
 	public void setMessagePattern(String message) {
+		checkSet();
 		this.message = message;
 	}
+
+	protected void checkSet() {
+		if (frozen) throw new IllegalStateException("Object is unmodifieble"); //$NON-NLS-1$
+	}
 }

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/model/CodanProblemCategory.java

@@ -41,40 +41,36 @@ public class CodanProblemCategory implements IProblemCategory, Cloneable {
 	}
 
 	public IProblemElement[] getChildren() {
-		return (IProblemElement[]) list.toArray(new IProblemElement[list.size()]);
+		return list.toArray(new IProblemElement[list.size()]);
 	}
 
 	public void addChild(IProblemElement p) {
 		list.add(p);
 	}
 
-	public IProblem findProblem(String id) {
+	public static IProblem findProblem(IProblemCategory c, String id) {
-		Object[] children = this.getChildren();
+		Object[] children = c.getChildren();
 		for (Object object : children) {
 			if (object instanceof IProblemCategory) {
 				IProblemCategory cat = (IProblemCategory) object;
-				IProblem found = cat.findProblem(id);
+				IProblem found = findProblem(cat, id);
-				if (found != null)
+				if (found != null) return found;
-					return found;
 			} else if (object instanceof IProblem) {
 				IProblem p = (IProblem) object;
-				if (p.getId().equals(id))
+				if (p.getId().equals(id)) return p;
-					return p;
 			}
 		}
 		return null;
 	}
 
-	public IProblemCategory findCategory(String id) {
+	public static IProblemCategory findCategory(IProblemCategory cat, String id) {
-		if (getId().equals(id))
+		if (cat.getId().equals(id)) return cat;
-			return this;
+		Object[] children = cat.getChildren();
-		Object[] children = getChildren();
 		for (Object object : children) {
 			if (object instanceof IProblemCategory) {
-				IProblemCategory cat = (IProblemCategory) object;
+				IProblemCategory cat2 = (IProblemCategory) object;
-				IProblemCategory found = cat.findCategory(id);
+				IProblemCategory found = findCategory(cat2, id);
-				if (found != null)
+				if (found != null) return found;
-					return found;
 			}
 		}
 		return null;
@@ -90,8 +86,7 @@ public class CodanProblemCategory implements IProblemCategory, Cloneable {
 		try {
 			CodanProblemCategory clone = (CodanProblemCategory) super.clone();
 			clone.list = new ArrayList<IProblemElement>();
-			for (Iterator<IProblemElement> iterator = this.list.iterator(); iterator
+			for (Iterator<IProblemElement> iterator = this.list.iterator(); iterator.hasNext();) {
-					.hasNext();) {
 				IProblemElement child = iterator.next();
 				clone.list.add((IProblemElement) child.clone());
 			}

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/model/CodanProblemLocation.java

@@ -0,0 +1,30 @@
+/*******************************************************************************
+ * Copyright (c) 2009 Alena Laskavaia 
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *    Alena Laskavaia  - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.cdt.codan.internal.core.model;
+
+import org.eclipse.cdt.codan.core.model.ProblemLocation;
+import org.eclipse.core.resources.IFile;
+
+/**
+ * Codan Problem Location, so far same as abstract class
+ *
+ */
+public class CodanProblemLocation extends ProblemLocation {
+
+	public CodanProblemLocation(IFile file, int startChar, int endChar) {
+		super(file, startChar, endChar);
+	}
+
+	protected CodanProblemLocation(IFile file, int line) {
+		super(file, line);
+	}
+
+}

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/model/ProblemLocationFactory.java

