From f369c6599a09abb89fcc3d36bfca47b808b91fc7 Mon Sep 17 00:00:00 2001
From: Dave Parker <dave.x.parker@gmail.com>
Date: Fri, 29 Jun 2012 18:35:01 +0000
Subject: [PATCH] Re-factor SBML-to-PRISM translator.

git-svn-id: https://www.prismmodelchecker.org/svn/prism/prism/trunk@5405 bbc10eb1-c90d-0410-af57-cb519fbb1720
---
 prism/src/prism/Reactions2Prism.java | 14 +++++++++++---
 prism/src/prism/SBML2Prism.java      | 18 +++++++++---------
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/prism/src/prism/Reactions2Prism.java b/prism/src/prism/Reactions2Prism.java
index e74a4339..c4d8247c 100644
--- a/prism/src/prism/Reactions2Prism.java
+++ b/prism/src/prism/Reactions2Prism.java
@@ -56,12 +56,15 @@ public class Reactions2Prism
 	protected ArrayList<Parameter> parameterList;
 	protected ArrayList<Reaction> reactionList;
 
+	// Config
+	
+	/** Maximum amount of each species (unless some initial amound is higher). */
+	protected int maxAmount = 100;
+
 	// Optional PRISM code header/footer
 	protected String prismCodeHeader;
 	protected String prismCodeFooter;
-
-	protected int maxAmount;
-
+	
 	// Constructors
 
 	public Reactions2Prism()
@@ -74,6 +77,11 @@ public class Reactions2Prism
 		this.mainLog = mainLog;
 	}
 
+	public void setMaxAmount(int maxAmount)
+	{
+		this.maxAmount = maxAmount;
+	}
+	
 	/**
 	 * Print the currently loaded reaction set model (for testing purposes).
 	 */
diff --git a/prism/src/prism/SBML2Prism.java b/prism/src/prism/SBML2Prism.java
index c5f263b8..33a1ac6c 100644
--- a/prism/src/prism/SBML2Prism.java
+++ b/prism/src/prism/SBML2Prism.java
@@ -62,7 +62,13 @@ public class SBML2Prism extends Reactions2Prism implements EntityResolver
 				System.exit(1);
 			}
 			SBML2Prism sbml2prism = new SBML2Prism(errLog);
-			sbml2prism.translate(new File(args[0]), (args.length > 1) ? args[1] : "100");
+			try {
+				if (args.length > 1)
+					sbml2prism.setMaxAmount(Integer.parseInt(args[1]));
+			} catch (NumberFormatException e) {
+				throw new PrismException("Invalid max amount \"" + args[1] + "\"");
+			}
+			sbml2prism.translate(new File(args[0]));
 		} catch (PrismException e) {
 			errLog.println("Error: " + e.getMessage() + ".");
 		}
@@ -81,16 +87,10 @@ public class SBML2Prism extends Reactions2Prism implements EntityResolver
 	}
 
 	/**
-	 * Main method: load SBML file, process and sent resulting PRISM file to stdout
+	 * Main method: load SBML file, process and send resulting PRISM file to stdout
 	 */
-	public void translate(File f, String maxAmount) throws PrismException
+	public void translate(File f) throws PrismException
 	{
-		// translate
-		try {
-			this.maxAmount = Integer.parseInt(maxAmount);
-		} catch (NumberFormatException e) {
-			throw new PrismException("Invalid max amount \"" + maxAmount + "\"");
-		}
 		// Read in SBML
 		Document doc = parseSBML(f);
 		checkSBMLVersion(doc);