Add documentation in commands folder

src/main/java/metapenta/commands/ConnectedComponents.java

@@ -4,6 +4,10 @@
 import metapenta.model.MetaPenta;
 import metapenta.tools.io.writers.ConnectedComponentsWriter;
 
+/**
+ * args[0] Metabolic network in XML format
+ * args[1] Output file
+ */
 public class ConnectedComponents {
 	public static void main(String[] args) throws Exception {
 		MetaPenta network = new MetaPenta(args[0]);

src/main/java/metapenta/commands/GetMetabolicNetworkInterception.java

@@ -7,6 +7,11 @@
 
 public class GetMetabolicNetworkInterception {
 
+    /**
+     * args[0]: Metabolic network 1 in XML format
+     * args[1]: Metabolic network 2 in XML format
+     * args[2]: Output file
+     */
     public static void main(String[] args) throws Exception {
         MetabolicNetworkXMLLoader loader = new MetabolicNetworkXMLLoader();
 
@@ -15,7 +20,7 @@ public static void main(String[] args) throws Exception {
 
         MetabolicNetwork resultNetwork = firstNetwork.interception(secondNetwork);
 
-        Writer metabolicNetworkWriter = new MetabolicNetworkJSONWriter(resultNetwork, args[3]);
+        Writer metabolicNetworkWriter = new MetabolicNetworkJSONWriter(resultNetwork, args[2]);
         metabolicNetworkWriter.write();
     }
 }

src/main/java/metapenta/commands/NetworkBoundaryFinder.java

@@ -5,6 +5,10 @@
 import metapenta.tools.io.writers.NetworkBoundaryWriter;
 
 public class NetworkBoundaryFinder {
+    /**
+     * args[0]: Metabolic network in XML format
+     * args[1]: Output file
+     */
     public static void main(String[] args) throws Exception {
         MetaPenta network = new MetaPenta(args[0]);
         NetworkBoundaryDTO networkBoundary = network.findNetworkBoundary();

src/main/java/metapenta/commands/WriteMetabolicNetworkInCSV.java

@@ -5,12 +5,13 @@
 import metapenta.tools.io.writers.MetabolicNetworkCSVWriter;
 import metapenta.tools.io.writers.Writer;
 
-/**
- * args[0]: Metabolic network in XML format
- * args[1]: Output file
- */
+
 public class WriteMetabolicNetworkInCSV {
 
+    /**
+     * args[0]: Metabolic network in XML format
+     * args[1]: Output file
+     */
     public static void main(String[] args) throws Exception {
         MetabolicNetworkXMLLoader loader = new MetabolicNetworkXMLLoader();
         MetabolicNetwork network = loader.loadNetwork(args[0]);