Update readme to reflect new default caching behavior.

readme.md

@@ -29,17 +29,13 @@ Unfortunately, it's a fairly new algorithm, and not yet implemented by the graph
 So this program instead uses the Fibonacci heap-based algorithm of Fredman and Tarjan (1987), which has a worst-case
 runtime of **O(n (n log(n) + m))**. The algorithm is implemented as described in Melhorn and Näher (1999).
 
-The current version of the program uses a pairing heap instead of a Fibonacci heap for its priority queue,
-which has lower theoretical efficiency but also lower complexity overhead, and is often equivalently performant
-in practice.
-
 ## USAGE
 
 ### RUNNING THE PROGRAM
 
 [Download the current version of BiGpairSEQ_Sim.](https://gitea.ejsf.synology.me/efischer/BiGpairSEQ/releases)
 
-BiGpairSEQ_Sim is an executable .jar file. Requires Java 11 or higher. [OpenJDK 17](https://jdk.java.net/17/)
+BiGpairSEQ_Sim is an executable .jar file. Requires Java 14 or higher. [OpenJDK 17](https://jdk.java.net/17/)
 recommended.
 
 Run with the command:
@@ -65,6 +61,7 @@ Please select an option:
 2) Generate a sample plate of T cells
 3) Generate CDR3 alpha/beta occupancy data and overlap graph
 4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ)
+8) Options
 9) About/Acknowledgments
 0) Exit
 ```
@@ -77,18 +74,21 @@ To run the simulation, the program reads and writes 4 kinds of files:
 * Graph/Data files in binary object serialization format
 * Matching Results files in CSV format
 
-These files are often generated in sequence. To save file I/O time, the most recent instance of each of these four
+These files are often generated in sequence. When entering filenames, it is not necessary to include the file extension
-files either generated or read from disk is cached in program memory. This is especially important for Graph/Data files,
+(.csv or .ser). When reading or writing files, the program will automatically add the correct extension to any filename without one.
+
+To save file I/O time, the most recent instance of each of these four
+files either generated or read from disk can be cached in program memory. This is could be important for Graph/Data files,
 which can be several gigabytes in size. Since some simulations may require running multiple, 
-differntly-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached drastically reduces 
+differently-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached may reduce execution time.
-execution time. 
+(The manipulation necessary to re-use a graph incurs its own performance overhead, though, which may scale with graph
+size faster than file I/O does. If so, caching is best for smaller graphs.)
 
-Subsequent uses of the same data file won't need to be read in again until another file of that type is used or generated.
+When caching is active, subsequent uses of the same data file won't need to be read in again until another file of that type is used or generated,
-The program checks whether it needs to update its cached data by comparing filenames as entered by the user. On 
+or caching is turned off for that file type. The program checks whether it needs to update its cached data by comparing
-encountering a new filename, the program flushes its cache and reads in the new file.
+filenames as entered by the user. On encountering a new filename, the program flushes its cache and reads in the new file.
 
-When entering filenames, it is not necessary to include the file extension (.csv or .ser). When reading or
+The program's caching behavior can be controlled in the Options menu. By default, all caching is OFF.
-writing files, the program will automatically add the correct extension to any filename without one. 
 
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
@@ -253,7 +253,8 @@ slightly less time than the simulation itself. Real elapsed time from start to f
 * ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
 * Hold graph data in memory until another graph is read-in? ~~ABANDONED~~ ~~UNABANDONED~~ DONE
   * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~
-  * Might have figured out a way to do it, by taking edges out and then putting them back into the graph. This may actually be possible. If so, awesome.
+  * Might have figured out a way to do it, by taking edges out and then putting them back into the graph. This may actually be possible.
+  * It is possible, though the modifications to the graph incur their own performance penalties. Need testing to see which option is best.
 * 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~~ 
@@ -267,9 +268,10 @@ slightly less time than the simulation itself. Real elapsed time from start to f
 * Re-implement CDR1 matching method
 * Implement Duan and Su's maximum weight matching algorithm
   * Add controllable algorithm-type parameter?
-* Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm
+* ~~Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm~~ DONE
-  * in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage
+  * ~~in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage~~
-  * Add controllable heap-type parameter?
+  * ~~Add controllable heap-type parameter?~~
+    * Parameter implemented. For large graphs, Fibonacci heap wins. Now the new default.
