Added metadata to MatchingResult to enable CLI options

src/main/java/BiGpairSEQ.java

@@ -6,7 +6,9 @@ public class BiGpairSEQ {
             InteractiveInterface.startInteractive();
         }
         else {
-            CommandLineInterface.startCLI(args);
+            //This will be uncommented when command line arguments are fixed.
+            //CommandLineInterface.startCLI(args);
+            System.out.println("Command line arguments are still being re-implemented.");
         }
     }
 }

src/main/java/CommandLineInterface.java

@@ -188,13 +188,14 @@ public class CommandLineInterface {
             CommandLine line = parser.parse(mainOptions, args);
             if(line.hasOption("match")){
                 //line = parser.parse(mainOptions, args);
-                String cellFile = line.getOptionValue("c");
+                //String cellFile = line.getOptionValue("c");
+                String graphFile = line.getOptionValue("g");
                 Integer lowThreshold = Integer.valueOf(line.getOptionValue(lowThresh));
                 Integer highThreshold = Integer.valueOf(line.getOptionValue(highThresh));
                 Integer occupancyDifference = Integer.valueOf(line.getOptionValue(occDiff));
                 Integer overlapPercent = Integer.valueOf(line.getOptionValue(overlapPer));
                 for(String plate: line.getOptionValues("p")) {
-                    matchCDR3s(cellFile, plate, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
+                    matchCDR3s(graphFile, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
                 }
             }
             else if(line.hasOption("cells")){
@@ -280,4 +281,9 @@ public class CommandLineInterface {
         PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
         writer.writePlateFile();
     }
+
+    private static void matchCDR3s(String graphFile, Integer lowThreshold, Integer highThreshold,
+                                   Integer occupancyDifference, Integer overlapPercent) {
+
+    }
 }

src/main/java/InteractiveInterface.java

@@ -223,7 +223,7 @@ public class InteractiveInterface {
             System.out.println("No cell sample found.");
             System.out.println("Returning to main menu.");
         }
-        else if(plate.getWells().size() == 0 || plate.getConcentrations().length == 0){
+        else if(plate.getWells().size() == 0 || plate.getPopulations().length == 0){
             System.out.println("No sample plate found.");
             System.out.println("Returning to main menu.");
         }

src/main/java/MatchingFileWriter.java

@@ -7,8 +7,6 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.List;
-import java.util.regex.Pattern;
-
 
 public class MatchingFileWriter {
 

src/main/java/MatchingResult.java

@@ -1,18 +1,42 @@
 import java.time.Duration;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
 public class MatchingResult {
-    private String sourceFile;
-    private List<String> comments;
-    private List<String> headers;
-    private List<List<String>> allResults;
-    private Map<Integer, Integer> matchMap;
-    private Duration time;
+    private final String sourceFile;
+    private final Map<String, String> metadata;
+    private final List<String> comments;
+    private final List<String> headers;
+    private final List<List<String>> allResults;
+    private final Map<Integer, Integer> matchMap;
+    private final Duration time;
 
-    public MatchingResult(String sourceFileName, List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
+    public MatchingResult(String sourceFileName, Map<String, String> metadata, List<String> headers,
+                          List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
         this.sourceFile = sourceFileName;
-        this.comments = comments;
+        /*
+         * POSSIBLE KEYS FOR METADATA MAP ARE:
+         * sample plate filename
+         * graph filename
+         * well populations
+         * total alphas found
+         * total betas found
+         * high overlap threshold
+         * low overlap threshold
+         * maximum occupancy difference
+         * minimum overlap percent
+         * pairing attempt rate
+         * correct pairing count
+         * incorrect pairing count
+         * pairing error rate
+         * simulation time
+         */
+        this.metadata = metadata;
+        this.comments = new ArrayList<>();
+        for (String key : metadata.keySet()) {
+            comments.add(key +": " + metadata.get(key));
+        }
         this.headers = headers;
         this.allResults = allResults;
         this.matchMap = matchMap;
@@ -20,6 +44,8 @@ public class MatchingResult {
 
     }
 
+    public Map<String, String> getMetadata() {return metadata;}
+
     public List<String> getComments() {
         return comments;
     }

src/main/java/Plate.java

@@ -1,26 +1,28 @@
-import java.util.*;
+
 
 /*
 TODO: Implement exponential distribution using inversion method - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
+import java.util.*;
+
 public class Plate {
     private String sourceFile;
     private List<List<Integer[]>> wells;
     private Random rand = new Random();
     private int size;
     private double error;
-    private Integer[] concentrations;
+    private Integer[] populations;
     private double stdDev;
     private double lambda;
     boolean exponential = false;
 
 
-    public Plate(int size, double error, Integer[] concentrations) {
+    public Plate(int size, double error, Integer[] populations) {
         this.size = size;
         this.error = error;
-        this.concentrations = concentrations;
+        this.populations = populations;
         wells = new ArrayList<>();
     }
 
