added d3 example

.gitignore

@@ -3,3 +3,7 @@
 .settings
 *~
 target
+/.gradle/
+/bin/
+/build/
+/test-output/

build.gradle

@@ -0,0 +1,48 @@
+buildscript {
+    repositories {
+        mavenCentral()
+    }
+    dependencies {
+        classpath("org.springframework.boot:spring-boot-gradle-plugin:1.1.7.RELEASE")
+    }
+}
+
+apply plugin: 'java'
+apply plugin: 'eclipse'
+apply plugin: 'spring-boot'
+
+repositories{
+	mavenLocal()
+	mavenCentral()
+}
+
+sourceSets{
+	test {
+    	java {
+      		srcDir 'src/testdummies/java'
+    	}
+  	}
+}
+
+dependencies{
+		 compile("org.springframework.boot:spring-boot-starter-web") {
+	        exclude module: "spring-boot-starter-jetty"
+    	}
+
+		compile 'org.neo4j:neo4j:1.4.M06'
+		compile 'commons-io:commons-io:1.4'
+		compile 'org.springframework:spring-beans:3.0.5.RELEASE'
+		compile 'org.springframework:spring-context:3.0.5.RELEASE'
+		compile 'javassist:javassist:3.12.1.GA'
+		compile 'ch.qos.logback:logback-core:0.9.29'
+		compile 'org.slf4j:slf4j-api:1.6.1'
+		compile 'ch.qos.logback:logback-classic:0.9.29'
+		compile 'org.xeustechnologies:jtar:1.0.4'
+		compile 'org.codehaus.jackson:jackson-mapper-asl:1.9.10'
+		
+		testCompile 'junit:junit:4.8.2'
+		testCompile 'org.mockito:mockito-core:1.9.5'
+		testCompile 'org.springframework:spring-test:3.0.5.RELEASE'
+		testCompile 'javax.annotation:jsr250-api:1.0'
+}
+

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Mon Sep 29 15:43:34 CEST 2014
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.0-bin.zip

gradlew

@@ -0,0 +1,164 @@
+#!/usr/bin/env bash
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+esac
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched.
+if $cygwin ; then
+    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+fi
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >&-
+APP_HOME="`pwd -P`"
+cd "$SAVED" >&-
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+function splitJvmOpts() {
+    JVM_OPTS=("$@")
+}
+eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+
+exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"

gradlew.bat

@@ -0,0 +1,90 @@
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windowz variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+if "%@eval[2+2]" == "4" goto 4NT_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+goto execute
+
+:4NT_args
+@rem Get arguments from the 4NT Shell from JP Software
+set CMD_LINE_ARGS=%$
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

src/main/java/yooze/ClassCache.java

@@ -1,32 +1,50 @@
 package yooze;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 
 import yooze.domain.ClassModel;
 
 public class ClassCache {
-	private final static Map<String, ClassModel> entries = new ConcurrentHashMap<String, ClassModel>();
+	private final Map<String, ClassModel> entries = new ConcurrentHashMap<String, ClassModel>();
+	private InclusionDecider inclusionDecider;
 
-	public static boolean contains(String classname) {
+	public boolean contains(String classname) {
 		return entries.containsKey(classname);
 	}
 
-	public static ClassModel createNewDummyModel(String name) {
+	public ClassModel createNewDummyModel(String name) {
 		ClassModel classModel = new ClassModel(name);
 		entries.put(name, classModel);
 		return classModel;
 	}
 
-	public static ClassModel get(String className) {
+	public ClassModel get(String className) {
 		return entries.get(className);
 	}
 
-	public static void add(String className, ClassModel model) {
+	public void add(String className, ClassModel model) {
 		entries.put(className, model);
 	}
 
-	public static void clear() {
+	public List<ClassModel> values() {
+		List<ClassModel> models = new ArrayList<ClassModel>();
+		for (ClassModel model : entries.values()) {
+			if (!inclusionDecider.shouldSkip(model.getName())) {
+				models.add(model);
+			}
+		}
+		return models;
+	}
+
+	public void clear() {
 		entries.clear();
 	}
+
+	public void setInclusionDecider(InclusionDecider inclusionDecider) {
+		this.inclusionDecider = inclusionDecider;
+	}
+
 }

src/main/java/yooze/ClassModelBuilder.java

@@ -1,8 +1,6 @@
 package yooze;
 
 import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javassist.ClassPool;
 import javassist.CtClass;
@@ -23,19 +21,15 @@ import yooze.domain.MethodModel;
 public class ClassModelBuilder {
 	private static Logger log = LoggerFactory.getLogger(ClassModelBuilder.class);
 