 
 
   

src/main/java/BiGpairSEQ.java

@@ -10,6 +10,10 @@ public class BiGpairSEQ {
     private static String plateFilename = null;
     private static GraphWithMapData graphInMemory = null;
     private static String graphFilename = null;
+    private static boolean cacheCells = false;
+    private static boolean cachePlate = false;
+    private static boolean cacheGraph = false;
+    private static String priorityQueueHeapType = "FIBONACCI";
 
     public static void main(String[] args) {
         if (args.length == 0) {
@@ -30,66 +34,134 @@ public class BiGpairSEQ {
         return cellSampleInMemory;
     }
 
-    public static void setCellSampleInMemory(CellSample cellSampleInMemory) {
+    public static void setCellSampleInMemory(CellSample cellSample, String filename) {
-        BiGpairSEQ.cellSampleInMemory = cellSampleInMemory;
+        if(cellSampleInMemory != null) {
+            clearCellSampleInMemory();
+        }
+        cellSampleInMemory = cellSample;
+        cellFilename = filename;
+        System.out.println("Cell sample file " + filename + " cached.");
     }
 
     public static void clearCellSampleInMemory() {
         cellSampleInMemory = null;
+        cellFilename = null;
         System.gc();
+        System.out.println("Cell sample file cache cleared.");
+
     }
 
     public static String getCellFilename() {
         return cellFilename;
     }
 
-    public static void setCellFilename(String cellFilename) {
-        BiGpairSEQ.cellFilename = cellFilename;
-    }
-
     public static Plate getPlateInMemory() {
         return plateInMemory;
     }
 
-    public static void setPlateInMemory(Plate plateInMemory) {
+    public static void setPlateInMemory(Plate plate, String filename) {
-        BiGpairSEQ.plateInMemory = plateInMemory;
+        if(plateInMemory != null) {
+            clearPlateInMemory();
+        }
+        plateInMemory = plate;
+        plateFilename = filename;
+        System.out.println("Sample plate file " + filename + " cached.");
     }
 
     public static void clearPlateInMemory() {
         plateInMemory = null;
+        plateFilename = null;
         System.gc();
+        System.out.println("Sample plate file cache cleared.");
+
     }
 
     public static String getPlateFilename() {
         return plateFilename;
     }
 
-    public static void setPlateFilename(String plateFilename) {
+
-        BiGpairSEQ.plateFilename = plateFilename;
+    public static GraphWithMapData getGraphInMemory() {return graphInMemory;
     }
 
-    public static GraphWithMapData getGraphInMemory() {
+    public static void setGraphInMemory(GraphWithMapData g, String filename) {
-        return graphInMemory;
-    }
-
-    public static void setGraphInMemory(GraphWithMapData g) {
         if (graphInMemory != null) {
             clearGraphInMemory();
         }
         graphInMemory = g;
+        graphFilename = filename;
+        System.out.println("Graph and data file " + filename + " cached.");
     }
 
     public static void clearGraphInMemory() {
         graphInMemory = null;
+        graphFilename = null;
         System.gc();
+        System.out.println("Graph and data file cache cleared.");
     }
 
     public static String getGraphFilename() {
         return graphFilename;
     }
 
-    public static void setGraphFilename(String filename) {
+
-        graphFilename = filename;
+    public static boolean cacheCells() {
+        return cacheCells;
     }
 
+    public static void setCacheCells(boolean cacheCells) {
+        //if not caching, clear the memory
+        if(!cacheCells){
+            BiGpairSEQ.clearCellSampleInMemory();
+            System.out.println("Cell sample file caching: OFF.");
+        }
+        else {
+            System.out.println("Cell sample file caching: ON.");
+        }
+        BiGpairSEQ.cacheCells = cacheCells;
+    }
+
+    public static boolean cachePlate() {
+        return cachePlate;
+    }
+
+    public static void setCachePlate(boolean cachePlate) {
+        //if not caching, clear the memory
+        if(!cachePlate) {
+            BiGpairSEQ.clearPlateInMemory();
+            System.out.println("Sample plate file caching: OFF.");
+        }
+        else {
+            System.out.println("Sample plate file caching: ON.");
+        }
+        BiGpairSEQ.cachePlate = cachePlate;
+    }
+
+    public static boolean cacheGraph() {
+        return cacheGraph;
+    }
+
+    public static void setCacheGraph(boolean cacheGraph) {
+        //if not caching, clear the memory
+        if(!cacheGraph) {
+            BiGpairSEQ.clearGraphInMemory();
+            System.out.println("Graph/data file caching: OFF.");
+        }
+        else {
+            System.out.println("Graph/data file caching: ON.");
+        }
+        BiGpairSEQ.cacheGraph = cacheGraph;
+    }
+
+    public static String getPriorityQueueHeapType() {
+        return priorityQueueHeapType;
+    }
+
+    public static void setPairingHeap() {
+        priorityQueueHeapType = "PAIRING";
+    }
+
+    public static void setFibonacciHeap() {
+        priorityQueueHeapType = "FIBONACCI";
+    }
 }

src/main/java/GraphModificationFunctions.java

@@ -6,59 +6,74 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-public abstract class GraphModificationFunctions {