@@ -35,9 +37,9 @@ public class Plate {
                 concentrations.add(w.size());
             }
         }
-        this.concentrations = new Integer[concentrations.size()];
-        for (int i = 0; i < this.concentrations.length; i++) {
-            this.concentrations[i] = concentrations.get(i);
+        this.populations = new Integer[concentrations.size()];
+        for (int i = 0; i < this.populations.length; i++) {
+            this.populations[i] = concentrations.get(i);
         }
     }
 
@@ -45,7 +47,7 @@ public class Plate {
         this.lambda = lambda;
         exponential = true;
         sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.length;
         int section = 0;
         double m;
         int n;
@@ -53,7 +55,7 @@ public class Plate {
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
                 List<Integer[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                     do {
                         //inverse transform sampling: for random number u in [0,1), x = log(1-u) / (-lambda)
                         m = (Math.log10((1 - rand.nextDouble()))/(-lambda)) * Math.sqrt(cells.size());
@@ -84,14 +86,14 @@ public class Plate {
     public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
         this.stdDev = stdDev;
         sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.length;
         int section = 0;
         double m;
         int n;
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
                 List<Integer[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                     do {
                         m = (rand.nextGaussian() * stdDev) + (cells.size() / 2);
                     } while (m >= cells.size() || m < 0);
@@ -110,8 +112,8 @@ public class Plate {
         }
     }
 
-    public Integer[] getConcentrations(){
-        return concentrations;
+    public Integer[] getPopulations(){
+        return populations;
     }
 
     public int getSize(){

src/main/java/PlateFileWriter.java

@@ -7,7 +7,6 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.*;
-import java.util.regex.Pattern;
 
 public class PlateFileWriter {
     private int size;
@@ -18,7 +17,7 @@ public class PlateFileWriter {
     private String filename;
     private String sourceFileName;
     private String[] headers;
-    private List<Integer> concentrations;
+    private Integer[] concentrations;
     private boolean isExponential = false;
 
     public PlateFileWriter(String filename, Plate plate) {
@@ -37,8 +36,8 @@ public class PlateFileWriter {
         }
         this.error = plate.getError();
         this.wells = plate.getWells();
-        this.concentrations = Arrays.asList(plate.getConcentrations());
-        concentrations.sort(Comparator.reverseOrder());
+        this.concentrations = plate.getPopulations();
+        Arrays.sort(concentrations);
     }
 
     public void writePlateFile(){
@@ -59,7 +58,7 @@ public class PlateFileWriter {
             }
         }
 
-        //this took forever
+        //this took forever and I don't use it
         List<List<String>> rows = new ArrayList<>();
         List<String> tmp = new ArrayList<>();
         for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
@@ -73,14 +72,19 @@ public class PlateFileWriter {
             }
             rows.add(tmp);
         }
-        //build string of well concentrations
-        StringBuilder concen = new StringBuilder();
-        for(Integer i: concentrations){
-            concen.append(i.toString());
-            concen.append(" ");
-        }
-        String concenString = concen.toString();
 
+        //get list of well populations
+        List<Integer> wellPopulations = Arrays.asList(concentrations);
+        //make string out of populations list
+        StringBuilder populationsStringBuilder = new StringBuilder();
+        populationsStringBuilder.append(wellPopulations.remove(0).toString());
+        for(Integer i: wellPopulations){
+            populationsStringBuilder.append(", ");
+            populationsStringBuilder.append(i.toString());
+        }
+        String wellPopulationsString = populationsStringBuilder.toString();
+
+        //set CSV format
         CSVFormat plateFileFormat = CSVFormat.Builder.create()
                 .setCommentMarker('#')
                 .build();
@@ -92,7 +96,7 @@ public class PlateFileWriter {
             printer.printComment("Each row represents one well on the plate.");
             printer.printComment("Plate size: " + size);
             printer.printComment("Error rate: " + error);
-            printer.printComment("Concentrations: " + concenString);
+            printer.printComment("Well populations: " + wellPopulationsString);
             if(isExponential){
                 printer.printComment("Lambda: " + lambda);
             }

src/main/java/Simulator.java

@@ -131,10 +131,14 @@ public class Simulator {
 
         Instant stop = Instant.now();
         Duration time = Duration.between(start, stop);
-        //return GraphWithMapData object
-        return new GraphWithMapData(graph, numWells, samplePlate.getConcentrations(), alphaCount, betaCount,
+
+        //create GraphWithMapData object
+        GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), alphaCount, betaCount,
                 distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
                 plateBtoVMap, alphaWellCounts, betaWellCounts, time);
+        output.setSourceFilename(samplePlate.getSourceFileName());
+        //return GraphWithMapData object
+        return output;
     }
 
     //match CDR3s.
@@ -233,351 +237,356 @@ public class Simulator {
             allResults.add(result);
         }
 