-	private Pattern[] packageIncludePatterns;
-	private Pattern[] packageExcludePatterns;
 	private ClassPool pool;
-
+	private InclusionDecider inclusionDecider;
-	public ClassModelBuilder(ClassPool pool) {
+	private ClassCache classCache;
-		this.pool = pool;
-	}
 
 	public ClassModel scanClassOrSkip(String className) {
-		if (shouldSkip(className))
+		if (inclusionDecider.shouldSkip(className))
 			return null;
-		if (ClassCache.contains(className)) {
+		if (classCache.contains(className)) {
-			return ClassCache.get(className);
+			return classCache.get(className);
 		}
 		log.info("scanning {}", className);
 
@@ -45,21 +39,27 @@ public class ClassModelBuilder {
 
 	private ClassModel scan(String className) {
 		ClassModel model = new ClassModel(className);
-		ClassCache.add(className, model);
+		classCache.add(className, model);
 		return tryScan(className, model);
 	}
 
 	private ClassModel tryScan(String className, ClassModel model) {
 		CtClass ctClass = getClassFromJavassist(className);
+		model.setClass(ctClass);
 		if (isScannable(ctClass)) {
+			try {
 				ConstPool constPool = ctClass.getClassFile().getConstPool();
 
 				addClassReferences(model, constPool);
 				addMethods(model, ctClass);
 				resolveMethodReferences();
 				return model;
+			} catch (Exception e) {
+				System.out.println(e.getClass().getName() + ":" + e.getMessage());
+				return null;
+			}
 		} else {
-			throw new ClassNotFound(className);
+			return null;
 		}
 	}
 
@@ -110,60 +110,15 @@ public class ClassModelBuilder {
 		}
 	}
 
-	private boolean shouldSkip(String className) {
+	public void setInclusionDecider(InclusionDecider inclusionDecider) {
-		if (!isIncluded(className)) {
+		this.inclusionDecider = inclusionDecider;
-			log.debug("skipping {}", className);
-			return true;
-		}
-		if (isExcluded(className)) {
-			log.debug("skipping {}", className);
-			return true;
 	}
 
-		return false;
+	public void setPool(ClassPool pool) {
+		this.pool = pool;
 	}
 
-	private boolean isExcluded(String className) {
+	public void setClassCache(ClassCache classCache) {
-		if (packageExcludePatterns != null) {
+		this.classCache = classCache;
-			for (Pattern excludePattern : packageExcludePatterns) {
-				Matcher matcher = excludePattern.matcher(className);
-				if (matcher.matches()) {
-					return true;
-				}
-			}
-		}
-		return false;
-	}
-
-	private boolean isIncluded(String className) {
-		if (packageIncludePatterns != null) {
-			for (Pattern includePattern : packageIncludePatterns) {
-				Matcher matcher = includePattern.matcher(className);
-				if (matcher.matches()) {
-					return true;
-				}
-			}
-		}
-		return false;
-	}
-
-	public void setPackageIncludePatterns(String... packageIncludePatterns) {
-		if (packageIncludePatterns != null) {
-			this.packageIncludePatterns = new Pattern[packageIncludePatterns.length];
-			int i = 0;
-			for (String pattern : packageIncludePatterns) {
-				this.packageIncludePatterns[i++] = Pattern.compile(pattern);
-			}
-		}
-	}
-
-	public void setPackageExcludePatterns(String... packageExcludePatterns) {
-		if (packageExcludePatterns != null) {
-			this.packageExcludePatterns = new Pattern[packageExcludePatterns.length];
-			int i = 0;
-			for (String pattern : packageExcludePatterns) {
-				this.packageExcludePatterns[i++] = Pattern.compile(pattern);
-			}
-		}
 	}
 }

src/main/java/yooze/GraphBuilder.java

@@ -10,13 +10,12 @@ import yooze.domain.ClassModel;
 import yooze.domain.Graph;
 