+public interface GraphModificationFunctions {
 
     //remove over- and under-weight edges
-    public static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+    static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
-                                                            int low, int high) {
+                                                            int low, int high, boolean saveEdges) {
         List<Integer[]> removedEdges = new ArrayList<>();
         for (DefaultWeightedEdge e : graph.edgeSet()) {
             if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
+                if(saveEdges) {
                     Integer source = graph.getEdgeSource(e);
                     Integer target = graph.getEdgeTarget(e);
                     Integer weight = (int) graph.getEdgeWeight(e);
                     Integer[] edge = {source, target, weight};
                     removedEdges.add(edge);
                 }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
                 }
+            }
+        }
+        if(saveEdges) {
             for (Integer[] edge : removedEdges) {
                 graph.removeEdge(edge[0], edge[1]);
             }
+        }
         return removedEdges;
     }
 
     //Remove edges for pairs with large occupancy discrepancy
-    public static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+    static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
                                                   Map<Integer, Integer> alphaWellCounts,
                                                   Map<Integer, Integer> betaWellCounts,
                                                   Map<Integer, Integer> plateVtoAMap,
                                                   Map<Integer, Integer> plateVtoBMap,
-                                                  Integer maxOccupancyDifference) {
+                                                  Integer maxOccupancyDifference, boolean saveEdges) {
         List<Integer[]> removedEdges = new ArrayList<>();
         for (DefaultWeightedEdge e : graph.edgeSet()) {
             Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
             Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
             if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
+                if (saveEdges) {
                     Integer source = graph.getEdgeSource(e);
                     Integer target = graph.getEdgeTarget(e);
                     Integer weight = (int) graph.getEdgeWeight(e);
                     Integer[] edge = {source, target, weight};
                     removedEdges.add(edge);
                 }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
                 }
+            }
+        }
+        if(saveEdges) {
             for (Integer[] edge : removedEdges) {
                 graph.removeEdge(edge[0], edge[1]);
             }
+        }
         return removedEdges;
     }
 
     //Remove edges for pairs where overlap size is significantly lower than the well occupancy
-    public static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+    static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
                                                          Map<Integer, Integer> alphaWellCounts,
                                                          Map<Integer, Integer> betaWellCounts,
                                                          Map<Integer, Integer> plateVtoAMap,
                                                          Map<Integer, Integer> plateVtoBMap,
-                                                         Integer minOverlapPercent) {
+                                                         Integer minOverlapPercent,
+                                                         boolean saveEdges) {
         List<Integer[]> removedEdges = new ArrayList<>();
         for (DefaultWeightedEdge e : graph.edgeSet()) {
             Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
@@ -66,20 +81,27 @@ public abstract class GraphModificationFunctions {
             double weight = graph.getEdgeWeight(e);
             double min = minOverlapPercent / 100.0;
             if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
+                if(saveEdges) {
                     Integer source = graph.getEdgeSource(e);
                     Integer target = graph.getEdgeTarget(e);
                     Integer intWeight = (int) graph.getEdgeWeight(e);
                     Integer[] edge = {source, target, intWeight};
                     removedEdges.add(edge);
                 }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
                 }
+            }
+        }
+        if(saveEdges) {
             for (Integer[] edge : removedEdges) {
                 graph.removeEdge(edge[0], edge[1]);
             }
+        }
         return removedEdges;
     }
 
-    public static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+    static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
                                        List<Integer[]> removedEdges) {
         for (Integer[] edge : removedEdges) {
             DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);

src/main/java/InteractiveInterface.java

