Merge remote-tracking branch 'origin/master'

readme.md

@@ -357,6 +357,8 @@ roughly as though it had a constant well population equal to the plate's average
     * Add controllable algorithm-type parameter?
     * This would be fun and valuable, but probably take more time than I have for a hobby project.
 * Implement Vose's alias method for arbitrary statistical distributions of cells
+  * Should probably refactor to use apache commons rng for this
+* Use commons JCS for caching
   
   
 ## CITATIONS

src/main/java/Simulator.java

@@ -23,6 +23,7 @@ public class Simulator implements GraphModificationFunctions {
     private static final int cdr1AlphaIndex = 2;
     private static final int cdr1BetaIndex = 3;
 
+
     //Make the graph needed for matching CDR3s
     public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
         Instant start = Instant.now();
@@ -34,7 +35,7 @@ public class Simulator implements GraphModificationFunctions {
 
         if(verbose){System.out.println("Making cell maps");}
         //HashMap keyed to Alphas, values Betas
-        Map<Integer, Integer> distCellsMapAlphaKey = makeSequenceToSequenceMap(distinctCells, 0, 1);
+        Map<Integer, Integer> distCellsMapAlphaKey = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr3BetaIndex);
         if(verbose){System.out.println("Cell maps made");}
 
         if(verbose){System.out.println("Making well maps");}
@@ -46,10 +47,11 @@ public class Simulator implements GraphModificationFunctions {
         if(verbose){System.out.println("All betas count: " + betaCount);}
         if(verbose){System.out.println("Well maps made");}
 
-        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
-        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
-        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
-        if(verbose){System.out.println("Sequences removed");}
+
+//        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
+//        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
+//        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
+//        if(verbose){System.out.println("Sequences removed");}
         int pairableAlphaCount = allAlphas.size();
         if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
         int pairableBetaCount = allBetas.size();
@@ -238,6 +240,8 @@ public class Simulator implements GraphModificationFunctions {
         //Metadata comments for CSV file
         String algoType = "LEDA book with heap: " + heapType;
         int min = Math.min(alphaCount, betaCount);
+        //matching weight
+        BigDecimal totalMatchingWeight = maxWeightMatching.getMatchingWeight();
         //rate of attempted matching
         double attemptRate = (double) (trueCount + falseCount) / min;
         BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
@@ -268,6 +272,7 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("sample plate filename", data.getSourceFilename());
         metadata.put("graph filename", dataFilename);
         metadata.put("algorithm type", algoType);
+        metadata.put("matching weight", totalMatchingWeight.toString());
         metadata.put("well populations", wellPopulationsString);
         metadata.put("total alphas found", alphaCount.toString());
         metadata.put("total betas found", betaCount.toString());