Mavenize project for easier project setup.

README.md

@@ -1,6 +1,6 @@
 #<a id="top"></a>Anonymouth
 
-![](src/edu/drexel/psal/resources/graphics/readme_Logo.png)
+![](src/main/resources/graphics/readme_Logo.png)
 
 Document Anonymization Tool, Version 0.5<br>
 
@@ -38,17 +38,19 @@ Though Anonymouth and it's team works hard to provide you with tools to help rem
 
 ###<a id="dependencies"></a>Dependencies
 
-Java 7 is required to run Anonymouth. If you don't yet have it, get it at <a href="http://java.com/en/download/index.jsp">Oracle's website here</a> and follow the installation instructions provided there.
+Java 7 (or higher) and Maven are required to run Anonymouth. If you don't yet have it, get it at <a href="http://java.com/en/download/index.jsp">Oracle's website here</a> and [Maven Download](https://maven.apache.org/download.cgi). Follow the installation instructions provided there.
 
 If you are unsure whether or not you have it installed, follow these steps to see:
-* OS X:
-	1.  Open up Terminal (Applications/Utilities)
-	2.  Type "java -version" without the quotes
-	3.  If you see something like `java version "1.7.x_xx"` then you're ready to go! If not, then that means you most likely don't have Java 7 installed, in which case you should go to the download link above
-* Windows:
-	1.  Follow the instructions here: http://www.java.com/en/download/help/version_manual.xml. if you have version "1.7.x_xx", then you're good to go! If not, then that means you most likely don't have Java 7 installed, in which case you should go to the download link above
-
-If you are using Eclipse, also make sure that Java 7 is your selected compiler by checking `Preferences/Java/Compiler` and is an included Library in your java Build Path (Not sure how to do this? Google is your friend).
+1. Open up a terminal
+    Linux: Bash/ZSH/...
+    OS X: Applications/Utilities
+    Windows: Press Windows key + R and execute cmd
+2. Type `java -version`
+3. If you don't see something like `java version "1.7.x_xx" or "1.8.x_xx"` then please install the required Java version
+4. Check if Maven installed by running `mvn`. Note that Maven sometimes comes bundled within your favorite IDE.
+    If not please install it using [this](https://maven.apache.org/install.html)
+
+Please make sure that you import the project as Maven project in your favorite IDE.
 
 Anonymouth requires the included `jsan_resources` directory in it's running directory (The main Anonymouth directory containing lib, src, etc.). It should be in the correct directy by default.
 

pom.xml

@@ -0,0 +1,123 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>edu.drexel.psal</groupId>
+    <artifactId>anonymouth</artifactId>
+    <packaging>jar</packaging>
+
+    <version>1.0-SNAPSHOT</version>
+    <name>anonymouth</name>
+    <url>https://psal.cs.drexel.edu/index.php/JStylo-Anonymouth</url>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.6.1</version>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.0.2</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <mainClass>edu.drexel.psal.anonymouth.gooie.ThePresident</mainClass>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <repositories>
+        <repository>
+            <id>jitpack.io</id>
+            <url>https://jitpack.io</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.github.mark-watson</groupId>
+            <artifactId>fasttag_v2</artifactId>
+            <version>e769975e70</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.github.jaytaylor</groupId>
+            <artifactId>jaws</artifactId>
+            <version>1.3.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.memetix</groupId>
+            <artifactId>microsoft-translator-java-api</artifactId>
+            <version>0.6.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>nz.ac.waikato.cms.weka</groupId>
+            <artifactId>weka-stable</artifactId>
+            <version>3.8.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>net.sf.jcommon</groupId>
+            <artifactId>jcommon</artifactId>
+            <version>1.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>jfreechart</groupId>
+            <artifactId>jfreechart</artifactId>
+            <version>1.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>com.miglayout</groupId>
+            <artifactId>miglayout-swing</artifactId>
+            <version>4.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.annolab.tt4j</groupId>
+            <artifactId>org.annolab.tt4j</artifactId>
+            <version>1.0.15</version>
+        </dependency>
+
+        <dependency>
+            <groupId>gov.nist.math</groupId>
+            <artifactId>jama</artifactId>
+            <version>1.0.3</version>
+        </dependency>
+
+        <!-- System libraries -->
+        <dependency>
+            <groupId>jgaap-5.2.0-lite</groupId>
+            <artifactId>jgaap-5.2.0-lite</artifactId>
+            <scope>system</scope>
+            <version>5.2.0</version>
+            <systemPath>${basedir}/lib/jgaap-5.2.0-lite.jar</systemPath>
+        </dependency>
+
+        <dependency>
+            <groupId>ui</groupId>
+            <artifactId>ui</artifactId>
+            <scope>system</scope>
+            <version>1.0-SNAPSHOT</version>
+            <systemPath>${basedir}/lib/ui.jar</systemPath>
+        </dependency>
+
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+</project>

src/edu/drexel/psal/ANONConstants.java → src/main/java/edu/drexel/psal/ANONConstants.java