@@ -27,6 +27,7 @@ public class InteractiveInterface {
                 //Need to re-do the CDR3/CDR1 matching to correspond to new pattern
                 //System.out.println("5) Generate CDR3/CDR1 occupancy graph");
                 //System.out.println("6) Simulate CDR3/CDR1 T cell matching");
+                System.out.println("8) Options");
                 System.out.println("9) About/Acknowledgments");
                 System.out.println("0) Exit");
                 try {
@@ -37,9 +38,10 @@ public class InteractiveInterface {
                         case 3 -> makeCDR3Graph();
                         case 4 -> matchCDR3s();
                         //case 6 -> matchCellsCDR1();
+                        case 8 -> mainOptions();
                         case 9 -> acknowledge();
                         case 0 -> quit = true;
-                        default -> throw new InputMismatchException("Invalid input.");
+                        default -> System.out.println("Invalid input.");
                     }
                 } catch (InputMismatchException | IOException ex) {
                     System.out.println(ex);
@@ -78,11 +80,9 @@ public class InteractiveInterface {
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
         System.out.println("Cell sample written to: " + filename);
-        if(BiGpairSEQ.getCellSampleInMemory() != null) {
+        if(BiGpairSEQ.cacheCells()) {
-            BiGpairSEQ.clearCellSampleInMemory();
+            BiGpairSEQ.setCellSampleInMemory(sample, filename);
         }
-        BiGpairSEQ.setCellSampleInMemory(sample);
-        BiGpairSEQ.setCellFilename(filename);
     }
 
     //Output a CSV of sample plate
@@ -219,9 +219,9 @@ public class InteractiveInterface {
             System.out.println("Reading Cell Sample file: " + cellFile);
             CellFileReader cellReader = new CellFileReader(cellFile);
             cells = cellReader.getCellSample();
-            BiGpairSEQ.clearCellSampleInMemory();
+            if(BiGpairSEQ.cacheCells()) {
-            BiGpairSEQ.setCellSampleInMemory(cells);
+                BiGpairSEQ.setCellSampleInMemory(cells, cellFile);
-            BiGpairSEQ.setCellFilename(cellFile);
+            }
         }
         assert filename != null;
         Plate samplePlate;
@@ -242,8 +242,9 @@ public class InteractiveInterface {
         System.out.println("Writing Sample Plate to file");
         writer.writePlateFile();
         System.out.println("Sample Plate written to file: " + filename);
-        BiGpairSEQ.setPlateInMemory(samplePlate);
+        if(BiGpairSEQ.cachePlate()) {
-        BiGpairSEQ.setPlateFilename(filename);
+            BiGpairSEQ.setPlateInMemory(samplePlate, filename);
+        }
     }
 
     //Output serialized binary of GraphAndMapData object
@@ -271,16 +272,16 @@ public class InteractiveInterface {
         assert cellFile != null;
         CellSample cellSample;
         //check if cells are already in memory
-        if(cellFile.equals(BiGpairSEQ.getCellFilename())) {
+        if(cellFile.equals(BiGpairSEQ.getCellFilename()) && BiGpairSEQ.getCellSampleInMemory() != null) {
             cellSample = BiGpairSEQ.getCellSampleInMemory();
         }
         else {
-            BiGpairSEQ.clearCellSampleInMemory();
             System.out.println("Reading Cell Sample file: " + cellFile);
             CellFileReader cellReader = new CellFileReader(cellFile);
             cellSample = cellReader.getCellSample();
-            BiGpairSEQ.setCellSampleInMemory(cellSample);
+            if(BiGpairSEQ.cacheCells()) {
-            BiGpairSEQ.setCellFilename(cellFile);
+                BiGpairSEQ.setCellSampleInMemory(cellSample, cellFile);
+            }
         }
 
         assert plateFile != null;
@@ -290,12 +291,12 @@ public class InteractiveInterface {
             plate = BiGpairSEQ.getPlateInMemory();
         }
         else {
-            BiGpairSEQ.clearPlateInMemory();
             System.out.println("Reading Sample Plate file: " + plateFile);
             PlateFileReader plateReader = new PlateFileReader(plateFile);
             plate = new Plate(plateReader.getFilename(), plateReader.getWells());
-            BiGpairSEQ.setPlateInMemory(plate);
+            if(BiGpairSEQ.cachePlate()) {
-            BiGpairSEQ.setPlateFilename(plateFile);
+                BiGpairSEQ.setPlateInMemory(plate, plateFile);
+            }
         }
         if (cellSample.getCells().size() == 0){
             System.out.println("No cell sample found.");
@@ -312,9 +313,10 @@ public class InteractiveInterface {
             GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
             dataWriter.writeDataToFile();
             System.out.println("Graph and Data file written to: " + filename);
-            BiGpairSEQ.setGraphInMemory(data);
+            if(BiGpairSEQ.cacheGraph()) {
-            BiGpairSEQ.setGraphFilename(filename);
+                BiGpairSEQ.setGraphInMemory(data, filename);
-            System.out.println("Graph and Data file " + filename + " cached.");
+
+            }
         }
     }
 
@@ -366,17 +368,15 @@ public class InteractiveInterface {
         assert graphFilename != null;
         //check if this is the same graph we already have in memory.
