Corrected packet naming

Makefile

@@ -15,10 +15,10 @@ all: classes doc jar
 
 classes:
 	mkdir -p classes
-	$(JAVAC) $(JAVAFLAGS) $(JAVACLASSPATH) src/fr/imag/Scidetect/*/*.java 
+	$(JAVAC) $(JAVAFLAGS) $(JAVACLASSPATH) src/fr/imag/forge/Scidetect/*/*.java 
 
 doc:
-	$(JAVADOC) src/*/*/*/*/*
+	$(JAVADOC) src/*/*/*/*/*/*
 
 jar:
 	cd classes ; jar -cfvm ../ScigenChecker_Local`date +%Y-%m-%d`.jar ../MANIFEST.MF *; cd ..

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

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.imag.Scidetect.Checker;
+package fr.imag.forge.Scidetect.Checker;
 
 import java.io.BufferedReader;
 import java.io.File;

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

+/*
+ * Copyright (C) 2015 UNIVERSITE JOSEPH FOURIER (Grenoble 1)/ Springer-Verlag GmbH
+ * author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+package fr.imag.Scidetect.Checker;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.HashMap;
+
+/**
+ *
+ * @author tien
+ */
+public class Classifier {
+
+    HashMap<String, Double[]> Threshold = new HashMap<String, Double[]>();
+
+    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_
+            }
+        }
+
+    }
+
+    public String classify(HashMap<String, HashMap<String, Double>> 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));
+            //System.out.println(result);
+            //System.out.println(key);
+            //System.out.println(result);
+            String[] a = checkdistant(result).split("\n");
+
+            if (a[0].length() == 0) {
+                conclusion += key + "\t" + "cant classify\t1\tnull\n";
+            } else {
+                for (int i = 0; i < a.length; i++) {
+
+                    conclusion += key + "\t" + a[i] + "\n";
+                }
+            }
+
+        }
+        //System.out.println(conclusion);
+        return conclusion;
+
+    }
+
+    private String checkdistant(String result) {
+        String conclution = "";
+        String[] eachtype = result.split("\n");
+
+        for (int i = 0; i < eachtype.length; i++) {
+            String[] eachNN = eachtype[i].split("\t");
+            //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]);
+            } else {
+                threshold = Threshold.get("Default");
+            }
+            //check distant with threshold
+            if (Double.parseDouble(eachNN[1]) < threshold[0]) {
+                conclution += "is a " + eachNN[0] + "\t" + eachNN[1] + "\t" + eachNN[2] + "\n";
+            } else if (Double.parseDouble(eachNN[1]) < threshold[1]) {
+                conclution += "is suppected " + eachNN[0] + "\t" + eachNN[1] + "\t" + eachNN[2] + "\n";
+            }
+
+        }
+        if (conclution == "") {
+            conclution = findmindistant(result);
+        }
+        return conclution;
+    }
+
+    private String findmindistant(String result) {
+        Double mindistant = 1.0;
+        String[] eachtype = result.split("\n");
+
+        String conclu = "";
+        for (int i = 0; i < eachtype.length; i++) {
+            String[] eachNN = eachtype[i].split("\t");
+            if (Double.parseDouble(eachNN[1]) < mindistant) {
+                mindistant = Double.parseDouble(eachNN[1]);
+                conclu = "is Genuine \t" + eachNN[1] + "\t" + eachNN[2] + "\n";
+            }
+        }
+        return conclu;
+    }
+
+    private String gettype(String indexpath) {
+        File indexfile = new File(indexpath);
+        String parent = indexfile.getParent();
+        // String type = parent.substring(0, parent.lastIndexOf("/"));
+        parent = parent.substring(parent.lastIndexOf("/") + 1, parent.length());
+        return parent;
+    }
+
+    private String find_NN(HashMap<String, Double> distantto) {
+        HashMap<String, Double> distotype = new HashMap<String, Double>();
+        HashMap<String, String> NNname = new HashMap<String, String>();
+        Double MinNN = 1.0;
+        String NN = "";
+
+        for (String key : distantto.keySet()) {
+            String type = gettype(key);
+            if (!distotype.containsKey(type)) {
+                distotype.put(type, distantto.get(key));
+                NNname.put(type, key);
+            } else if (distantto.get(key) < distotype.get(type)) {
+                distotype.put(type, distantto.get(key));
+                NNname.put(type, key);
+            }
+
+        }
+        // it returns the path to the NN
+        String result = "";
+        for (String key : distotype.keySet()) {
+            result += key + "\t" + distotype.get(key) + "\t" + NNname.get(key) + "\n";
+        }
+        return result;
+    }
+}

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

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.imag.Scidetect.Checker;
+package fr.imag.forge.Scidetect.Checker;
 
 import java.util.HashMap;
 import java.util.HashSet;

