changes to the project

.classpath

@@ -28,6 +28,5 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="C:/Users/Asus/Downloads/Java_Binding_1_1/WolframAlphaJavaLibrary/WolframAlpha-1.1.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

pom.xml

@@ -16,7 +16,8 @@
         <maven.build.timestamp.format>yyyy</maven.build.timestamp.format>
         <pt.uminho.ceb.biosystems.merlin.version>4.0.0-SNAPSHOT</pt.uminho.ceb.biosystems.merlin.version>
         <pt.uminho.ceb.biosystems.merlin.groupId>pt.uminho.ceb.biosystems.merlin</pt.uminho.ceb.biosystems.merlin.groupId>
-        <merlin.plugins.directory>${project.basedir}/../merlin-aibench/plugins</merlin.plugins.directory>
+        <merlin.plugins.directory>${project.basedir}/../merlin-project/merlin-gui/plugins</merlin.plugins.directory>
+		<merlin.plugins_bin.directory>${project.basedir}/../merlin-project/merlin-gui/plugins_bin/merlin-bigg</merlin.plugins_bin.directory>
         <slf4j.version>1.8.0-beta4</slf4j.version>
     </properties>
     <repositories>
@@ -53,7 +54,7 @@
                             <goal>copy-resources</goal>
                         </goals>
                         <configuration>
-                            <outputDirectory>../merlin-aibench/plugins_bin/merlin-bigg</outputDirectory>
+                            <outputDirectory>../merlin-project/merlin-gui/plugins_bin/merlin-bigg</outputDirectory>
                             <resources>
                                 <resource>
                                     <directory>target/classes</directory>
@@ -101,10 +102,11 @@
             <version>1.3.2</version>
         </dependency>
         <dependency>
-            <groupId>${pt.uminho.ceb.biosystems.merlin.groupId}</groupId>
-            <artifactId>merlin-aibench</artifactId>
-            <version>${pt.uminho.ceb.biosystems.merlin.version}</version>
-        </dependency>
+			<groupId>pt.uminho.ceb.biosystems.merlin</groupId>
+			<artifactId>merlin-gui</artifactId>
+			<version>4.0.2-RELEASE</version>
+		</dependency>
+
         <dependency>
             <groupId>${pt.uminho.ceb.biosystems.merlin.groupId}</groupId>
             <artifactId>merlin-core</artifactId>
@@ -121,10 +123,10 @@
             <version>1.1.1</version>
         </dependency>
         <dependency>
-    		<groupId>com.bpodgursky</groupId>
-    		<artifactId>jbool_expressions</artifactId>
-    		<version>1.23</version>
-		</dependency>
+        	<groupId>pt.uminho.ceb.biosystems.merlin</groupId>
+			<artifactId>merlin-alignments</artifactId>
+			<version>4.0.05-SNAPSHOT</version>
+        </dependency>
         <!-- </dependency> <groupId>org.sing_group</groupId> <artifactId>gc4s</artifactId> 
             <version>1.2.2</version> </dependency> -->
     </dependencies>

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/DatabaseLoader.java

+package pt.uminho.ceb.biosystems.merlin.bigg.blast;
+
+public class DatabaseLoader {
+
+}

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/ProvideBiggReactionsToGenes.java

@@ -17,6 +17,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
@@ -25,6 +26,7 @@ import org.json.JSONObject;
 
 import pt.uminho.ceb.biosystems.merlin.bigg.data.BiggDataCenter;
 import pt.uminho.ceb.biosystems.merlin.core.datatypes.WorkspaceInitialData;
+import pt.uminho.ceb.biosystems.merlin.services.DatabaseServices;
 import pt.uminho.ceb.biosystems.merlin.services.WorkspaceInitialDataServices;
 
 public class ProvideBiggReactionsToGenes {
@@ -453,7 +455,9 @@ public class ProvideBiggReactionsToGenes {
     	
     	try {
     		
+    		AtomicBoolean cancel = new AtomicBoolean(false);
     		
+//    		DatabaseServices.readxmldb(workspaceName, workFolderID + "Bigg_Files/BiggDatabaseDump/", cancel, this);
     		
     		WorkspaceInitialData databaseInitialData = WorkspaceInitialDataServices.retrieveAllData(workspaceName);
         	

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/operation/CreateModelfromBigg.java

@@ -4,7 +4,7 @@ import es.uvigo.ei.aibench.core.operation.annotation.Direction;
 import es.uvigo.ei.aibench.core.operation.annotation.Operation;
 import es.uvigo.ei.aibench.core.operation.annotation.Port;
 import es.uvigo.ei.aibench.workbench.Workbench;
-import pt.uminho.ceb.biosystems.merlin.aibench.datatypes.WorkspaceAIB;
+import pt.uminho.ceb.biosystems.merlin.gui.datatypes.WorkspaceAIB;
 
 @Operation(name="CreateModelfromBigg", description="Create model from BiGG data.")
 public class CreateModelfromBigg {