@@ -21,8 +21,7 @@ public class ANONConstants {
 	//DO NOT DELETE, for use when bundling Anonymouth in an OS X app.
 	//public static final String LOG_DIR = System.getProperty("user.home")+"/Desktop/anonymouth_log";
 	public static final String LOG_DIR = WORKING_DIR + "anonymouth_log";
-	public static final String RESOURCE_PACKAGE = "/edu/drexel/psal/resources/";
-	public static final String GRAPHICS_PREFIX = RESOURCE_PACKAGE+"graphics/";
+	public static final String GRAPHICS_PREFIX = "graphics/";
 	public static final String EXTERNAL_RESOURCE_PACKAGE = ANONConstants.WORKING_DIR + "jsan_resources/";
 	public static final String CORPORA_PREFIX = EXTERNAL_RESOURCE_PACKAGE+"corpora/";
 	public static final String PROBLEMSETS_PREFIX = EXTERNAL_RESOURCE_PACKAGE+"problem_sets/";
@@ -31,7 +30,7 @@ public class ANONConstants {
 	public static final String DOC_MAGICIAN_WRITE_DIR = WORKING_DIR + ".edited_documents/";
 	public static final String KOPPEL_FUNCTION_WORDS = EXTERNAL_RESOURCE_PACKAGE+"koppel_function_words.txt";
 	public static final String SER_DIR = WORKING_DIR + ".serialized_objects/";
-	public static final String GRAPHICS = "/edu/drexel/psal/resources/graphics/";
+	public static final String GRAPHICS = "/graphics/";
 	public static final String PATH_TO_CLASSIFIER = SER_DIR+"saved_classifier.model";
 	public static final String ABBREVIATIONS_FILE = EXTERNAL_RESOURCE_PACKAGE+"abbreviations.txt";
 

src/edu/drexel/psal/anonymouth/gooie/PreProcessAdvancedDriver.java → src/main/java/edu/drexel/psal/anonymouth/gooie/PreProcessAdvancedDriver.java

@@ -6,6 +6,7 @@
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowListener;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import javax.swing.SwingUtilities;
@@ -523,10 +524,13 @@ protected void updateClassifierTab() {
 		Logger.logln(NAME+"Successfully loaded classifier: "+className);
 		//Add an -M option for SMO classifier
 		if (className.toLowerCase().contains("smo")) {
-			String options = advancedWindow.getOptionsStr(((OptionHandler)tmpClassifier).getOptions()) + " -M";
+			String[] optionsArray = ((OptionHandler) tmpClassifier).getOptions();
+			optionsArray = Arrays.copyOf(optionsArray, optionsArray.length + 1);
+			optionsArray[optionsArray.length - 1] = "-M";
 			try {
-				((OptionHandler)tmpClassifier).setOptions(options.split(" "));
+				((OptionHandler)tmpClassifier).setOptions(optionsArray);
 			} catch (Exception e) {
+				e.printStackTrace();
 				Logger.logln(NAME+"Problem occured while tried to add -M flag to SMO classifier", LogOut.STDERR);
 			}
 		}
@@ -544,4 +548,4 @@ protected void updateClassifierTab() {
 
 		SwingUtilities.invokeLater(new ScrollToTop(new Point(0, 0), advancedWindow.classDescScrollPane));
 	}
-}
+}

src/edu/drexel/psal/anonymouth/gooie/StartWindow.java → src/main/java/edu/drexel/psal/anonymouth/gooie/StartWindow.java

@@ -635,4 +635,4 @@ public void actionPerformed(ActionEvent e) {
 		};
 		continueButton.addActionListener(continueListener);
 	}
-}
+}

src/edu/drexel/psal/jstylo/eventDrivers/MaxentPOSTagsEventDriverGeneric.java → src/main/java/edu/drexel/psal/jstylo/eventDrivers/MaxentPOSTagsEventDriverGeneric.java

@@ -6,7 +6,7 @@
 import edu.drexel.psal.jstylo.generics.Logger;
 import edu.drexel.psal.jstylo.generics.Logger.LogOut;
 import edu.stanford.nlp.ling.*;
-import edu.stanford.nlp.tagger.maxent.MaxentTagger; 
+import edu.stanford.nlp.tagger.maxent.MaxentTagger;
 
 import java.io.*;
 import java.util.*;

src/edu/drexel/psal/jstylo/generics/Analyzer.java → src/main/java/edu/drexel/psal/jstylo/generics/Analyzer.java

@@ -257,7 +257,7 @@ public Evaluation getTrainTestEval(List<Document> testDocs){ //TODO overhaul thi
 			allInstances.setClassIndex(allInstances.numAttributes()-1);
 			goodInstances = new Instances(allInstances,0,extractedAuthors.size());
 			smo.buildClassifier(goodInstances);
-			smo.setBuildLogisticModels(true);
+			smo.setBuildCalibrationModels(true);
 			eval = new Evaluation(allInstances);		
 		} catch (Exception e){
 			e.printStackTrace();

src/edu/drexel/psal/jstylo/generics/FeatureDriver.java → src/main/java/edu/drexel/psal/jstylo/generics/FeatureDriver.java

@@ -370,7 +370,7 @@ public NormBaselineEnum getNormBaseline() {
 	 * 		The normalization factor.
 	 */
 	public Double getNormFactor() {
-		return norm.getSecond() == null ? 1 : norm.getSecond();
+		return norm.getSecond() == null ? 1D : norm.getSecond();
 	}
 
 	/**