diff --git a/src/main/java/edu/odu/cs/cs350/DupDetector.java b/src/main/java/edu/odu/cs/cs350/DupDetector.java
index cbb7294..466fe39 100644
--- a/src/main/java/edu/odu/cs/cs350/DupDetector.java
+++ b/src/main/java/edu/odu/cs/cs350/DupDetector.java
@@ -1,6 +1,5 @@
 package edu.odu.cs.cs350;
 
-import java.io.FileNotFoundException;
 /**
  * DupDetector is the main class for the system. It will call
  * each subsystem of the program, passing input/output between
@@ -9,44 +8,13 @@
 public class DupDetector {
     
 	public static void main(String args[]) throws Exception {
-    	/**
-    	 * input file will be invoked using command line arguments
-    	 * args[0] is reserved for the number of suggestions the user wants to print
-    	 * args[1] is an optional input to load a properties file, if no properties 
-    	 * file is loaded, it will set to default properties
-    	 * args[i] i will be any number of files supplied in the command line
-    	 */
-    	if (args.length == 0) {
-            System.err.println ("Usage: java -jar build/libs/DupDetector.jar <nSuggestions> "
-            		+ "<properties file>[OPTIONAL] <path/of/file1> <path/of/file2>");
-            System.exit(-1);
-        }
-    	int nSuggestions = Integer.parseInt(args[0]);
-    	if(args[1].endsWith(".ini")) {
-    		for (int i = 2; i < args.length; i++) {	
-    			try {
-    				String startDir = args[i];
-    				RecursiveSearch r = new RecursiveSearch();
-					Output out = new Output();
-					out.setFiles(r.searchWithProperties(startDir, args[1]));
-					System.out.println(out.getSectionOne());
-    			} catch(FileNotFoundException e) {
-    				System.out.println(e.getMessage());
-    			}
-    		}
-		}
-    	else {
-    		for (int i = 1; i < args.length; i++) {
-        		try {
-                    String startDir = args[i];
-                    RecursiveSearch r = new RecursiveSearch();
-                    Output out = new Output();
-					out.setFiles(r.searchDirectory(startDir));
-					System.out.println(out.getSectionOne());
-                } catch(FileNotFoundException e) {
-                    System.out.println(e.getMessage());
-                }
-    		}
-    	}
+		Input input = new Input(args);
+		Recommender recommender = new Recommender(input.getTokens());
+		Output output = new Output(
+			input.getNSuggestions(),
+			input.getFiles(),
+			recommender.getRefactorings()
+		);
+		System.out.println(output.getCompleteOutput());
     }
 }
diff --git a/src/main/java/edu/odu/cs/cs350/Input.java b/src/main/java/edu/odu/cs/cs350/Input.java
new file mode 100644
index 0000000..632ee3d
--- /dev/null
+++ b/src/main/java/edu/odu/cs/cs350/Input.java
@@ -0,0 +1,82 @@
+package edu.odu.cs.cs350;
+
+import java.io.FileNotFoundException;
+import java.io.File;
+import java.util.*;
+
+/**
+ * Input file will be invoked using command line arguments.
+ * args[0] is reserved for the number of suggestions the user wants
+ * to print.
+ * args[1] is an optional input to load a properties file, if no
+ * properties file is loaded, it will set to default properties.
+ * args[i] i will be any number of files supplied in the command
+ * line.
+ */
+public class Input {
+
+    private int nSuggestions;
+    private List<File> files;
+    private List<Token> tokens;
+    
+    Input() {
+        this.nSuggestions = 0;
+        files = new ArrayList<File>();
+        tokens = new ArrayList<Token>();
+    }
+
+    Input(String args[]) throws Exception {
+        if (args.length == 0) {
+            System.err.println("Usage: java -jar build/libs/DupDetector.jar <nSuggestions> "
+            		+ "<properties file>[OPTIONAL] <path/of/file1> <path/of/file2>");
+            System.exit(-1);
+        }
+
+        this.nSuggestions = Integer.parseInt(args[0]);
+
+        if(args[1].endsWith(".ini")) {
+    		for (int i = 2; i < args.length; i++) {	
+    			try {
+    				String startDir = args[i];
+    				RecursiveSearch r = new RecursiveSearch();
+					this.files = r.searchWithProperties(startDir, args[1]);
+    			} catch(FileNotFoundException e) {
+    				System.out.println(e.getMessage());
+    			}
+    		}
+		}
+    	else {
+    		for (int i = 1; i < args.length; i++) {
+        		try {
+                    String startDir = args[i];
+                    RecursiveSearch r = new RecursiveSearch();
+					this.files = r.searchDirectory(startDir);
+                } catch(FileNotFoundException e) {
+                    System.out.println(e.getMessage());
+                }
+    		}
+    	}
+
+        this.setTokens();
+    }
+
+    public void setTokens() {
+        this.tokens = new ArrayList<Token>();
+        for (File file : this.getFiles()) {
+            TokenAnalyzer t = new TokenAnalyzer(file);
+            this.tokens.add(t.getTokens());
+        }
+    }
+
+    public List<File> getFiles() {
+        return this.files;
+    }
+
+    public List<Token> getTokens() {
+        return this.tokens;
+    }
+
+    public int getNSuggestions() {
+        return this.nSuggestions;
+    }
+}
diff --git a/src/main/java/edu/odu/cs/cs350/TokenAnalyzer.java b/src/main/java/edu/odu/cs/cs350/TokenAnalyzer.java
index 5cb622c..4d2e67f 100644
--- a/src/main/java/edu/odu/cs/cs350/TokenAnalyzer.java
+++ b/src/main/java/edu/odu/cs/cs350/TokenAnalyzer.java
@@ -1,5 +1,6 @@
 package edu.odu.cs.cs350;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.Reader;
 import java.util.List;
@@ -21,6 +22,8 @@ public class TokenAnalyzer implements Iterable<Token> {
 
     /** Token object found in the file. Contains necessary metadata defined in Token class. */
     private Token token;
+
+    private File file;
     
     /**
      * The default constructor for token analyzer.
@@ -42,6 +45,12 @@ public TokenAnalyzer(Reader input) {
         scanner = new LexerAnalyzer(input);
     }
 
+    public TokenAnalyzer(File file) {
+        tokensContainer = new LinkedList<Token>();
+        this.file = file;
+        scanner = new LexerAnalyzer(input);
+    }
+
     /**
      * Divides source codes into tokens.
      * The function will scan each token and add it to the 
@@ -84,4 +93,8 @@ public final Iterator<Token> iterator() {
     public String toString() {
         return Integer.toString(getFileTokenCount());
     }
+
+	public Token getTokens() {
+		return null;
+	}
 }