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

+/*
+ * Copyright (C) 2015 UNIVERSITE JOSEPH FOURIER (Grenoble 1)/ Springer-Verlag GmbH
+ * author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+package fr.imag.Scidetect.Checker;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ *
+ * @author tien
+ */
+public class DistantCalculator {
+
+    private HashMap<String, HashMap<String, Double>> distant = new HashMap<String, HashMap<String, Double>>();
+
+    public HashMap<String, HashMap<String, Double>> 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>();
+            for (String key2 : samples.keySet()) {
+                double distanttt = cal_textdistant(tests.get(key),
+                        samples.get(key2));
+				// System.out.println("distant between " + key + " and " + key2
+                // + ": " + distanttt);
+                distantto.put(key2, distanttt);
+
+            }
+            distant.put(key, distantto);
+        }
+
+        return distant;
+    }
+
+    private double cal_textdistant(HashMap<String, Integer> text1,
+            HashMap<String, Integer> text2) {
+        double nboftoken = 0.0;
+        double sum = 0.0;
+
+        Set<String> keys1 = text1.keySet();
+        Set<String> keys2 = text2.keySet();
+        Set<String> allkeys = new HashSet<String>();
+        allkeys.addAll(keys1);
+        allkeys.addAll(keys2);
+        Integer Na = 0, Nb = 0;
+        // get the nb of token in each text
+        for (String key : allkeys) {
+            Integer Fa = 0;
+            Integer Fb = 0;
+            if (text1.containsKey(key)) {
+                Fa = text1.get(key);
+            }
+            if (text2.containsKey(key)) {
+                Fb = text2.get(key);
+            }
+            Na += Fa;
+            Nb += Fb;
+        }
+        // reduce propotion for text of different lenght
+        if (Na <= Nb) {
+            for (String key : allkeys) {
+                Integer Fa = 0;
+                Integer Fb = 0;
+                if (text1.containsKey(key)) {
+                    Fa = text1.get(key);
+                }
+                if (text2.containsKey(key)) {
+                    Fb = text2.get(key);
+                }
+                sum += Math.abs(Fa - (double) Fb * (Na / (double) Nb));
+            }
+            return sum / (2 * Na);
+        } else {
+            for (String key : allkeys) {
+                Integer Fa = 0;
+                Integer Fb = 0;
+                if (text1.containsKey(key)) {
+                    Fa = text1.get(key);
+                }
+                if (text2.containsKey(key)) {
+                    Fb = text2.get(key);
+                }
+                sum += Math.abs(Fa * (Nb / (double) Na) - (double) Fb);
+            }
+            return sum / (2 * Nb);
+        }
+    }
+}

src/fr/imag/Scidetect/Checker/Indexer.java → src/fr/imag/forge/Scidetect/Checker/Indexer.java

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.imag.Scidetect.Checker;
+package fr.imag.forge.Scidetect.Checker;
 
 import java.io.File;
 import java.io.FileNotFoundException;

src/fr/imag/forge/Scidetect/Checker/Indexer.java~

+/*
+ * Copyright (C) 2015 UNIVERSITE JOSEPH FOURIER (Grenoble 1)/ Springer-Verlag GmbH
+ * author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+package fr.imag.Scidetect.Checker;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.util.HashMap;
+
+/**
+ *
+ * @author tien
+ */
+public class Indexer {
+
+    private Object content;
+
+    public void index(String content, File textfile) throws FileNotFoundException {
+        String filename = textfile.getName().substring(0,textfile.getName().lastIndexOf("."));
+        filename+=".txt";
+        String path = textfile.getParent();
+
+        String[] words = content.split(" ");
+        //System.out.println(words.length);
+        HashMap<String, Integer> counter = new HashMap<String, Integer>();
+        for (int i = 0; i < words.length; i++) {
+            if (!counter.containsKey(words[i])) {
+                counter.put(words[i], 1);
+            } else {
+                counter.put(words[i], counter.get(words[i]) + 1);
+            }
+        }
+
+        File indexout = new File(path + "/INDEX-" + filename);
+       // String filepath = (indexout.getPath());
+        PrintWriter out = new PrintWriter(indexout);
+
+        for (String key : counter.keySet()) {
+            out.println(key + "\t" + counter.get(key));
+        }
+        out.close();
+    }
+}

src/fr/imag/Scidetect/Checker/Reader.java → src/fr/imag/forge/Scidetect/Checker/Reader.java

@@ -14,10 +14,10 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.imag.Scidetect.Checker;
+package fr.imag.forge.Scidetect.Checker;
 