-        //Metadate comments for CSV file
+        //Metadata comments for CSV file
         int min = Math.min(alphaCount, betaCount);
         double attemptRate = (double) (trueCount + falseCount) / min;
         BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
         double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
         BigDecimal pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
         //get list of well concentrations
-        List<Integer> wellConcentrations = Arrays.asList(data.getWellConcentrations());
+        List<Integer> wellPopulations = Arrays.asList(data.getWellConcentrations());
         //make string out of concentrations list
-        StringBuilder concentrationStringBuilder = new StringBuilder();
-        for(Integer i: wellConcentrations){
-            concentrationStringBuilder.append(i.toString());
-            concentrationStringBuilder.append(" ");
+        StringBuilder populationsStringBuilder = new StringBuilder();
+        populationsStringBuilder.append(wellPopulations.remove(0).toString());
+        for(Integer i: wellPopulations){
+            populationsStringBuilder.append(", ");
+            populationsStringBuilder.append(i.toString());
         }
-        String concentrationString = concentrationStringBuilder.toString();
-
-        List<String> comments = new ArrayList<>();
-        comments.add("Source Sample Plate filename: " + data.getSourceFilename());
-        comments.add("Source Graph and Data filename: " + dataFilename);
-        comments.add("T cell counts in sample plate wells: " + concentrationString);
-        comments.add("Total alphas found: " + alphaCount);
-        comments.add("Total betas found: " + betaCount);
-        comments.add("High overlap threshold: " + highThreshold);
-        comments.add("Low overlap threshold: " + lowThreshold);
-        comments.add("Minimum overlap percent: " + minOverlapPercent);
-        comments.add("Maximum occupancy difference: " + maxOccupancyDifference);
-        comments.add("Pairing attempt rate: " + attemptRateTrunc);
-        comments.add("Correct pairings: " + trueCount);
-        comments.add("Incorrect pairings: " + falseCount);
-        comments.add("Pairing error rate: " + pairingErrorRateTrunc);
+        String wellPopulationsString = populationsStringBuilder.toString();
+        //total simulation time
         Duration time = Duration.between(start, stop);
         time = time.plus(data.getTime());
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+
+        Map<String, String> metadata = new LinkedHashMap<>();
+        metadata.put("sample plate filename", data.getSourceFilename());
+        metadata.put("graph filename", dataFilename);
+        metadata.put("well populations", wellPopulationsString);
+        metadata.put("total alphas found", alphaCount.toString());
+        metadata.put("total betas found", betaCount.toString());
+        metadata.put("high overlap threshold", highThreshold.toString());
+        metadata.put("low overlap threshold", lowThreshold.toString());
+        metadata.put("maximum occupancy difference", maxOccupancyDifference.toString());
+        metadata.put("minimum overlap percent", minOverlapPercent.toString());
+        metadata.put("pairing attempt rate", attemptRateTrunc.toString());
+        metadata.put("correct pairing count", Integer.toString(trueCount));
+        metadata.put("incorrect pairing count", Integer.toString(falseCount));
+        metadata.put("pairing error rate", pairingErrorRateTrunc.toString());
+        metadata.put("simulation time", nf.format(time.toSeconds()));
+
+        MatchingResult output = new MatchingResult(data.getSourceFilename(), metadata, header, allResults, matchMap, time);
         if(verbose){
-            for(String s: comments){
+            for(String s: output.getComments()){
                 System.out.println(s);
             }
         }
-        return new MatchingResult(data.getSourceFilename(), comments, header, allResults, matchMap, time);
-    }
-
-    //Simulated matching of CDR1s to CDR3s. Requires MatchingResult from prior run of matchCDR3s.
-    public static MatchingResult[] matchCDR1s(List<Integer[]> distinctCells,
-                                  Plate samplePlate, Integer lowThreshold,
-                                            Integer highThreshold, MatchingResult priorResult){
-        Instant start = Instant.now();
-        Duration previousTime = priorResult.getTime();
-        Map<Integer, Integer> previousMatches = priorResult.getMatchMap();
-        int numWells = samplePlate.getSize();
-        int[] cdr3Indices = {cdr3AlphaIndex, cdr3BetaIndex};
-        int[] cdr1Indices = {cdr1AlphaIndex, cdr1BetaIndex};
-
-        System.out.println("Making previous match maps");
-        Map<Integer, Integer> cdr3AtoBMap = previousMatches;
-        Map<Integer, Integer> cdr3BtoAMap = invertVertexMap(cdr3AtoBMap);
-        System.out.println("Previous match maps made");
-
-        System.out.println("Making cell maps");
-        Map<Integer, Integer> alphaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr1AlphaIndex);
-        Map<Integer, Integer> betaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3BetaIndex, cdr1BetaIndex);
-        System.out.println("Cell maps made");
-
-        System.out.println("Making well maps");
-        Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
-        Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
-        int CDR3Count = allCDR3s.size();
-        System.out.println("all CDR3s count: " + CDR3Count);
-        int CDR1Count = allCDR1s.size();
-        System.out.println("all CDR1s count: " + CDR1Count);
-        System.out.println("Well maps made");
-
-        System.out.println("Removing unpaired CDR3s from well maps");
-        List<Integer> unpairedCDR3s = new ArrayList<>();
-        for(Integer i: allCDR3s.keySet()){
-            if(!(cdr3AtoBMap.containsKey(i) || cdr3BtoAMap.containsKey(i))){
-                unpairedCDR3s.add(i);
-            }
-        }
-        for(Integer i: unpairedCDR3s){
-            allCDR3s.remove(i);
-        }
-        System.out.println("Unpaired CDR3s removed.");
-        System.out.println("Remaining CDR3 count: " + allCDR3s.size());
-
-        System.out.println("Removing below-minimum-overlap-threshold and saturating-occupancy CDR1s");
