Bug fix: output may be empty

Author: guanmingwu

src/main/java/org/reactome/cytoscape/pathway/FactorGraphBatchAnalyzer.java

@@ -88,6 +88,9 @@ protected void runFactorGraphAnalysis() {
             List<FactorGraph> failedFGs = new ArrayList<FactorGraph>();
             boolean isAborted = false;
             for (FactorGraph fg : factorGraphs) {
+//                if (!fg.getName().contains("71737"))
+//                    continue;
+                System.out.println("Handling " + fg.getName() + " (" + count + "/" + factorGraphs.size() + ")");
                 progressPane.setText("Analyzing " + fg.getName() + 
                                      " (" + count + "/" + factorGraphs.size() + ")");
                 // Since progressPane is used by other process, show the progress in the title

src/main/java/org/reactome/cytoscape/util/PlugInUtilities.java

@@ -285,6 +285,9 @@ private static Collection<FileChooserFilter> getAnalysisResultFilters() {
      */
     public static double calculateCombinedPValue(List<Double> pvalues,
                                          List<List<Double>> values) throws MathException {
+        if (pvalues.size() == 0) {
+            return Double.MAX_VALUE; // Nothing to do. Mark this as the largest pvalue.
+        }
         // Have to make sure no 0 in the pvalues list in order to make the implementation in MathUtility work
         List<Double> pvalueCopy = new ArrayList<Double>();
         for (Double pvalue : pvalues) {