 /**
- * Builds a class dependency graph from given classpath. Delegates to ClassModelBuilder.
+ * Builds a class dependency graph from given classpath. Delegates to
+ * ClassModelBuilder.
  */
 public class GraphBuilder {
 	private Scanner scanner;
 	private ClassModelBuilder classModelBuilder;
-	private String[] packageIncludePatterns;
-	private String[] packageExcludePatterns;
 
 	public GraphBuilder(Scanner scanner) {
 		this.scanner = scanner;
@@ -27,7 +26,8 @@ public class GraphBuilder {
 	 * 
 	 * @param archiveFilename
 	 * @param className
-	 *            the name of the class that is the starting point. Only classes referenced from here will be included.
+	 *            the name of the class that is the starting point. Only classes
+	 *            referenced from here will be included.
 	 * @return a Graph containing all calculated dependencies
 	 * @throws IOException
 	 *             when file reading fails
@@ -35,7 +35,7 @@ public class GraphBuilder {
 	public Graph build(String archiveFilename, String className) throws IOException {
 		return buildClassDepencyGraph(new File(archiveFilename), className, new IncludeDecision() {
 			public boolean shouldIncludeClass(String name, String startingpointname) {
-				return name.equals(startingpointname);
+				return startingpointname == null || name.equals(startingpointname);
 			}
 		});
 	}
@@ -49,7 +49,8 @@ public class GraphBuilder {
 	}
 
 	/**
-	 * Builds a graph for all classes (all included via package patterns and not excluded)
+	 * Builds a graph for all classes (all included via package patterns and not
+	 * excluded)
 	 * 
 	 * @param archiveFilename
 	 * @return a Graph containing all calculated dependencies
@@ -80,13 +81,12 @@ public class GraphBuilder {
 	private Graph createClassDependencyGraph(ClassPool pool, List<InspectableClasspath> classpath, String className,
 			IncludeDecision decide) {
 		Graph graph = new Graph();
-		classModelBuilder = new ClassModelBuilder(pool);
+		classModelBuilder.setPool(pool);
-		classModelBuilder.setPackageExcludePatterns(packageExcludePatterns);
+
-		classModelBuilder.setPackageIncludePatterns(packageIncludePatterns);
 		for (InspectableClasspath lib : classpath) {
 			for (String name : lib.getClasses()) {
 				if (decide.shouldIncludeClass(name, className)) {
-					ClassModel newModel = classModelBuilder.scanClassOrSkip(className);
+					ClassModel newModel = classModelBuilder.scanClassOrSkip(name);
 					if (newModel != null) {
 						graph.add(newModel);
 					}
@@ -96,15 +96,11 @@ public class GraphBuilder {
 		return graph;
 	}
 
-	public void setPackageIncludePatterns(String... packageIncludePatterns) {
-		this.packageIncludePatterns = packageIncludePatterns;
-	}
-
-	public void setPackageExcludePatterns(String... packageExcludePatterns) {
-		this.packageExcludePatterns = packageExcludePatterns;
-	}
-
 	interface IncludeDecision {
 		boolean shouldIncludeClass(String name, String startingpointname);
 	}
+
+	public void setClassModelBuilder(ClassModelBuilder classModelBuilder) {
+		this.classModelBuilder = classModelBuilder;
+	}
 }

src/main/java/yooze/MethodCache.java

@@ -29,4 +29,8 @@ public class MethodCache {
 	public Collection<MethodModel> getMethods() {
 		return entries.values();
 	}
+
+	public void reset() {
+		entries.clear();
+	}
 }

src/main/java/yooze/application/GraphBuilderFactory.java

@@ -3,6 +3,7 @@ package yooze.application;
 import yooze.GraphBuilder;
 import yooze.scanner.ArchiveScanner;
 import yooze.scanner.ClassesDirScanner;
+import yooze.scanner.JarScanner;
 import yooze.scanner.LibScanner;
 import yooze.scanner.TgzScanner;
 import yooze.scanner.WarScanner;
@@ -20,21 +21,30 @@ public class GraphBuilderFactory {
 	 */
 	public static GraphBuilder getDefaultTgzBuilder() {
 		GraphBuilder tgzBuilder = new GraphBuilder(new TgzScanner());
-		tgzBuilder.setPackageExcludePatterns("java.*", "sun.*", "com.sun.*");
 		return tgzBuilder;
 	}
 