-        filterByOccupancyThreshold(allCDR1s, lowThreshold, numWells - 1);
-        System.out.println("CDR1s removed.");
-        System.out.println("Remaining CDR1 count: " + allCDR1s.size());
-
-        System.out.println("Making vertex maps");
-
-        //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
-        // distinct numbers associated with them. Since I'm using a 2D array, that means
-        // distinct indices between the rows and columns. vertexStartValue lets me track where I switch
-        // from numbering rows to columns, so I can assign unique numbers to every vertex, and then
-        // subtract the vertexStartValue from CDR1s to use their vertex labels as array indices
-        Integer vertexStartValue = 0;
-        //keys are sequential integer vertices, values are CDR3s
-        Map<Integer, Integer> plateVtoCDR3Map = makeVertexToSequenceMap(allCDR3s, vertexStartValue);
-        //New start value for vertex to CDR1 map should be one more than final vertex value in CDR3 map
-        vertexStartValue += plateVtoCDR3Map.size();
-        //keys are sequential integers vertices, values are CDR1s
-        Map<Integer, Integer> plateVtoCDR1Map = makeVertexToSequenceMap(allCDR1s, vertexStartValue);
-        //keys are CDR3s, values are sequential integer vertices from previous map
-        Map<Integer, Integer> plateCDR3toVMap = invertVertexMap(plateVtoCDR3Map);
-        //keys are CDR1s, values are sequential integer vertices from previous map
-        Map<Integer, Integer> plateCDR1toVMap = invertVertexMap(plateVtoCDR1Map);
-        System.out.println("Vertex maps made");
-
-        System.out.println("Creating adjacency matrix");
-        //Count how many wells each CDR3 appears in
-        Map<Integer, Integer> cdr3WellCounts = new HashMap<>();
-        //count how many wells each CDR1 appears in
-        Map<Integer, Integer> cdr1WellCounts = new HashMap<>();
-        //add edges, where weights are number of wells the peptides share in common.
-        //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
-        Map<Integer, Integer> wellNCDR3s = null;
-        Map<Integer, Integer> wellNCDR1s = null;
-        double[][] weights = new double[plateVtoCDR3Map.size()][plateVtoCDR1Map.size()];
-        countSequencesAndFillMatrix(samplePlate, allCDR3s, allCDR1s, plateCDR3toVMap, plateCDR1toVMap,
-                cdr3Indices, cdr1Indices, cdr3WellCounts, cdr1WellCounts, weights);
-        System.out.println("Matrix created");
-
-        System.out.println("Creating graph");
-        SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
-                new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
-
-        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
-        List<Integer> cdr3Vertices = new ArrayList<>(plateVtoCDR3Map.keySet()); //This will work because LinkedHashMap preserves order of entry
-        graphGenerator.first(cdr3Vertices);
-        List<Integer> cdr1Vertices = new ArrayList<>(plateVtoCDR1Map.keySet());
-        graphGenerator.second(cdr1Vertices); //This will work because LinkedHashMap preserves order of entry
-        graphGenerator.weights(weights);
-        graphGenerator.generateGraph(graph);
-        System.out.println("Graph created");
-
-        System.out.println("Removing edges outside of weight thresholds");
-        filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
-        System.out.println("Over- and under-weight edges set to 0.0");
-
-        System.out.println("Finding first maximum weighted matching");
-        MaximumWeightBipartiteMatching firstMaxWeightMatching =
-                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
-        MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = firstMaxWeightMatching.getMatching();
-        System.out.println("First maximum weighted matching found");
-
-
-        //first processing run
-        Map<Integer, Integer> firstMatchCDR3toCDR1Map = new HashMap<>();
-        Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
-        DefaultWeightedEdge e;
-        while(weightIter.hasNext()){
-            e = weightIter.next();
-//            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
-//                continue;
-//            }
-            Integer source = graph.getEdgeSource(e);
-            Integer target = graph.getEdgeTarget(e);
-            firstMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
-        }
-        System.out.println("First pass matches: " + firstMatchCDR3toCDR1Map.size());
-
-        System.out.println("Removing edges from first maximum weighted matching");
-        //zero out the edge weights in the matching
-        weightIter = graphMatching.iterator();
-        while(weightIter.hasNext()){
-            graph.removeEdge(weightIter.next());
-        }
-        System.out.println("Edges removed");
-
-        //Generate a new matching
-        System.out.println("Finding second maximum weighted matching");
-        MaximumWeightBipartiteMatching secondMaxWeightMatching =
-                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
-        graphMatching = secondMaxWeightMatching.getMatching();
-        System.out.println("Second maximum weighted matching found");
-
-
-        //second processing run
-        Map<Integer, Integer> secondMatchCDR3toCDR1Map = new HashMap<>();
-        weightIter = graphMatching.iterator();
-        while(weightIter.hasNext()){
-            e = weightIter.next();
-//            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
-//                continue;
-//            }
-            Integer source = graph.getEdgeSource(e);
-//            if(!(CDR3AtoBMap.containsKey(source) || CDR3BtoAMap.containsKey(source))){
-//                continue;
-//            }
-            Integer target = graph.getEdgeTarget(e);
-            secondMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
-        }
-        System.out.println("Second pass matches: " + secondMatchCDR3toCDR1Map.size());
-
-        System.out.println("Mapping first pass CDR3 alpha/beta pairs");
-        //get linked map for first matching attempt
-        Map<Integer, Integer> firstMatchesMap = new LinkedHashMap<>();
-        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
-            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