         GraphWithMapData data;
-        if(!(graphFilename.equals(BiGpairSEQ.getGraphFilename())) || BiGpairSEQ.getGraphInMemory() == null) {
+        if(graphFilename.equals(BiGpairSEQ.getGraphFilename())) {
-            BiGpairSEQ.clearGraphInMemory();
+            data = BiGpairSEQ.getGraphInMemory();
-            //read object data from file
-            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
-            data = dataReader.getData();
-            //set new graph in memory and new filename
-            BiGpairSEQ.setGraphInMemory(data);
-            BiGpairSEQ.setGraphFilename(graphFilename);
         }
         else {
-            data = BiGpairSEQ.getGraphInMemory();
+            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
+            data = dataReader.getData();
+            if(BiGpairSEQ.cacheGraph()) {
+                BiGpairSEQ.setGraphInMemory(data, graphFilename);
+            }
         }
         //simulate matching
         MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
@@ -493,6 +493,75 @@ public class InteractiveInterface {
 //        }
 //    }
 
+    private static void mainOptions(){
+        boolean backToMain = false;
+        while(!backToMain) {
+            System.out.println("\n--------------OPTIONS---------------");
+            System.out.println("1) Turn " + getOnOff(!BiGpairSEQ.cacheCells()) + " cell sample file caching");
+            System.out.println("2) Turn " + getOnOff(!BiGpairSEQ.cachePlate()) + " plate file caching");
+            System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
+            System.out.println("4) Maximum weight matching algorithm options");
+            System.out.println("0) Return to main menu");
+            try {
+                input = sc.nextInt();
+                switch (input) {
+                    case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
+                    case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
+                    case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
+                    case 4 -> algorithmOptions();
+                    case 0 -> backToMain = true;
+                    default -> System.out.println("Invalid input");
+                }
+            } catch (InputMismatchException ex) {
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+    }
+
+    /**
+     * Helper function for printing menu items in mainOptions(). Returns a string based on the value of parameter.
+     *
+     * @param b - a boolean value
+     * @return String "on" if b is true, "off" if b is false
+     */
+    private static String getOnOff(boolean b) {
+        if (b) { return "on";}
+        else { return "off"; }
+    }
+
+    private static void algorithmOptions(){
+        boolean backToOptions = false;
+        while(!backToOptions) {
+            System.out.println("\n---------ALGORITHM OPTIONS----------");
+            System.out.println("1) Use scaling algorithm by Duan and Su.");
+            System.out.println("2) Use LEDA book algorithm with Fibonacci heap priority queue");
+            System.out.println("3) Use LEDA book algorithm with pairing heap priority queue");
+            System.out.println("0) Return to Options menu");
+            try {
+                input = sc.nextInt();
+                switch (input) {
+                    case 1 -> System.out.println("This option is not yet implemented. Choose another.");
+                    case 2 -> {
+                        BiGpairSEQ.setFibonacciHeap();
+                        System.out.println("MWM algorithm set to LEDA with Fibonacci heap");
+                        backToOptions = true;
+                    }
+                    case 3 -> {
+                        BiGpairSEQ.setPairingHeap();
+                        System.out.println("MWM algorithm set to LEDA with pairing heap");
+                        backToOptions = true;
+                    }
+                    case 0 -> backToOptions = true;
+                    default -> System.out.println("Invalid input");
+                }
+            } catch (InputMismatchException ex) {
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+    }
+
     private static void acknowledge(){
         System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
         System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");

src/main/java/Simulator.java

@@ -3,6 +3,7 @@ import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
 import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
 import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
+import org.jheaps.tree.FibonacciHeap;
 import org.jheaps.tree.PairingHeap;
 
 import java.math.BigDecimal;
@@ -16,7 +17,7 @@ import java.util.stream.IntStream;