 	/**
-	 * Factory method for getting a builder that scans a lib directory (containing jars)
+	 * Factory method for getting a builder that scans a lib directory
+	 * (containing jars)
 	 */
 	public static GraphBuilder getLibDirectoryBuilder() {
 		return new GraphBuilder(new LibScanner());
 	}
 
 	/**
-	 * Factory method for getting a builder that scans a directory containing classes
+	 * Factory method for getting a builder that scans a directory containing
+	 * classes
 	 */
 	public static GraphBuilder getClassesDirectoryBuilder() {
 		return new GraphBuilder(new ClassesDirScanner());
 	}
+
+	/**
+	 * Factory method for getting a builder that scans a directory containing
+	 * classes
+	 */
+	public static GraphBuilder getJarBuilder() {
+		return new GraphBuilder(new JarScanner());
+	}
 }

src/main/java/yooze/application/Yooze.java

@@ -2,7 +2,9 @@ package yooze.application;
 
 import java.io.IOException;
 
+import yooze.ClassModelBuilder;
 import yooze.GraphBuilder;
+import yooze.InclusionDecider;
 import yooze.domain.ClassModel;
 import yooze.domain.Graph;
 
@@ -27,8 +29,13 @@ public class Yooze {
 	public void createNeoGraph(String archive, String packageIncludePatterns, String packageExcludePatterns,
 			String startingClass) throws IOException {
 		GraphBuilder libDirectoryBuilder = GraphBuilderFactory.getLibDirectoryBuilder();
-		libDirectoryBuilder.setPackageExcludePatterns(packageExcludePatterns);
+
-		libDirectoryBuilder.setPackageIncludePatterns(packageIncludePatterns);
+		InclusionDecider i = new InclusionDecider();
+		i.setPackageExcludePatterns(packageExcludePatterns);
+		i.setPackageIncludePatterns(packageIncludePatterns);
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		libDirectoryBuilder.setClassModelBuilder(classModelBuilder);
 
 		Graph graph = libDirectoryBuilder.build(archive, startingClass);
 

src/main/java/yooze/domain/ClassModel.java

@@ -3,6 +3,7 @@ package yooze.domain;
 import java.util.ArrayList;
 import java.util.List;
 
+import javassist.CtClass;
 
 /**
  * 
@@ -12,6 +13,7 @@ public class ClassModel {
 
 	final private List<ClassModel> references = new ArrayList<ClassModel>();
 	final private List<MethodModel> methods = new ArrayList<MethodModel>();
+	private CtClass classDefinition;
 
 	public ClassModel(String name) {
 		super();
@@ -59,9 +61,14 @@ public class ClassModel {
 		if (name == null) {
 			if (other.name != null)
 				return false;
-		} else if (!name.equals(other.name))
+		} else if (!name.equals(other.name)) {
 			return false;
+		}
 		return true;
 	}
 
+	public void setClass(CtClass ctClass) {
+		this.classDefinition = ctClass;
+	}
+
 }

src/main/java/yooze/domain/MethodCallModel.java

@@ -2,7 +2,6 @@ package yooze.domain;
 
 import javassist.NotFoundException;
 import javassist.expr.MethodCall;
-import yooze.ClassCache;
 import yooze.MethodCache;
 
 public class MethodCallModel {
@@ -13,7 +12,8 @@ public class MethodCallModel {
 	}
 
 	public ClassModel getCalledClass() {
-		return ClassCache.get(methodCall.getClassName());
+		// return ClassCache.get(methodCall.getClassName());
+		return null;
 	}
 
 	public MethodModel getCalledMethod() {

src/main/java/yooze/domain/ParameterModel.java

@@ -1,6 +1,5 @@
 package yooze.domain;
 
-import yooze.ClassCache;
 import javassist.CtClass;
 
 public class ParameterModel {
@@ -9,10 +8,10 @@ public class ParameterModel {
 
 	public ParameterModel(CtClass typeAsCtClass) {
 		String classname = typeAsCtClass.getName();
-		type = ClassCache.get(classname);
+		// type = ClassCache.get(classname);
-		if (type == null) {
+		// if (type == null) {
-			type = ClassCache.createNewDummyModel(classname);
+		// type = ClassCache.createNewDummyModel(classname);
-		}
+		// }
 		name = "";// javassist doesn't give me this (?)
 	}
 

src/test/java/yooze/GraphTest.java

@@ -6,9 +6,10 @@ import java.io.IOException;
 
 import junit.framework.Assert;
 