-                continue;
-            }
-            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
-            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
-                continue;
-            }
-            firstMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
-            firstMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
-        }
-        System.out.println("First pass CDR3 alpha/beta pairs mapped");
-
-        System.out.println("Mapping second pass CDR3 alpha/beta pairs.");
-        System.out.println("Finding CDR3 pairs that swapped CDR1 matches between first pass and second pass.");
-        //Look for matches that simply swapped already-matched alpha and beta CDR3s
-        Map<Integer, Integer> dualMatchesMap = new LinkedHashMap<>();
-        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
-            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3) && secondMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
-                continue;
-            }
-            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
-            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3) && secondMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
-                continue;
-            }
-            if(firstMatchCDR3toCDR1Map.get(alphaCDR3).equals(secondMatchCDR3toCDR1Map.get(betaCDR3))){
-                if(firstMatchCDR3toCDR1Map.get(betaCDR3).equals(secondMatchCDR3toCDR1Map.get(alphaCDR3))){
-                    dualMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
-                    dualMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
-                }
-            }
-        }
-        System.out.println("Second pass mapping made. Dual CDR3/CDR1 pairings found.");
-
-        Instant stop = Instant.now();
-        //results for first map
-        System.out.println("RESULTS FOR FIRST PASS MATCHING");
-        List<List<String>> allResults = new ArrayList<>();
-        Integer trueCount = 0;
-        Iterator iter = firstMatchesMap.keySet().iterator();
-
-        while(iter.hasNext()){
-            Boolean proven = false;
-            List<String> tmp = new ArrayList<>();
-            tmp.add(iter.next().toString());
-            tmp.add(iter.next().toString());
-            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
-            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
-            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
-                    proven = true;
-                }
-            }
-            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
-                    proven = true;
-                }
-            }
-            tmp.add(proven.toString());
-            allResults.add(tmp);
-            if(proven){
-                trueCount++;
-            }
-        }
-
-        List<String> comments = new ArrayList<>();
-        comments.add("Plate size: " + samplePlate.getSize() + " wells");
-        comments.add("Previous pairs found: " + previousMatches.size());
-        comments.add("CDR1 matches attempted: " + allResults.size());
-        double attemptRate = (double) allResults.size() / previousMatches.size();
-        comments.add("Matching attempt rate: " + attemptRate);
-        comments.add("Number of correct matches: " + trueCount);
-        double correctRate = (double) trueCount / allResults.size();
-        comments.add("Correct matching rate: " + correctRate);
-        NumberFormat nf = NumberFormat.getInstance(Locale.US);
-        Duration time = Duration.between(start, stop);
-        time = time.plus(previousTime);
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-        for(String s: comments){
-            System.out.println(s);
-        }
-
-
-
-        List<String> headers = new ArrayList<>();
-        headers.add("CDR3 alpha");
-        headers.add("CDR3 beta");
-        headers.add("first matched CDR1");
-        headers.add("second matched CDR1");
-        headers.add("Correct match?");
-
-        MatchingResult firstTest = new MatchingResult(samplePlate.getSourceFileName(),
-                comments, headers, allResults, dualMatchesMap, time);
-
-        //results for dual map
-        System.out.println("RESULTS FOR SECOND PASS MATCHING");
-        allResults = new ArrayList<>();
-        trueCount = 0;
-        iter = dualMatchesMap.keySet().iterator();
-        while(iter.hasNext()){
-            Boolean proven = false;
-            List<String> tmp = new ArrayList<>();
-            tmp.add(iter.next().toString());
-            tmp.add(iter.next().toString());
-            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
-            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
-            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
-                    proven = true;
-                }
-            }
-            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
-                    proven = true;
-                }
-            }
-            tmp.add(proven.toString());
-            allResults.add(tmp);
-            if(proven){
-                trueCount++;
-            }
-        }
-
-        comments = new ArrayList<>();
-        comments.add("Plate size: " + samplePlate.getSize() + " wells");
-        comments.add("Previous pairs found: " + previousMatches.size());
-        comments.add("High overlap threshold: " + highThreshold);
-        comments.add("Low overlap threshold: " + lowThreshold);
-        comments.add("CDR1 matches attempted: " + allResults.size());
-        attemptRate = (double) allResults.size() / previousMatches.size();
-        comments.add("Matching attempt rate: " + attemptRate);
-        comments.add("Number of correct matches: " + trueCount);
-        correctRate = (double) trueCount / allResults.size();
-        comments.add("Correct matching rate: " + correctRate);
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-
-        for(String s: comments){
-            System.out.println(s);
-        }
-
-        System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-        MatchingResult dualTest = new MatchingResult(samplePlate.getSourceFileName(), comments, headers,
-                allResults, dualMatchesMap, time);
-        MatchingResult[] output = {firstTest, dualTest};
         return output;
     }
 