 import static java.lang.Float.*;
 
 //NOTE: "sequence" in method and variable names refers to a peptide sequence from a simulated T cell
-public class Simulator {
+public class Simulator implements GraphModificationFunctions {
     private static final int cdr3AlphaIndex = 0;
     private static final int cdr3BetaIndex = 1;
     private static final int cdr1AlphaIndex = 2;
@@ -146,8 +147,8 @@ public class Simulator {
                                             Integer highThreshold, Integer maxOccupancyDifference,
                                             Integer minOverlapPercent, boolean verbose) {
         Instant start = Instant.now();
-        //Integer arrays will contain TO VERTEX, FROM VERTEX, and WEIGHT (which I'll need to cast to double)
         List<Integer[]> removedEdges = new ArrayList<>();
+        boolean saveEdges = BiGpairSEQ.cacheGraph();
         int numWells = data.getNumWells();
         Integer alphaCount = data.getAlphaCount();
         Integer betaCount = data.getBetaCount();
@@ -160,33 +161,50 @@ public class Simulator {
 
         //remove edges with weights outside given overlap thresholds, add those to removed edge list
         if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
-        removedEdges.addAll(GraphModificationFunctions.filterByOverlapThresholds(graph, lowThreshold, highThreshold));
+        removedEdges.addAll(GraphModificationFunctions.filterByOverlapThresholds(graph, lowThreshold, highThreshold, saveEdges));
         if(verbose){System.out.println("Over- and under-weight edges removed");}
 
         //remove edges between vertices with too small an overlap size, add those to removed edge list
         if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
                 " percent of vertex occupancy value.");}
         removedEdges.addAll(GraphModificationFunctions.filterByOverlapPercent(graph, alphaWellCounts, betaWellCounts,
-                plateVtoAMap, plateVtoBMap, minOverlapPercent));
+                plateVtoAMap, plateVtoBMap, minOverlapPercent, saveEdges));
         if(verbose){System.out.println("Edges with weights too far below a vertex occupancy value removed");}
 
         //Filter by relative occupancy
         if(verbose){System.out.println("Eliminating edges between vertices with occupancy difference > "
                 + maxOccupancyDifference);}
         removedEdges.addAll(GraphModificationFunctions.filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts,
-                plateVtoAMap, plateVtoBMap, maxOccupancyDifference));
+                plateVtoAMap, plateVtoBMap, maxOccupancyDifference, saveEdges));
         if(verbose){System.out.println("Edges between vertices of with excessively different occupancy values " +
                 "removed");}
 
         //Find Maximum Weighted Matching
         //using jheaps library class PairingHeap for improved efficiency
         if(verbose){System.out.println("Finding maximum weighted matching");}
-        //Attempting to use addressable heap to improve performance
+        MaximumWeightBipartiteMatching maxWeightMatching;
-        MaximumWeightBipartiteMatching maxWeightMatching =
+        //Use correct heap type for priority queue
-                new MaximumWeightBipartiteMatching(graph,
+        String heapType = BiGpairSEQ.getPriorityQueueHeapType();
+        switch (heapType) {
+            case "PAIRING" -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
                         plateVtoAMap.keySet(),
                         plateVtoBMap.keySet(),
                         i -> new PairingHeap(Comparator.naturalOrder()));
+            }
+            case "FIBONACCI" -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
+                        plateVtoAMap.keySet(),
+                        plateVtoBMap.keySet(),
+                        i -> new FibonacciHeap(Comparator.naturalOrder()));
+            }
+            default -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
+                        plateVtoAMap.keySet(),
+                        plateVtoBMap.keySet());
+            }
+        }
+        //get the matching
         MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = maxWeightMatching.getMatching();
         if(verbose){System.out.println("Matching completed");}
         Instant stop = Instant.now();
@@ -292,10 +310,11 @@ public class Simulator {
             }
         }
 
+        if(saveEdges) {
             //put the removed edges back on the graph
             System.out.println("Restoring removed edges to graph.");
             GraphModificationFunctions.addRemovedEdges(graph, removedEdges);
-
+        }
         //return MatchingResult object
         return output;
     }