Remove testing code, add garbage collection calls

readme.md

@@ -222,9 +222,10 @@ using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et a
 
 ## TODO
 
-* Try invoking GC at end of workloads to reduce paging to disk
+* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
 * ~~Hold graph data in memory until another graph is read-in?~~
   * No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.
+* ~~See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows~~ DONE
 * Enable GraphML output in addition to serialized object binaries, for data portability
   * Custom vertex type with attribute for sequence occupancy?
 * Re-implement CDR1 matching method
@@ -237,10 +238,7 @@ using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et a
 * Implement sample plates with random numbers of T cells per well
   * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well populations; pairSEQ is not.
     * preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
-* See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows
-  * Problem is variable number of cells in a well
-  * Apache Commons CSV library writes entries a row at a time
-    * Can possibly sort the wells by length first, then construct entries 
+
   
 ## CITATIONS
 * Howie, B., Sherwood, A. M., et al. ["High-throughput pairing of T cell receptor alpha and beta sequences."](https://pubmed.ncbi.nlm.nih.gov/26290413/) Sci. Transl. Med. 7, 301ra131 (2015)

src/main/java/UserInterface.java

@@ -319,6 +319,7 @@ public class UserInterface {
         assert filename != null;
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
+        System.gc();
     }
 
 //    //for calling from command line
@@ -465,6 +466,7 @@ public class UserInterface {
             System.out.println("Writing Sample Plate to file");
             writer.writePlateFile();
             System.out.println("Sample Plate written to file: " + filename);
+            System.gc();
         }
     }
 
@@ -496,14 +498,6 @@ public class UserInterface {
         assert plateFile != null;
         PlateFileReader plateReader = new PlateFileReader(plateFile);
         Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
-
-        //TAKE THIS OUT
-        PlateFileWriter writer = new PlateFileWriter(filename + "_plate", plate);
-        System.out.println("Writing Sample Plate to file");
-        writer.writePlateFile();
-        System.out.println("Sample Plate written to file: " + filename + "_plate");
-        //
-
         if (cellReader.getCells().size() == 0){
             System.out.println("No cell sample found.");
             System.out.println("Returning to main menu.");
@@ -521,6 +515,7 @@ public class UserInterface {
             System.out.println("File I/O time is not included in results.");
             dataWriter.writeDataToFile();
             System.out.println("Graph and Data file written to: " + filename);
+            System.gc();
         }
     }
 
@@ -575,6 +570,7 @@ public class UserInterface {
         System.out.println("Writing results to file");
         writer.writeResultsToFile();
         System.out.println("Results written to file: " + filename);
+        System.gc();
     }
 
     ///////