-import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.DirtiesContext.ClassMode;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
@@ -18,23 +19,23 @@ import yooze.domain.Graph;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
+@DirtiesContext(classMode = ClassMode.AFTER_EACH_TEST_METHOD)
 public class GraphTest {
 
-	@Before
-	public void clearClassCache() {
-		ClassCache.clear();
-	}
-
 	@Test
 	public void buildGraph() throws IOException {
 		// new Yooze("/tmp/test").createNeoGraph("target/test-classes",
 		// ".*?.Class.");
-		GraphBuilder libDirectoryBuilder = GraphBuilderFactory
+		GraphBuilder libDirectoryBuilder = GraphBuilderFactory.getClassesDirectoryBuilder();
-				.getClassesDirectoryBuilder();
+
-		libDirectoryBuilder.setPackageIncludePatterns(".*?.Class.");
+		InclusionDecider i = new InclusionDecider();
-		libDirectoryBuilder.setPackageExcludePatterns("");
+		i.setPackageIncludePatterns(".*?.Class.");
-		Graph graph = libDirectoryBuilder.build("target/test-classes",
+		i.setPackageExcludePatterns("");
-				"yooze.Class1");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		libDirectoryBuilder.setClassModelBuilder(classModelBuilder);
+
+		Graph graph = libDirectoryBuilder.build("target/test-classes", "yooze.Class1");
 		ClassModel class1 = graph.getChildren().get(0);
 		Assert.assertNotNull(class1);
 

src/test/java/yooze/LargePackageTest.java

@@ -6,6 +6,8 @@ import java.io.IOException;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.DirtiesContext.ClassMode;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
@@ -15,6 +17,7 @@ import yooze.output.DotPrinter;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
+@DirtiesContext(classMode = ClassMode.AFTER_EACH_TEST_METHOD)
 public class LargePackageTest {
 
 	@Autowired
@@ -23,8 +26,14 @@ public class LargePackageTest {
 	@Test
 	public void largePackage() throws IOException {
 		GraphBuilder earBuilder = GraphBuilderFactory.getEarBuilder();
-		earBuilder.setPackageIncludePatterns("");
+
-		earBuilder.setPackageExcludePatterns("java.*");
+		InclusionDecider i = new InclusionDecider();
+		i.setPackageIncludePatterns("");
+		i.setPackageExcludePatterns("java.*");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		earBuilder.setClassModelBuilder(classModelBuilder);
+
 		Graph graph = earBuilder.build(config.getEarFile(), "java.lang.String");
 		DotPrinter dotPrinter = new DotPrinter(new FileOutputStream("/tmp/example.dot"));
 		dotPrinter.print(graph);

src/test/java/yooze/MethodReferencesTest.java

@@ -8,8 +8,11 @@ import junit.framework.Assert;
 
 import org.codehaus.jackson.JsonGenerator;
 import org.codehaus.jackson.map.ObjectMapper;
+import org.junit.After;
 import org.junit.Test;
 import org.junit.runner.RunWith;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.DirtiesContext.ClassMode;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
@@ -19,11 +22,24 @@ import yooze.dto.MethodDto;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
+@DirtiesContext(classMode = ClassMode.AFTER_EACH_TEST_METHOD)
 public class MethodReferencesTest {
+
+	@After
+	public void reset() {
+		MethodCache.getInstance().reset();
+	}
+
 	@Test
 	public void test() throws IOException {
 		GraphBuilder directoryBuilder = GraphBuilderFactory.getClassesDirectoryBuilder();
-		directoryBuilder.setPackageIncludePatterns("yooze.Class.*");
+
+		InclusionDecider i = new InclusionDecider();
+		i.setPackageIncludePatterns("yooze.Class.*");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		directoryBuilder.setClassModelBuilder(classModelBuilder);
+
 		directoryBuilder.build("target/test-classes", "yooze.Class1");
 		MethodModel mm1 = MethodCache.getInstance().get("yooze.Class1.rup(int)");
 		Assert.assertNotNull(mm1);

src/test/java/yooze/TgzBuilderTest.java

@@ -25,8 +25,14 @@ public class TgzBuilderTest {
 	@Test
 	public void tgzBuilder() throws IOException {
 		GraphBuilder tgzBuilder = GraphBuilderFactory.getDefaultTgzBuilder();
-		tgzBuilder.setPackageIncludePatterns("nl.*");
+
-		tgzBuilder.setPackageExcludePatterns("");
+		InclusionDecider i = new InclusionDecider();
+		i.setPackageIncludePatterns("nl.*");
+		i.setPackageExcludePatterns("");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		tgzBuilder.setClassModelBuilder(classModelBuilder);
+
 		Graph graph = tgzBuilder.build(config.getTgzFile(), "nl.jssl.jas.Main");
 
