Fixed bug with the manifest file in FBACometsLoader and FBAParameters.

briehl · Mar 12, 2014 · 1b49c7b · 1b49c7b
1 parent 02ed9d1
commit 1b49c7b
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/comets_simplified/src/edu/bu/segrelab/comets/fba/FBACometsLoader.java b/comets_simplified/src/edu/bu/segrelab/comets/fba/FBACometsLoader.java
@@ -189,13 +189,14 @@ public int loadLayoutFile(String filename, Comets c, boolean useGui) throws IOEx
 		//Write the file name in the manifest file.
 		try
 		{
-			FileWriter manifestWriter=new FileWriter(new File(path+File.separatorChar+pParams.getManifestFileName()),false);
+			FileWriter manifestWriter=new FileWriter(new File(path+File.separatorChar+pParams.getNopathManifestFileName()),false);
 			manifestWriter.write("LayoutFileName: "+filename+System.getProperty("line.separator"));
 			manifestWriter.close();
-			pParams.setManifestFileName(path+File.separatorChar+pParams.getManifestFileName());
+			pParams.setManifestFileName(path+File.separatorChar+pParams.getNopathManifestFileName());
 		}
 		catch (IOException e)
 		{
+			System.out.println(e.getMessage());
 			System.out.println("Unable to initialize manifest file. \nContinuing without writing manifest file.");
 		}		
 

diff --git a/comets_simplified/src/edu/bu/segrelab/comets/fba/FBAParameters.java b/comets_simplified/src/edu/bu/segrelab/comets/fba/FBAParameters.java
@@ -140,6 +140,7 @@ public static ExchangeStyle findByName(String name)
 				   totalBiomassLogName;
 
 	private String manifestFileName = "COMETS_manifest.txt";
+	private final String nopathManifestFileName="COMETS_manifest.txt";
 
 	private int numRunThreads = 1,
 				numDiffPerStep = 10,
@@ -809,6 +810,14 @@ public LogFormat getFluxLogFormat()
 		return fluxLogFormat; 
 	}
 
+	/** Gets the name of the manifest file
+	 *  without the path prepended.
+	 * 
+	 */
+	public String getNopathManifestFileName()
+	{
+		return nopathManifestFileName;
+	}
 
 	/** Gets the name of the manifest file
 	 *