Cache graph data on creation

readme.md

@@ -159,8 +159,10 @@ Structure:
 Graph and Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
 Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file 
 (to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a 
-Sample Plate file (to construct the associated occupancy graph). These files can be several gigabytes in size.
-Writing them to a file lets us generate a graph and its metadata once, then use it for multiple different BiGpairSEQ simulations.
+Sample Plate file (to construct the associated occupancy graph).
+
+These files can be several gigabytes in size. Writing them to a file lets us generate a graph and its metadata once,
+then use it for multiple different BiGpairSEQ simulations.
 
 Options for creating a Graph and Data file:
 * The Cell Sample file to use
@@ -172,7 +174,11 @@ portable data format may be implemented in the future. The tricky part is encodi
 ---
 
 #### Matching Results Files 
-Matching results files consist of the results of a BiGpairSEQ matching simulation.
+Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a Graph and 
+Data file. To save file I/O time, the data from the most recent Graph and Data file read or generated is cached
+by the simulator. Subsequent BiGpairSEQ simulations run with the same input filename will use the cached version
+rather than reading in again from disk.
+
 Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
 Metadata about the matching simulation is included as comments. Comments are preceded by `#`.
 

src/main/java/InteractiveInterface.java

@@ -75,7 +75,6 @@ public class InteractiveInterface {
         assert filename != null;
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
-        System.gc();
     }
 
     //Output a CSV of sample plate
@@ -187,7 +186,6 @@ public class InteractiveInterface {
             System.out.println("Writing Sample Plate to file");
             writer.writePlateFile();
             System.out.println("Sample Plate written to file: " + filename);
-            System.gc();
         }
     }
 
@@ -234,7 +232,9 @@ public class InteractiveInterface {
             GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
             dataWriter.writeDataToFile();
             System.out.println("Graph and Data file written to: " + filename);
-            System.gc();
+            BiGpairSEQ.setGraph(data);
+            BiGpairSEQ.setGraphFilename(filename);
+            System.out.println("Graph and Data file " + filename + " cached.");
         }
     }
 
@@ -296,7 +296,6 @@ public class InteractiveInterface {
         System.out.println("Writing results to file");
         writer.writeResultsToFile();
         System.out.println("Results written to file: " + filename);
-        System.gc();
     }
 
     ///////