properly read the functions file

Author: danv61

vcell-core/src/main/java/cbit/vcell/simdata/DataSetControllerImpl.java

@@ -2406,13 +2406,11 @@ public LangevinBatchResultSet getLangevinBatchResultSet(VCDataIdentifier vcdID)
 		ODEDataInfo odeDataInfo = new ODEDataInfo(vcdID.getOwner(), vcdID.getID(),
 									simData.getDataBlockTimeStamp(ODE_DATA, 0));
 		int keepAtMost = 10000;
-		File functionsFile = null;
+		File functionsFile = simData.getJobFunctionsFile();
 		LangevinBatchResultSet lbrs = new LangevinBatchResultSet(odeDataInfo);
 
 		File avg_file = simData.getLangevinFile(LangevinBatchResultSet.LangevinFileType.Avg);
 		if (avg_file != null && avg_file.exists()) {
-			// want to keep all results, so pass 0 for keepAtMost
-			// don't care about functions, so pass null for functionsFile
 			ODESimData odeSimData_avg = ODESimData.readIDADataFile(vcdID, avg_file, keepAtMost, functionsFile);
 			lbrs.setOdeSimDataAvg(odeSimData_avg);
 		}

vcell-core/src/main/java/cbit/vcell/simdata/MergedData.java

@@ -1160,5 +1160,10 @@ public ComsolSimFiles getComsolSimFiles() throws FileNotFoundException, DataAcce
 	throw new RuntimeException("MergedData.getComsolSimFiles() not yet implemented");
 }
 
+@Override
+public File getJobFunctionsFile() throws FileNotFoundException {
+	throw new RuntimeException("MergedData.getJobFunctionsFile() not yet implemented");
+}
+
 
 }

vcell-core/src/main/java/cbit/vcell/simdata/SimulationData.java

@@ -626,8 +626,8 @@ private synchronized File getFirstJobFunctionsFile() throws FileNotFoundExceptio
 	}
 }
 
-
-private synchronized File getJobFunctionsFile() throws FileNotFoundException {
+@Override
+public synchronized File getJobFunctionsFile() throws FileNotFoundException {
 	File functionsFile = null;
 	functionsFile = amplistorHelper.getFunctionsFile(false);
 	if (functionsFile.exists()){

vcell-core/src/main/java/cbit/vcell/simdata/VCData.java

@@ -226,4 +226,6 @@ public final double[][][] getSimDataTimeSeries(
 
 public abstract boolean isComsol() throws DataAccessException, IOException;
 
+public abstract File getJobFunctionsFile() throws FileNotFoundException;
+
 }

vcell-core/src/main/java/cbit/vcell/solver/ode/ODESimData.java

@@ -512,16 +512,6 @@ public static ODESimData readIDADataFile(VCDataIdentifier vcdId, File dataFile,
 	}
 
 	// read functions file
-	if(functionsFile == null) {
-		// functionFile is being initialized in SimulationData.getJobFunctionsFile() which already
-		// throws is the file doesn't exist, so we call explicitly with null here to skip functions loading
-		// for langevin batch simulation results (where functionFile is meaningless)
-		if (keepMost > 0) {
-			odeSimData.trimRows(keepMost);
-		}
-		return odeSimData;
-	}
-
 	if (!odeSimData.getColumnDescriptions(0).getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME)) {
 		Vector<AnnotatedFunction> funcList;
 		try {