@@ -0,0 +1,35 @@
+/*******************************************************************************
+ * Copyright (c) 2009 Alena Laskavaia 
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *    Alena Laskavaia  - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.cdt.codan.internal.core.model;
+
+import org.eclipse.cdt.codan.core.model.IProblemLocation;
+import org.eclipse.cdt.codan.core.model.IProblemLocationFactory;
+import org.eclipse.core.resources.IFile;
+
+/**
+ * Factory class that allows to create problem locations
+ *
+ */
+public class ProblemLocationFactory implements IProblemLocationFactory {
+	/* (non-Javadoc)
+	 * @see org.eclipse.cdt.codan.core.model.IProblemLocationFactory#createProblemLocation(org.eclipse.core.resources.IFile, int)
+	 */
+	public IProblemLocation createProblemLocation(IFile file, int line) {
+		return new CodanProblemLocation(file, line);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.cdt.codan.core.model.IProblemLocationFactory#createProblemLocation(org.eclipse.core.resources.IFile, int, int)
+	 */
+	public IProblemLocation createProblemLocation(IFile file, int startChar, int endChar) {
+		return new CodanProblemLocation(file, startChar, endChar);
+	}
+}

codan/org.eclipse.cdt.codan.core/src/org/eclipse/cdt/codan/internal/core/model/ProblemProfile.java

@@ -22,8 +22,7 @@ import org.eclipse.cdt.codan.core.model.IProblemProfile;
  * 
  */
 public class ProblemProfile implements IProblemProfile, Cloneable {
-	private IProblemCategory rootCategory = new CodanProblemCategory("root",
+	private IProblemCategory rootCategory = new CodanProblemCategory("root", "root"); //$NON-NLS-1$ //$NON-NLS-2$
-			"root");
 
 	/*
 	 * (non-Javadoc)
@@ -33,7 +32,7 @@ public class ProblemProfile implements IProblemProfile, Cloneable {
 	 * .String)
 	 */
 	public IProblem findProblem(String id) {
-		return getRoot().findProblem(id);
+		return CodanProblemCategory.findProblem(getRoot(), id);
 	}
 
 	/*
@@ -51,8 +50,7 @@ public class ProblemProfile implements IProblemProfile, Cloneable {
 	 * @param root
 	 * @param problems
 	 */
-	protected void collectProblems(IProblemCategory parent,
+	protected void collectProblems(IProblemCategory parent, Collection<IProblem> problems) {
-			Collection<IProblem> problems) {
 		Object[] children = parent.getChildren();
 		for (Object object : children) {
 			if (object instanceof IProblemCategory) {
@@ -69,13 +67,12 @@ public class ProblemProfile implements IProblemProfile, Cloneable {
 	}
 
 	public void addProblem(IProblem p, IProblemCategory cat) {
-		if (cat == null)
+		if (cat == null) cat = getRoot();
-			cat = getRoot();
 		((CodanProblemCategory) cat).addChild(p);
 	}
 
 	public IProblemCategory findCategory(String id) {
-		return getRoot().findCategory(id);
+		return CodanProblemCategory.findCategory(getRoot(), id);
 	}
 
 	/*
@@ -87,8 +84,7 @@ public class ProblemProfile implements IProblemProfile, Cloneable {
 	public Object clone() {
 		try {
 			ProblemProfile clone = (ProblemProfile) super.clone();
-			clone.rootCategory = (IProblemCategory) ((CodanProblemCategory) this.rootCategory)
+			clone.rootCategory = (IProblemCategory) ((CodanProblemCategory) this.rootCategory).clone();
-					.clone();
 			return clone;
 		} catch (CloneNotSupportedException e) {
 			return this;

codan/org.eclipse.cdt.codan.ui/.project

@@ -20,9 +20,15 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>

codan/org.eclipse.cdt.codan.ui/.settings/.api_filters

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<component id="org.eclipse.cdt.codan.ui" version="2">
+    <resource path="src/org/eclipse/cdt/codan/internal/ui/preferences/CodanPreferencePage.java" type="org.eclipse.cdt.codan.internal.ui.preferences.CodanPreferencePage">
+        <filter id="640712815">
+            <message_arguments>
+                <message_argument value="ICheckersRegistry"/>
+                <message_argument value="CodanPreferencePage"/>
+                <message_argument value="updateProfile(IResource, IProblemProfile)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>

