Javadoc / unix makefile and manifest

Makefile

@@ -8,6 +8,7 @@ JAVAC = javac
 JAVADOC = javadoc -d doc
 JAVAFLAGS = -O -d classes -encoding utf-8
 JAVACLASSPATH = -cp lib/pdfbox-app-1.8.8.jar
+SRC = src/fr/imag/forge/scidetect/Checker/Utils/*.java src/fr/imag/forge/scidetect/Checker/*.java src/fr/imag/forge/scidetect/Corpus/*.java src/fr/imag/forge/scidetect/Logger/*.java src/fr/imag/forge/scidetect/SciDetect_local/*.java src/fr/imag/forge/scidetect/TextExtractor/*.java
 
 default: all
 
@@ -15,10 +16,10 @@ all: classes doc jar run
 
 classes:
 	mkdir -p classes
-	$(JAVAC) $(JAVAFLAGS) $(JAVACLASSPATH) src/fr/imag/forge/scidetect/*/*.java 
+	$(JAVAC) $(JAVAFLAGS) $(JAVACLASSPATH) $(SRC) 
 
 doc:
-	$(JAVADOC) src/*/*/*/*/*/*
+	$(JAVADOC) $(SRC)
 
 jar:
 	cd classes ; jar -cfvm ../SciDetect_Local`date +%Y-%m-%d`.jar ../manifest.mf *; cd ..

manifest.mf

 Manifest-Version: 1.0
 Class-Path: lib/pdfbox-app-1.8.8.jar
 X-COMMENT: Main-Class will be added automatically by build
-Main-Class: fr.imag.forge.Scidetect.scigenchecker_local.ScigenChecker_Local
+Main-Class: fr.imag.forge.scidetect.SciDetect_local.SciDetect_Local
 

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

@@ -37,7 +37,7 @@ public class Classifier {
     private ThresholdsSet SetOfThresholds;
 
     /**
-     *
+     * Build a new classifier, thresholds are read in the configuration file
      */
     public Classifier() {
         this.SetOfThresholds = new ThresholdsSet();
@@ -86,10 +86,10 @@ public class Classifier {
      *
      * @param result a string composed having for each classes the value of its
      * NN
-     * @return
+     * @return a string composed of the classes and the distances to the nearest neighbor in each class.
      */
     private String checkdistant(String result) {
-        String conclution = "";
+        String conclusion = "";
         String[] eachtype = result.split("\n");
 
         for (int i = 0; i < eachtype.length; i++) {
@@ -105,16 +105,16 @@ public class Classifier {
             }
             //check distant with threshold
             if (Double.parseDouble(eachNN[1]) < threshold[0]) {
-                conclution += "is a " + eachNN[0] + "\t" + eachNN[1] + "\t" + eachNN[2] + "\n";
+                conclusion += "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";
+                conclusion += "is suppected " + eachNN[0] + "\t" + eachNN[1] + "\t" + eachNN[2] + "\n";
             }
 
         }
-        if (conclution == "") {
-            conclution = findmindistant(result);
+        if (conclusion == "") {
+            conclusion = findmindistant(result);
         }
-        return conclution;
+        return conclusion;
     }
 
     /**

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

@@ -24,7 +24,7 @@ import fr.imag.forge.scidetect.Checker.Utils.DistancesSet;
 import fr.imag.forge.scidetect.Corpus.Corpus;
 
 /**
- *
+ * Compute distances between two sets of texts 
  * @author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
  */
 public class DistantCalculator {
@@ -33,10 +33,10 @@ public class DistantCalculator {
 	private DistancesSet distant = new DistancesSet();
 
     /**
-     *calculate the distant between 2 text corpus
+     * Compute distances between each text of a corpus and the samples
      * @param samples corpus
      * @param tests corpus
-     * @return DistancesSet from test to sample
+     * @return DistancesSet distances from text in test to text in sample
      */
     public DistancesSet caldistant(Corpus samples, Corpus tests) {
         for (String key : tests.keySet()) {
@@ -53,9 +53,13 @@ public class DistantCalculator {
 
         return distant;
     }
-/**
- *Calculate distant between 2 text index
- */
+
+    /**
+ 	 * Compute the distance between 2 texts index
+     * @param text1
+     * @param text2
+     * @return the distance between text 1 and text 2.
+     */
     private double cal_textdistant(HashMap<String, Integer> text1,
             HashMap<String, Integer> text2) {
         double nboftoken = 0.0;

src/fr/imag/forge/scidetect/Checker/Indexer.java

@@ -22,7 +22,7 @@ import java.io.PrintWriter;
 import java.util.HashMap;
 
 /**
- *
+ * Index texts (i.e. for each word computes its occurrence number
  * @author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
  */
 public class Indexer {
@@ -30,8 +30,8 @@ public class Indexer {
     private Object content;
 
     /**
-     * Index a text (count how many time each word appeared)
-     * and write to file under then name INDEX-filename.txt
+     * Index a text (count how many time each word is appearing)
+     * and writes results in a file INDEX-filename.txt
      * @param content
      * @param textfile
      * @throws FileNotFoundException

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

+/*
+ * Copyright (C) 2015 UNIVERSITE JOSEPH FOURIER (Grenoble 1)/ Springer-Verlag GmbH
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ */
 package fr.imag.forge.scidetect.Checker.Utils;
 
 import java.util.HashMap;
@@ -18,8 +34,8 @@ public class DistancesSet extends HashMap<String, HashMap<String, Double>>{
     
     /**
      * Get the value of the distance between A and B
-     * @param A
-     * @param B
+     * @param A text
+     * @param B text
      * @return the distance between A and B
      */
     public Double getDist(String A, String B){
@@ -28,9 +44,9 @@ public class DistancesSet extends HashMap<String, HashMap<String, Double>>{
 
     /**
      * Set the distance between A and B to the value d
-     * @param A
-     * @param B
-     * @param d
+     * @param A text
+     * @param B text
+     * @param d distance
      */
     public void setDist(String A, String B, Double d){
     	if (this.get(A) == null) {this.put(A,new HashMap<String, Double>());}

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

+/*
+ * Copyright (C) 2015 UNIVERSITE JOSEPH FOURIER (Grenoble 1)/ Springer-Verlag GmbH
+ *
+ * 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 3 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, see <http://www.gnu.org/licenses/>.
+ */
 
 package fr.imag.forge.scidetect.Checker.Utils;
 
@@ -18,8 +34,6 @@ public class ThresholdsSet extends HashMap<String, Double[]> {
     
     /**
      * Initialize the thresholds Set by reading the configuration file
-     * @throws FileNotFoundException
-     * @throws IOException
      */
     public void Init() {
     	try{

src/fr/imag/forge/scidetect/TextExtractor/pdfextractor.java

@@ -27,7 +27,7 @@ import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.util.PDFTextStripper;
 
 /**
- * extract raw txt from a pdf File
+ * Extract raw txt from a pdf File
  * @author Nguyen Minh Tien - minh-tien.nguyen@imag.fr
  */
 public class pdfextractor {