 		ArrayList<String> names = new ArrayList<String>();

src/test/java/yooze/output/DotPrinterTest.java

@@ -5,14 +5,14 @@ import java.io.IOException;
 
 import junit.framework.Assert;
 
-import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
-import yooze.ClassCache;
+import yooze.ClassModelBuilder;
 import yooze.GraphBuilder;
+import yooze.InclusionDecider;
 import yooze.application.GraphBuilderFactory;
 import yooze.domain.Graph;
 
@@ -20,16 +20,15 @@ import yooze.domain.Graph;
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
 public class DotPrinterTest {
 
-	@Before
-	public void clearClassCache() {
-		ClassCache.clear();
-	}
-
 	@Test
 	public void dotPrinting() throws IOException {
 		GraphBuilder directoryBuilder = GraphBuilderFactory.getClassesDirectoryBuilder();
-		directoryBuilder.setPackageExcludePatterns(".*?Class4");
+		InclusionDecider i = new InclusionDecider();
-		directoryBuilder.setPackageIncludePatterns(".*?.Class.");
+		i.setPackageExcludePatterns(".*?Class4");
+		i.setPackageIncludePatterns(".*?.Class.");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		directoryBuilder.setClassModelBuilder(classModelBuilder);
 		Graph graph = directoryBuilder.build("target/test-classes", "yooze.Class1");
 
 		ByteArrayOutputStream bytes = new ByteArrayOutputStream(500);
@@ -56,8 +55,14 @@ public class DotPrinterTest {
 	@Test
 	public void noReference() throws IOException {
 		GraphBuilder directoryBuilder = GraphBuilderFactory.getClassesDirectoryBuilder();
-		directoryBuilder.setPackageExcludePatterns("");
+
-		directoryBuilder.setPackageIncludePatterns("yooze.Class4");
+		InclusionDecider i = new InclusionDecider();
+		i.setPackageExcludePatterns("");
+		i.setPackageIncludePatterns("yooze.Class4");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		directoryBuilder.setClassModelBuilder(classModelBuilder);
+
 		Graph graph = directoryBuilder.build("target/test-classes", "yooze.Class4");
 		ByteArrayOutputStream bytes = new ByteArrayOutputStream(1000);
 		DotPrinter d = new DotPrinter(bytes);

src/test/java/yooze/output/JsonPrinterTest.java

@@ -5,25 +5,27 @@ import java.io.IOException;
 
 import junit.framework.Assert;
 
-import org.junit.Before;
 import org.junit.Test;
 
-import yooze.ClassCache;
+import yooze.ClassModelBuilder;
 import yooze.GraphBuilder;
+import yooze.InclusionDecider;
 import yooze.application.GraphBuilderFactory;
 import yooze.domain.Graph;
 
 public class JsonPrinterTest {
-	@Before
-	public void clearClassCache() {
-		ClassCache.clear();
-	}
 
 	@Test
 	public void jsonShouldBeWellFormed() throws IOException {
 		GraphBuilder directoryBuilder = GraphBuilderFactory.getClassesDirectoryBuilder();
-		directoryBuilder.setPackageExcludePatterns(".*?Class4");
+
-		directoryBuilder.setPackageIncludePatterns(".*?.Class.");
+		InclusionDecider i = new InclusionDecider();
+		i.setPackageExcludePatterns(".*?Class4");
+		i.setPackageIncludePatterns(".*?.Class.");
+		ClassModelBuilder classModelBuilder = new ClassModelBuilder();
+		classModelBuilder.setInclusionDecider(i);
+		directoryBuilder.setClassModelBuilder(classModelBuilder);
+
 		Graph graph = directoryBuilder.build("target/test-classes", "yooze.Class1");
 
 		ByteArrayOutputStream bytes = new ByteArrayOutputStream(500);