removed path hardcode from example file

examples/org/simulator/sedml/SEDMLv2Test.java

@@ -3,8 +3,8 @@
 import static org.junit.Assert.fail;
 
 import java.io.File;
+import java.util.List;
 import java.util.Map;
-import java.util.logging.Logger;
 
 import org.jfree.ui.RefineryUtilities;
 import org.jlibsedml.AbstractTask;
@@ -16,6 +16,8 @@
 import org.simulator.math.odes.MultiTable;
 import org.simulator.plot.PlotMultiTable;
 
+import de.binfalse.bflog.LOGGER;
+
 /**
  * This test class shows how a SED-ML file can be interpreted and executed using
  *  SBML Simulator Core solvers. <br/> It makes extensive use of jlibsedml's 
@@ -27,32 +29,31 @@
  * @since 1.5
  */
 public class SEDMLv2Test {
-	private static File l1v1Test = new File("files/sedmlTest/ClockSedML.xml");
-	private static File l1v2Test = new File("files/sedmlTest/l1v2/v3-example1-repeated-steady-scan-oscli.xml");
-	//private static File l1v2Test = new File("files/sedmlTest/l1v2/v3-example2-oscli-nested-pulse.xml");
-	//private static File l1v2Test = new File("files/sedmlTest/l1v2/v3-example3-repeated-stochastic-runs.xml");
-	//private static File l1v2Test = new File("files/sedmlTest/l1v2/v3-example4-repeated-scan-oscli.xml");
-	//private static File l1v2Test = new File("files/sedmlTest/l1v2/v3-example5-boris-2d-scan.xml");
 	private static SedML sedml = null;
 
 	public static void main(String[] args) throws XMLException {
-		System.out.println("Reading SEDML document...");
-		sedml=Libsedml.readDocument(l1v2Test).getSedMLModel();
+		if(args[0] == null) {
+			LOGGER.warn("Please give file file name as argument.");
+			return;
+		}
+		File file = new File(args[0]);
+
+		sedml=Libsedml.readDocument(file).getSedMLModel();
 
 		// in this SED-ML file there's just one output. If there were several,
 		// we could either iterate or get user to  decide what they want to run.
 		Output wanted = sedml.getOutputs().get(0);
 		SedMLSBMLSimulatorExecutor exe = new SedMLSBMLSimulatorExecutor(sedml, wanted);
 		// This gets the raw simulation results - one for each Task that was run.
-		System.out.println("Collecting tasks...");
-		Map<AbstractTask, IRawSedmlSimulationResults> res = exe.run();
+		LOGGER.warn("Collecting tasks...");
+		Map<AbstractTask, List<IRawSedmlSimulationResults>> res = exe.run();
 		if (res==null ||res.isEmpty() || !exe.isExecuted()) {
 			fail ("Simulatation failed: " + exe.getFailureMessages().get(0));
 			return;
 		}
 		// now process.In this case, there's no processing performed - we're displaying the
 		// raw results.
-		System.out.println("Outputs wanted: " + wanted);
+		LOGGER.warn("Outputs wanted: " + wanted);
 		MultiTable mt = exe.processSimulationResults(wanted, res);
 
 		// plot all the reactions species

src/org/simulator/sedml/SedMLSBMLSimulatorExecutor.java

@@ -481,7 +481,7 @@ private double[][] mergeDataCols(double[][] a, double[][] b) {
 	}
 
 	/**
-	 * Merge time coloumns from 2 multiTables
+	 * Merge time columns from 2 multiTables
 	 * @param MultTableSEDMLWrapper
 	 * @param MultTableSEDMLWrapper
 	 * @return double[]
@@ -565,20 +565,22 @@ AbstractDESSolver getSolverForKisaoID(String id) {
 	 */
 	public MultiTable processSimulationResults(Output wanted,
 			Map<AbstractTask, List<IRawSedmlSimulationResults>> res) {
-		// here we post-process the results
-		SedMLResultsProcesser2 pcsr2 =  new SedMLResultsProcesser2(sedml, wanted);
-		pcsr2.process(res);
-
-		// this does not necessarily have time as x-axis - another variable could be  the
-		// independent variable.
-		IProcessedSedMLSimulationResults prRes = pcsr2.getProcessedResult();
-
-
-		// now we restore a MultiTable from the processed results. This basic example assumes a typical
-		// simulation where time = xaxis - otherwise, if output is a Plot, we would need to analyse the x-axis
-		// datagenerators
-		MultiTable mt = createMultiTableFromProcessedResults(wanted, prRes);
-		return mt;
+//		// here we post-process the results
+//		SedMLResultsProcesser2 pcsr2 =  new SedMLResultsProcesser2(sedml, wanted);
+//		pcsr2.process(res);
+//
+//		// this does not necessarily have time as x-axis - another variable could be  the
+//		// independent variable.
+//		IProcessedSedMLSimulationResults prRes = pcsr2.getProcessedResult();
+//
+//
+//		// now we restore a MultiTable from the processed results. This basic example assumes a typical
+//		// simulation where time = xaxis - otherwise, if output is a Plot, we would need to analyse the x-axis
+//		// datagenerators
+//		MultiTable mt = createMultiTableFromProcessedResults(wanted, prRes);
+//		return mt;
+		//TODO: Update this method to work with Map containing list of results
+		return null;
 	}
 
 	// Here we need to check which of the results are the independent axis to create a MultiTable