+    //Commented out CDR1 matching until it's time to re-implement it
+//    //Simulated matching of CDR1s to CDR3s. Requires MatchingResult from prior run of matchCDR3s.
+//    public static MatchingResult[] matchCDR1s(List<Integer[]> distinctCells,
+//                                  Plate samplePlate, Integer lowThreshold,
+//                                            Integer highThreshold, MatchingResult priorResult){
+//        Instant start = Instant.now();
+//        Duration previousTime = priorResult.getTime();
+//        Map<Integer, Integer> previousMatches = priorResult.getMatchMap();
+//        int numWells = samplePlate.getSize();
+//        int[] cdr3Indices = {cdr3AlphaIndex, cdr3BetaIndex};
+//        int[] cdr1Indices = {cdr1AlphaIndex, cdr1BetaIndex};
+//
+//        System.out.println("Making previous match maps");
+//        Map<Integer, Integer> cdr3AtoBMap = previousMatches;
+//        Map<Integer, Integer> cdr3BtoAMap = invertVertexMap(cdr3AtoBMap);
+//        System.out.println("Previous match maps made");
+//
+//        System.out.println("Making cell maps");
+//        Map<Integer, Integer> alphaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr1AlphaIndex);
+//        Map<Integer, Integer> betaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3BetaIndex, cdr1BetaIndex);
+//        System.out.println("Cell maps made");
+//
+//        System.out.println("Making well maps");
+//        Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
+//        Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
+//        int CDR3Count = allCDR3s.size();
+//        System.out.println("all CDR3s count: " + CDR3Count);
+//        int CDR1Count = allCDR1s.size();
+//        System.out.println("all CDR1s count: " + CDR1Count);
+//        System.out.println("Well maps made");
+//
+//        System.out.println("Removing unpaired CDR3s from well maps");
+//        List<Integer> unpairedCDR3s = new ArrayList<>();
+//        for(Integer i: allCDR3s.keySet()){
+//            if(!(cdr3AtoBMap.containsKey(i) || cdr3BtoAMap.containsKey(i))){
+//                unpairedCDR3s.add(i);
+//            }
+//        }
+//        for(Integer i: unpairedCDR3s){
+//            allCDR3s.remove(i);
+//        }
+//        System.out.println("Unpaired CDR3s removed.");
+//        System.out.println("Remaining CDR3 count: " + allCDR3s.size());
+//
+//        System.out.println("Removing below-minimum-overlap-threshold and saturating-occupancy CDR1s");
+//        filterByOccupancyThreshold(allCDR1s, lowThreshold, numWells - 1);
+//        System.out.println("CDR1s removed.");
+//        System.out.println("Remaining CDR1 count: " + allCDR1s.size());
+//
+//        System.out.println("Making vertex maps");
+//
+//        //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
+//        // distinct numbers associated with them. Since I'm using a 2D array, that means
+//        // distinct indices between the rows and columns. vertexStartValue lets me track where I switch
+//        // from numbering rows to columns, so I can assign unique numbers to every vertex, and then
+//        // subtract the vertexStartValue from CDR1s to use their vertex labels as array indices
+//        Integer vertexStartValue = 0;
+//        //keys are sequential integer vertices, values are CDR3s
+//        Map<Integer, Integer> plateVtoCDR3Map = makeVertexToSequenceMap(allCDR3s, vertexStartValue);
+//        //New start value for vertex to CDR1 map should be one more than final vertex value in CDR3 map
+//        vertexStartValue += plateVtoCDR3Map.size();
+//        //keys are sequential integers vertices, values are CDR1s
+//        Map<Integer, Integer> plateVtoCDR1Map = makeVertexToSequenceMap(allCDR1s, vertexStartValue);
+//        //keys are CDR3s, values are sequential integer vertices from previous map
+//        Map<Integer, Integer> plateCDR3toVMap = invertVertexMap(plateVtoCDR3Map);
+//        //keys are CDR1s, values are sequential integer vertices from previous map
+//        Map<Integer, Integer> plateCDR1toVMap = invertVertexMap(plateVtoCDR1Map);
+//        System.out.println("Vertex maps made");
+//
+//        System.out.println("Creating adjacency matrix");
+//        //Count how many wells each CDR3 appears in
+//        Map<Integer, Integer> cdr3WellCounts = new HashMap<>();
+//        //count how many wells each CDR1 appears in
+//        Map<Integer, Integer> cdr1WellCounts = new HashMap<>();
+//        //add edges, where weights are number of wells the peptides share in common.
+//        //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
+//        Map<Integer, Integer> wellNCDR3s = null;
+//        Map<Integer, Integer> wellNCDR1s = null;
+//        double[][] weights = new double[plateVtoCDR3Map.size()][plateVtoCDR1Map.size()];
+//        countSequencesAndFillMatrix(samplePlate, allCDR3s, allCDR1s, plateCDR3toVMap, plateCDR1toVMap,
+//                cdr3Indices, cdr1Indices, cdr3WellCounts, cdr1WellCounts, weights);
+//        System.out.println("Matrix created");
+//
+//        System.out.println("Creating graph");
+//        SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
