Add proper support for building with Maven

.classpath

@@ -21,10 +21,10 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="target/Libraries/align.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/alignsvc.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/ontowrap.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/procalign.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/spmf.jar"/>
+	<classpathentry kind="lib" path="lib/align.jar"/>
+	<classpathentry kind="lib" path="lib/alignsvc.jar"/>
+	<classpathentry kind="lib" path="lib/ontowrap.jar"/>
+	<classpathentry kind="lib" path="lib/procalign.jar"/>
+	<classpathentry kind="lib" path="lib/spmf.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

.gitignore

@@ -1 +1,2 @@
 /.apt_generated/
+target/

README.md

@@ -10,9 +10,28 @@ An automatic data linking tool developed by [DOREMUS][3].
 3. **Indexing and Instance matching**: We apply standard NLP techniques to index the instance profiles by using a term frequency vector model. The threshold value of Legato applies to the similarity computed at this stage. Low thresholds are recommended to ensure high recall (default 0.2). 
 4. **Link repairing**: A post-processing step to repair erroneous links generated in the matching step by clustering highly similar instances together and applying a key-identification adn ranking algorthims.
 
-<b> How to run <i> Legato </i> </b>
+<b> How to build <i> Legato </i> </b>
 ========
-For running <b> <i> Legato </i> </b> through the GUI, please run the "main.java" class in the "legato" package. Then, select the source, the target and a reference alignement (if availble). Then, you can choose between two treatment's modes:
+### Using Maven
+The first time you build this project, run the following command to generate Maven dependencies:
+```
+mvn initialize
+```
+Then, everytime you want to build:
+```
+mvn clean package
+```
+To run:
+```
+mvn exec:java
+```
+
+### Manually
+For running <b> <i> Legato </i> </b> through the GUI, please run the "main.java" class in the "legato" package.
+
+<b> How to use <i> Legato </i> </b>
+========
+Select the source, the target and a reference alignement (if availble). Then, you can choose between two treatment's modes:
 - Automatic allows to filter resources by fixing only the classes to compare.
 - Manual allows to filter resources by classe and comparate by a set of selected properties.
 The field "threshold value" allows to define Legato's threshold in the Instance matching step. Legato will consider only resources with a similarity higher than the threshold value.

pom.xml

@@ -18,6 +18,134 @@
           <target>1.8</target>
         </configuration>
       </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>exec-maven-plugin</artifactId>
+        <version>1.6.0</version>
+        <executions>
+          <execution>
+          <goals>
+            <goal>java</goal>
+          </goals>
+          </execution>
+        </executions>
+        <configuration>
+          <mainClass>legato.Main</mainClass>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.1.1</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-jar-plugin</artifactId>
+        <version>2.4</version>
+        <configuration>
+          <archive>
+            <manifest>
+              <mainClass>legato.Main</mainClass>
+              <addClasspath>true</addClasspath>
+              <classpathPrefix>libs/</classpathPrefix>
+            </manifest>
+          </archive>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-install-plugin</artifactId>
+        <version>2.5.2</version>
+        <executions>
+          <!-- SPMF -->
+          <execution>
+            <id>install-spmf</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/spmf.jar</file>
+              <groupId>ca.pfv.spmf</groupId>
+              <artifactId>SPMF</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- align -->
+          <execution>
+            <id>install-align</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/align.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>align</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- alignsvc -->
+          <execution>
+            <id>install-alignsvc</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/alignsvc.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>alignsvc</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- ontowrap -->
+          <execution>
+            <id>install-ontowrap</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/ontowrap.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>ontowrap</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- proc-align -->
+          <execution>
+            <id>install-proc-align</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/procalign.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>proc-align</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
   </build>
 
@@ -119,6 +247,41 @@
 	</dependency>
 
 
+	<!-- lib/spmf.jar -->
+	<dependency>
+	<groupId>ca.pfv.spmf</groupId>
+	<artifactId>SPMF</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/align.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>align</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/alignsvc.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>alignsvc</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/ontowrap.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>ontowrap</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/procalign.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>proc-align</artifactId>
+	<version>1.0</version>
+	</dependency>
+
   </dependencies>
 
 </project>

src/legato/indexer/VectorGenerator.java

@@ -42,7 +42,7 @@ public DocVector[] GetDocumentVectors() throws IOException {
         for (int docId = 0; docId < totalNoOfDocumentInIndex; docId++) {
             Terms vector = indexReader.getTermVector(docId, LEGATO.getInstance().FIELD_CONTENT);
             TermsEnum termsEnum = null;
-            //Verification integrit� de vector
+            //Verification integrité de vector
             try
             {
             	termsEnum = vector.iterator(termsEnum);