codan/org.eclipse.cdt.codan.ui/META-INF/MANIFEST.MF

@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: Code Analyzers Framework
 Bundle-SymbolicName: org.eclipse.cdt.codan.ui; singleton:=true
 Bundle-Version: 1.0.0
-Bundle-Activator: org.eclipse.cdt.codan.ui.CodanUIActivator
+Bundle-Activator: org.eclipse.cdt.codan.internal.ui.CodanUIActivator
 Bundle-Vendor: Eclipse
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,

codan/org.eclipse.cdt.codan.ui/build.properties

@@ -3,7 +3,3 @@ output.. = bin/
 bin.includes = plugin.xml,\
                META-INF/,\
                .
-src.includes = src/,\
-               plugin.xml,\
-               build.properties,\
-               META-INF/

codan/org.eclipse.cdt.codan.ui/src/org/eclipse/cdt/codan/internal/ui/CodanCReconciler.java

@@ -40,7 +40,7 @@ public class CodanCReconciler implements ICReconcilingListener {
 	 * 
 	 */
 	private void initialize() {
-		// TODO Auto-generated method stub
+		// nothing?
 	}
 
 	/*
@@ -51,7 +51,7 @@ public class CodanCReconciler implements ICReconcilingListener {
 	 * ()
 	 */
 	public void aboutToBeReconciled() {
-		// TODO Auto-generated method stub
+		// nothing
 	}
 
 	/*

codan/org.eclipse.cdt.codan.ui/src/org/eclipse/cdt/codan/internal/ui/CodanUIActivator.java

@@ -1,4 +1,4 @@
-package org.eclipse.cdt.codan.ui;
+package org.eclipse.cdt.codan.internal.ui;
 
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Status;

codan/org.eclipse.cdt.codan.ui/src/org/eclipse/cdt/codan/internal/ui/preferences/BuildPropertyPage.java

@@ -21,7 +21,7 @@ public class BuildPropertyPage extends FieldEditorPreferencePage implements
 	 * 
 	 */
 	public BuildPropertyPage() {
-		setPreferenceStore(org.eclipse.cdt.codan.ui.CodanUIActivator.getDefault()
+		setPreferenceStore(org.eclipse.cdt.codan.internal.ui.CodanUIActivator.getDefault()
 				.getPreferenceStore());
 	}
 

codan/org.eclipse.cdt.codan.ui/src/org/eclipse/cdt/codan/internal/ui/preferences/CodanPreferencePage.java

@@ -71,7 +71,7 @@ public class CodanPreferencePage extends FieldEditorOverlayPage implements
 
 
 	protected String getPageId() {
-		return "org.eclipse.cdt.codan.internal.ui.preferences.CodanPreferencePage";
+		return "org.eclipse.cdt.codan.internal.ui.preferences.CodanPreferencePage"; //$NON-NLS-1$
 	}
 
 	/**
@@ -153,7 +153,7 @@ public class CodanPreferencePage extends FieldEditorOverlayPage implements
 	 */
 	@Override
 	public boolean performOk() {
-		if (isPropertyPage())
+		//if (isPropertyPage())
 			getRegistry().updateProfile((IResource) getElement(), null);
 		return super.performOk();
 	}

codan/org.eclipse.cdt.codan.ui/src/org/eclipse/cdt/codan/internal/ui/preferences/PreferenceInitializer.java

@@ -25,7 +25,7 @@ public class PreferenceInitializer extends AbstractPreferenceInitializer {
 	 * @see org.eclipse.core.runtime.preferences.AbstractPreferenceInitializer#initializeDefaultPreferences()
 	 */
 	public void initializeDefaultPreferences() {
-		IPreferenceStore store = org.eclipse.cdt.codan.ui.CodanUIActivator
+		IPreferenceStore store = org.eclipse.cdt.codan.internal.ui.CodanUIActivator
 				.getDefault().getPreferenceStore();
 		store.setDefault(PreferenceConstants.P_RUN_ON_BUILD, false);
 	}