-import fr.imag.Scidetect.TextExtractor.Xmlextractor;
-import fr.imag.Scidetect.TextExtractor.pdfextractor;
+import fr.imag.forge.Scidetect.TextExtractor.Xmlextractor;
+import fr.imag.forge.Scidetect.TextExtractor.pdfextractor;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;

src/fr/imag/forge/Scidetect/Checker/Reader.java~

+/*
+ * Copyright (C) 2015 UNIVERSITE JOSEPH FOURIER (Grenoble 1)/ Springer-Verlag GmbH
+ * author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+package fr.imag.Scidetect.Checker;
+
+import fr.imag.Scidetect.TextExtractor.Xmlextractor;
+import fr.imag.Scidetect.TextExtractor.pdfextractor;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+
+/**
+ *
+ * @author tien
+ */
+public class Reader {
+
+    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 int maxlength;
+
+    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("#")) {
+                // System.out.println(line);
+                String[] b = line.split("\t");
+                if (b[0].equals("samples")) {
+                    SamplesFolder = b[1];
+                }
+                //other config should be read over here
+                if (b[0].equals("Max_length")) {
+                    maxlength = Integer.parseInt(b[1]);
+                }
+            }
+        }
+
+    }
+
+    public HashMap<String, HashMap<String, Integer>> readsamples(String foldername) throws IOException {
+        File folder = new File(foldername);
+        File[] listOfFile = folder.listFiles();
+
+        for (int j = 0; j < listOfFile.length; j++) {
+            if (listOfFile[j].isDirectory()) {
+                readsamples(listOfFile[j].getPath());
+            } else if (listOfFile[j].getName().endsWith(".pdf")) {
+                // find if there is already index for it
+                String indexname = "INDEX-"
+                        + listOfFile[j].getName().substring(0,
+                                listOfFile[j].getName().lastIndexOf("."))
+                        + ".txt";
+                if (Arrays.asList(listOfFile).toString().contains(indexname)) {
+                    // System.out.println("lets read from index file");
+                    readindexfile(listOfFile[j].getParent() + "/" + indexname);
+                } else {
+                    pdfextractor a = new pdfextractor();
+                    String content = a.pdfextract(listOfFile[j]);
+                    Indexer b = new Indexer();
+                    b.index(content, listOfFile[j]);
+                    readindexfile(listOfFile[j].getParent() + "/" + indexname);
+                }
+            }
+        }
+        return samples;
+    }
+
+    private void readindexfile(String path) throws IOException {
+        File index = new File(path);
+        BufferedReader br;
+        br = new BufferedReader(new FileReader(index));
+        String line;
+        HashMap<String, Integer> a = new HashMap<String, Integer>();
+        while ((line = br.readLine()) != null) {
+            String[] b = line.split("\t");
+            a.put(b[0], Integer.parseInt(b[1]));
+        }
+        br.close();
+        if (path.contains(SamplesFolder)) {
+            samples.put(path, a);
+        } else {
+            tests.put(path, a);
+        }
+    }
+
+    private void readfile(File pdf) throws IOException {
+
+        String content = "";
+        if (pdf.getName().endsWith(".pdf")) {
+
+            pdfextractor a = new pdfextractor();
+            content = a.pdfextract(pdf);
+        } else if (pdf.getName().endsWith(".xml") || pdf.getName().endsWith(".xtx")) {
+            Xmlextractor a = new Xmlextractor();
+            content = a.xmlextract(pdf);
+        }
+
+        //lets deal with long file over here
+        //split content and the index part by part
+        if (content.length() < maxlength) {
+            String indexname = "INDEX-"
+                    + pdf.getName().substring(0,
+                            pdf.getName().lastIndexOf("."))
+                    + ".txt";
+
+            Indexer b = new Indexer();
+            b.index(content, pdf);
+
+            readindexfile(pdf.getParent() + "/" + indexname);
+        } else {
+            String[] part = splitcontent(content);
+            for (int i = 0; i < part.length; i++) {
+                String indexname = "INDEX-"
+                        + pdf.getName().substring(0,
+                                pdf.getName().lastIndexOf("."))
+                        + "_part" + i + ".txt";
+                String filename = pdf.getName().substring(0,
+                        pdf.getName().lastIndexOf("."))
+                        + "_part" + i + ".txt";
+                Indexer b = new Indexer();
+                File a = new File(pdf.getParent() + "/" + filename);
+                PrintWriter out = new PrintWriter(new FileWriter(a));
+                out.println(part[i]);
+                //System.out.println(text);
+                out.close();
+                b.index(part[i], a);
+
+                readindexfile(a.getParent() + "/" + indexname);
+
+            }
+        }
+    }
+
+    public HashMap<String, HashMap<String, Integer>> readtests(String testpath) throws IOException {
+        File folder = new File(testpath);
+
+        if (folder.isDirectory()) {
+            File[] listOfFile = folder.listFiles();
+
+            for (int j = 0; j < listOfFile.length; j++) {
+
+                if (listOfFile[j].isDirectory()) {
+                    readtests(listOfFile[j].getPath());
+                } else if (listOfFile[j].getName().endsWith(".pdf") || listOfFile[j].getName().endsWith(".xml") || listOfFile[j].getName().endsWith(".xtx")) {
+                    readfile(listOfFile[j]);
+                }
+            }
+        } else if (folder.getName().endsWith(".pdf") || folder.getName().endsWith(".xml") || folder.getName().endsWith(".xtx")) {
+            readfile(folder);
+
+        }
+        return tests;
+    }
+
+    private String[] splitcontent(String content) {
+
+        int nbofpart = content.length() / maxlength;
+        String[] part = new String[nbofpart + 1];
+        int lower = 0;