Utils package for Set of distance and set of thersholds

	modified:   src/fr/imag/forge/Scidetect/Checker/Classifier.java
	modified:   src/fr/imag/forge/Scidetect/Checker/DistantCalculator.java
	new file:   src/fr/imag/forge/Scidetect/Checker/Utils/DistancesSet.java
	new file:   src/fr/imag/forge/Scidetect/Checker/Utils/ThresholdsSet.java
	modified:   src/fr/imag/forge/Scidetect/TextExtractor/Xmlextractor.java
	modified:   src/fr/imag/forge/Scidetect/scigenchecker_local/ScigenChecker_Local.java

src/fr/imag/forge/Scidetect/Checker/Classifier.java

@@ -24,41 +24,30 @@ import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.HashMap;
 
+import fr.imag.forge.Scidetect.Checker.Utils.DistancesSet;
+import fr.imag.forge.Scidetect.Checker.Utils.ThresholdsSet;
+
 /**
  * Classifier is tagging input files has being of a certain class. Example of classes are SCIgen, Mathgen,...
  * The decision is made according to the distance between the tested file and its nearest neighbor 
- * in each class. Thresholds for assignation are read in file specified in the configuration file 
+ * in each class. Thresholds for assigning are read in file specified in the configuration file 
  * (default config.txt).
  * @author Nguyen Minh Tien - minh-tien.nguyen@imag.frs
  */
 public class Classifier {
-    /**
-     * The key is the class name and value is a couple of Double.
-     * This couple is composed of a threshold for quasi-certain classification and another for suspicion.
-     */
-    HashMap<String, Double[]> Threshold = new HashMap<String, Double[]>();
-    /**
-     * Reads threshold in the configuration file (default config.txt).
-     * @throws FileNotFoundException
-     * @throws IOException
-     */
-    public void readconfig() throws FileNotFoundException, IOException {
-        File conf = new File("config.txt");
-        BufferedReader br = new BufferedReader(new FileReader(conf));
-        String line;
-        while ((line = br.readLine()) != null) {
-            if (line.startsWith("Threshold_")) {
-                // System.out.println(line);
-                String[] b = line.split("\t");
-                Double[] temp = new Double[2];
-                temp[0] = Double.parseDouble(b[1]);
-                temp[1] = Double.parseDouble(b[2]);
-                Threshold.put(b[0].substring(10, b[0].length()), temp);
-                //10 because i want to cut Threshold_
-            }
-        }
 
-    }
+	private ThresholdsSet SetOfThresholds;
+	
+	/**
+	 * @throws Exception 
+	 * 
+	 */
+	public Classifier() {
+		this.SetOfThresholds = new ThresholdsSet();
+		this.SetOfThresholds.Init();
+	}
+	
+	
     /**
      * Classify is classifying each document given the matrix of distances (distant).
      * For each entry it gives the class (or more) to which the text can be assigned 
@@ -66,11 +55,11 @@ public class Classifier {
      * @return the assigned class
      * @throws IOException
      */
-    public String classify(HashMap<String, HashMap<String, Double>> distant) throws IOException {
+    public String classify(DistancesSet distant) throws IOException {
 
         String result = "";
         String conclusion = "";
-        readconfig();
+        
         for (String key : distant.keySet()) {
             //for each file in the test
             result = find_NN(distant.get(key));
@@ -107,10 +96,10 @@ public class Classifier {
             //System.out.println(eachtype[i]);
             //get threshold for the corresponding type
             Double[] threshold = new Double[2];
-            if (Threshold.containsKey(eachNN[0])) {
-                threshold = Threshold.get(eachNN[0]);
+            if (SetOfThresholds.containsKey(eachNN[0])) {
+                threshold = SetOfThresholds.get(eachNN[0]);
             } else {
-                threshold = Threshold.get("Default");
+                threshold = SetOfThresholds.get("Default");
             }
             //check distant with threshold
             if (Double.parseDouble(eachNN[1]) < threshold[0]) {

src/fr/imag/forge/Scidetect/Checker/DistantCalculator.java

@@ -20,26 +20,28 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Set;
 
+import fr.imag.forge.Scidetect.Checker.Utils.DistancesSet;
+
 /**
  *
  * @author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
  */
 public class DistantCalculator {
 
-    private HashMap<String, HashMap<String, Double>> distant = new HashMap<String, HashMap<String, Double>>();
+    //private HashMap<String, HashMap<String, Double>> distant = new HashMap<String, HashMap<String, Double>>();
+	private DistancesSet distant = new DistancesSet();
 