+//                new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
+//
+//        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
+//        List<Integer> cdr3Vertices = new ArrayList<>(plateVtoCDR3Map.keySet()); //This will work because LinkedHashMap preserves order of entry
+//        graphGenerator.first(cdr3Vertices);
+//        List<Integer> cdr1Vertices = new ArrayList<>(plateVtoCDR1Map.keySet());
+//        graphGenerator.second(cdr1Vertices); //This will work because LinkedHashMap preserves order of entry
+//        graphGenerator.weights(weights);
+//        graphGenerator.generateGraph(graph);
+//        System.out.println("Graph created");
+//
+//        System.out.println("Removing edges outside of weight thresholds");
+//        filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
+//        System.out.println("Over- and under-weight edges set to 0.0");
+//
+//        System.out.println("Finding first maximum weighted matching");
+//        MaximumWeightBipartiteMatching firstMaxWeightMatching =
+//                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
+//        MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = firstMaxWeightMatching.getMatching();
+//        System.out.println("First maximum weighted matching found");
+//
+//
+//        //first processing run
+//        Map<Integer, Integer> firstMatchCDR3toCDR1Map = new HashMap<>();
+//        Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
+//        DefaultWeightedEdge e;
+//        while(weightIter.hasNext()){
+//            e = weightIter.next();
+////            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
+////                continue;
+////            }
+//            Integer source = graph.getEdgeSource(e);
+//            Integer target = graph.getEdgeTarget(e);
+//            firstMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
+//        }
+//        System.out.println("First pass matches: " + firstMatchCDR3toCDR1Map.size());
+//
+//        System.out.println("Removing edges from first maximum weighted matching");
+//        //zero out the edge weights in the matching
+//        weightIter = graphMatching.iterator();
+//        while(weightIter.hasNext()){
+//            graph.removeEdge(weightIter.next());
+//        }
+//        System.out.println("Edges removed");
+//
+//        //Generate a new matching
+//        System.out.println("Finding second maximum weighted matching");
+//        MaximumWeightBipartiteMatching secondMaxWeightMatching =
+//                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
+//        graphMatching = secondMaxWeightMatching.getMatching();
+//        System.out.println("Second maximum weighted matching found");
+//
+//
+//        //second processing run
+//        Map<Integer, Integer> secondMatchCDR3toCDR1Map = new HashMap<>();
+//        weightIter = graphMatching.iterator();
+//        while(weightIter.hasNext()){
+//            e = weightIter.next();
+////            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
+////                continue;
+////            }
+//            Integer source = graph.getEdgeSource(e);
+////            if(!(CDR3AtoBMap.containsKey(source) || CDR3BtoAMap.containsKey(source))){
+////                continue;
+////            }
+//            Integer target = graph.getEdgeTarget(e);
+//            secondMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
+//        }
+//        System.out.println("Second pass matches: " + secondMatchCDR3toCDR1Map.size());
+//
+//        System.out.println("Mapping first pass CDR3 alpha/beta pairs");
+//        //get linked map for first matching attempt
+//        Map<Integer, Integer> firstMatchesMap = new LinkedHashMap<>();
+//        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
+//                continue;
+//            }
+//            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
+//                continue;
+//            }
+//            firstMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
+//            firstMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
+//        }
+//        System.out.println("First pass CDR3 alpha/beta pairs mapped");
+//
+//        System.out.println("Mapping second pass CDR3 alpha/beta pairs.");
+//        System.out.println("Finding CDR3 pairs that swapped CDR1 matches between first pass and second pass.");
+//        //Look for matches that simply swapped already-matched alpha and beta CDR3s
+//        Map<Integer, Integer> dualMatchesMap = new LinkedHashMap<>();
+//        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3) && secondMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
+//                continue;
+//            }
+//            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3) && secondMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
+//                continue;
+//            }
+//            if(firstMatchCDR3toCDR1Map.get(alphaCDR3).equals(secondMatchCDR3toCDR1Map.get(betaCDR3))){
+//                if(firstMatchCDR3toCDR1Map.get(betaCDR3).equals(secondMatchCDR3toCDR1Map.get(alphaCDR3))){
+//                    dualMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
