Merge pull request #1 from Gebbi8/master

DiViL extension

.gitignore

@@ -5,3 +5,7 @@ dist
 testfiles
 target
 lib
+.settings
+src/log4j.properties
+.project
+.classpath

pom.xml

@@ -3,7 +3,7 @@
     <groupId>de.unirostock.sems</groupId>
     <artifactId>BiVeS</artifactId>
     <packaging>jar</packaging>
-    <version>1.9.2</version>
+    <version>1.10.0</version>
     <name>BiVeS</name>
     <description>
         BiVeS - BioModel Version Control System
@@ -36,17 +36,17 @@
         <dependency>
             <groupId>de.unirostock.sems</groupId>
             <artifactId>BiVeS-SBML</artifactId>
-            <version>1.7.5</version>
+            <version>1.8.0</version>
         </dependency>
         <dependency>
             <groupId>de.unirostock.sems</groupId>
             <artifactId>BiVeS-CellML</artifactId>
-            <version>1.6.6</version>
+            <version>1.7.1</version>
         </dependency>
         <dependency>
             <groupId>de.unirostock.sems</groupId>
             <artifactId>BiVeS-Core</artifactId>
-            <version>1.7.2</version>
+            <version>1.8.1</version>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>
@@ -58,6 +58,12 @@
             <artifactId>log4j</artifactId>
             <version>1.2.17</version>
         </dependency>
+        <dependency>
+        	<groupId>de.unirostock.sems</groupId>
+        	<artifactId>BiVeS</artifactId>
+        	<version>1.9.1</version>
+        	<scope>provided</scope>
+        </dependency>
     </dependencies>
     <distributionManagement>
         <downloadUrl>http://mvn.sems.uni-rostock.de</downloadUrl>   

src/main/java/de/unirostock/sems/bives/Executer.java

@@ -81,6 +81,9 @@ public class Executer
 	public static final String REQ_WANT_REACTIONS_DOT = "reactionsDot";
 	public static final String REQ_WANT_REACTIONS_DOT2 = "crnDot";
 
+	/** The Constant REQ_WANT_REACTIONS_SBGN_JSON. */
+	public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson";
+
 	/** The Constant REQ_WANT_REACTIONS_JSON. */
 	public static final String REQ_WANT_REACTIONS_JSON = "reactionsJson";
 	public static final String REQ_WANT_REACTIONS_JSON2 = "crnJson";
@@ -188,6 +191,7 @@ private void fillOptions ()
 		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML).desc ("get the highlighted reaction network encoded in GraphML").build ());
 		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT).desc ("get the highlighted reaction network encoded in DOT language").build ());
 		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON).desc ("get the highlighted reaction network encoded in JSON").build ());
+		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_SBGN_JSON).desc ("get the highlighted reaction network encoded in an SBGN-JSON format").build ());
 		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML2).desc ("get the highlighted reaction network encoded in GraphML (deprecated version)").build ());
 		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT2).desc ("get the highlighted reaction network encoded in DOT language (deprecated version)").build ());
 		options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON2).desc ("get the highlighted reaction network encoded in JSON (deprecated version)").build ());
@@ -509,6 +513,17 @@ else if ((type & DocumentClassifier.XML) != 0)
 				errors.add (e);
 			}
 
+		if (line.hasOption (REQ_WANT_REACTIONS_SBGN_JSON))
+			try
+			{
+				hasOption = true;
+				toReturn.put (Executer.REQ_WANT_REACTIONS_SBGN_JSON, result (diff.getReactionsSbgnJsonGraph ()));
+			}
+			catch (Exception e)
+			{
+				errors.add (e);
+			}
+
 		if (line.hasOption (REQ_WANT_COMP_HIERARCHY_DOT))
 			try
 			{