-    public HashMap<String, HashMap<String, Double>> caldistant(HashMap<String, HashMap<String, Integer>> samples, HashMap<String, HashMap<String, Integer>> tests) {
+    public DistancesSet caldistant(HashMap<String, HashMap<String, Integer>> samples, HashMap<String, HashMap<String, Integer>> tests) {
         for (String key : tests.keySet()) {
-            HashMap<String, Double> distantto = new HashMap<String, Double>();
+            //HashMap<String, Double> distantto = new HashMap<String, Double>();
             for (String key2 : samples.keySet()) {
-                double distanttt = cal_textdistant(tests.get(key),
-                        samples.get(key2));
+                double distanttt = cal_textdistant(tests.get(key),samples.get(key2));
 				// System.out.println("distant between " + key + " and " + key2
                 // + ": " + distanttt);
-                distantto.put(key2, distanttt);
-
+                //distantto.put(key2, distanttt);
+                distant.setDist(key,key2,distanttt);
             }
-            distant.put(key, distantto);
+            //distant.put(key, distantto);
         }
 
         return distant;

src/fr/imag/forge/Scidetect/Checker/Utils/DistancesSet.java

+package fr.imag.forge.Scidetect.Checker.Utils;
+
+import java.util.HashMap;
+
+/**
+ * DistancesSet(A,B) Stores the distance between the two texts A and B 
+ *
+ */
+public class DistancesSet extends HashMap<String, HashMap<String, Double>>{
+	
+    /**
+     * Constructor
+     */
+    public DistancesSet() {
+	    super();
+    }
+    
+    
+    /**
+     * Get the value of the distance between A and B
+     * @param A
+     * @param B
+     * @return the distance between A and B
+     */
+    public Double getDist(String A, String B){
+    	return this.get(A).get(B);
+    }
+
+    /**
+     * Set the distance between A and B to the value d
+     * @param A
+     * @param B
+     * @param d
+     */
+    public void setDist(String A, String B, Double d){
+    	if (this.get(A) == null) {this.put(A,new HashMap<String, Double>());}
+    	this.get(A).put(B,d);
+    }
+    
+}

src/fr/imag/forge/Scidetect/Checker/Utils/ThresholdsSet.java

+
+package fr.imag.forge.Scidetect.Checker.Utils;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.HashMap;
+/**
+ * @author 
+ */
+public class ThresholdsSet extends HashMap<String, Double[]> {
+
+    public ThresholdsSet() {
+    		    super();
+    }
+    
+    /**
+     * Initialize the thresholds Set by reading the configuration file
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
+    public void Init() {
+    	try{
+    		this.readconfig();
+    	}
+    	catch (Exception E) { 
+    		System.out.println("*****");
+            System.out.println("***** Problem when reading Thresholds values");
+            System.out.println("***** Please check the config.txt file ");
+    		System.out.println("*****");
+    	};
+    }
+    
+    /**
+     * Reads threshold in the configuration file (default config.txt).
+     * @throws Exception 
+     */
+    private void readconfig() throws Exception {
+        File conf = new File("config.txt");
+        BufferedReader br = new BufferedReader(new FileReader(conf));
+        String line;
+        boolean foundClass= false;
+        while ((line = br.readLine()) != null) {
+            if (line.startsWith("Threshold_")) {
+                // System.out.println(line);
+            	foundClass=true;
+                String[] b = line.split("\t");
+                Double[] temp = new Double[2];
+                temp[0] = Double.parseDouble(b[1]);
+                temp[1] = Double.parseDouble(b[2]);
+                this.put(b[0].substring(10, b[0].length()), temp);
+                //10 because i want to cut Threshold_
+            }
+        }
+        br.close();
+        if (!foundClass){throw new Exception();};
+    }
+
+
+	
+}

src/fr/imag/forge/Scidetect/TextExtractor/Xmlextractor.java

@@ -62,11 +62,11 @@ public class Xmlextractor {
         //return text;
     }
     /**
-     *  <#Description#>
+     *  Extract txt from xml
      *
-     *  @param xml <#xml description#>
+     *  @param xml xml File
      *
-     *  @return <#return value description#>
+     *  @return extracted content
      */
     public String xmlextract(File xml) throws IOException {
         try {

src/fr/imag/forge/Scidetect/scigenchecker_local/ScigenChecker_Local.java

@@ -20,8 +20,10 @@ import fr.imag.forge.Scidetect.Checker.Classifier;
 import fr.imag.forge.Scidetect.Checker.DistantCalculator;
 import fr.imag.forge.Scidetect.Checker.Indexer;
 import fr.imag.forge.Scidetect.Checker.Reader;
+import fr.imag.forge.Scidetect.Checker.Utils.DistancesSet;
 import fr.imag.forge.Scidetect.Logger.Log;
 import fr.imag.forge.Scidetect.TextExtractor.pdfextractor;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -47,7 +49,8 @@ public class ScigenChecker_Local {
     private HashMap<String, HashMap<String, Integer>> samples = new HashMap<String, HashMap<String, Integer>>();
     private HashMap<String, HashMap<String, Integer>> tests = new HashMap<String, HashMap<String, Integer>>();
     private String SamplesFolder;
-    private HashMap<String, HashMap<String, Double>> distant = new HashMap<String, HashMap<String, Double>>();
+    //private HashMap<String, HashMap<String, Double>> distant = new HashMap<String, HashMap<String, Double>>();
+    DistancesSet distant = new DistancesSet();
     private Boolean savedetaillog = false;
 
     /**