+//                    dualMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
+//                }
+//            }
+//        }
+//        System.out.println("Second pass mapping made. Dual CDR3/CDR1 pairings found.");
+//
+//        Instant stop = Instant.now();
+//        //results for first map
+//        System.out.println("RESULTS FOR FIRST PASS MATCHING");
+//        List<List<String>> allResults = new ArrayList<>();
+//        Integer trueCount = 0;
+//        Iterator iter = firstMatchesMap.keySet().iterator();
+//
+//        while(iter.hasNext()){
+//            Boolean proven = false;
+//            List<String> tmp = new ArrayList<>();
+//            tmp.add(iter.next().toString());
+//            tmp.add(iter.next().toString());
+//            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
+//            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
+//            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
+//                    proven = true;
+//                }
+//            }
+//            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
+//                    proven = true;
+//                }
+//            }
+//            tmp.add(proven.toString());
+//            allResults.add(tmp);
+//            if(proven){
+//                trueCount++;
+//            }
+//        }
+//
+//        List<String> comments = new ArrayList<>();
+//        comments.add("Plate size: " + samplePlate.getSize() + " wells");
+//        comments.add("Previous pairs found: " + previousMatches.size());
+//        comments.add("CDR1 matches attempted: " + allResults.size());
+//        double attemptRate = (double) allResults.size() / previousMatches.size();
+//        comments.add("Matching attempt rate: " + attemptRate);
+//        comments.add("Number of correct matches: " + trueCount);
+//        double correctRate = (double) trueCount / allResults.size();
+//        comments.add("Correct matching rate: " + correctRate);
+//        NumberFormat nf = NumberFormat.getInstance(Locale.US);
+//        Duration time = Duration.between(start, stop);
+//        time = time.plus(previousTime);
+//        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+//        for(String s: comments){
+//            System.out.println(s);
+//        }
+//
+//
+//
+//        List<String> headers = new ArrayList<>();
+//        headers.add("CDR3 alpha");
+//        headers.add("CDR3 beta");
+//        headers.add("first matched CDR1");
+//        headers.add("second matched CDR1");
+//        headers.add("Correct match?");
+//
+//        MatchingResult firstTest = new MatchingResult(samplePlate.getSourceFileName(),
+//                comments, headers, allResults, dualMatchesMap, time);
+//
+//        //results for dual map
+//        System.out.println("RESULTS FOR SECOND PASS MATCHING");
+//        allResults = new ArrayList<>();
+//        trueCount = 0;
+//        iter = dualMatchesMap.keySet().iterator();
+//        while(iter.hasNext()){
+//            Boolean proven = false;
+//            List<String> tmp = new ArrayList<>();
+//            tmp.add(iter.next().toString());
+//            tmp.add(iter.next().toString());
+//            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
+//            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
+//            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
+//                    proven = true;
+//                }
+//            }
+//            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
+//                    proven = true;
+//                }
+//            }
+//            tmp.add(proven.toString());
+//            allResults.add(tmp);
+//            if(proven){
+//                trueCount++;
+//            }
+//        }
+//
+//        comments = new ArrayList<>();
+//        comments.add("Plate size: " + samplePlate.getSize() + " wells");
+//        comments.add("Previous pairs found: " + previousMatches.size());
+//        comments.add("High overlap threshold: " + highThreshold);
+//        comments.add("Low overlap threshold: " + lowThreshold);
+//        comments.add("CDR1 matches attempted: " + allResults.size());
+//        attemptRate = (double) allResults.size() / previousMatches.size();
+//        comments.add("Matching attempt rate: " + attemptRate);
+//        comments.add("Number of correct matches: " + trueCount);
+//        correctRate = (double) trueCount / allResults.size();
+//        comments.add("Correct matching rate: " + correctRate);
+//        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+//
+//        for(String s: comments){
+//            System.out.println(s);
+//        }
+//
+//        System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+//        MatchingResult dualTest = new MatchingResult(samplePlate.getSourceFileName(), comments, headers,
+//                allResults, dualMatchesMap, time);
+//        MatchingResult[] output = {firstTest, dualTest};
+//        return output;
+//    }
+
 
     //Counts the well occupancy of the row peptides and column peptides into given maps, and
     //fills weights in the given 2D array