diff --git a/out/artifacts/TCellSim_jar/TCellSim.jar b/out/artifacts/TCellSim_jar/TCellSim.jar index 189f0c5..eb9a41b 100644 Binary files a/out/artifacts/TCellSim_jar/TCellSim.jar and b/out/artifacts/TCellSim_jar/TCellSim.jar differ diff --git a/src/main/java/Plate.java b/src/main/java/Plate.java index 121a776..3a99c41 100644 --- a/src/main/java/Plate.java +++ b/src/main/java/Plate.java @@ -28,6 +28,11 @@ public class Plate { this.sourceFile = sourceFileName; this.wells = wells; this.size = wells.size(); + List concentrations = new ArrayList<>(); + for (List w: wells) { + concentrations.add(w.size()); + } + concentrations.toArray(this.concentrations); } public void fillWellsExponential(String sourceFileName, List cells, double lambda){ diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java index f9cc8cb..4315bca 100644 --- a/src/main/java/Simulator.java +++ b/src/main/java/Simulator.java @@ -240,18 +240,18 @@ public class Simulator { BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc); double pairingErrorRate = (double) falseCount / (trueCount + falseCount); BigDecimal pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc); - //make list of well concentrations + //get list of well concentrations List wellConcentrations = Arrays.asList(data.getWellConcentrations()); //make string out of concentrations list - StringBuilder concen = new StringBuilder(); + StringBuilder concentrationStringBuilder = new StringBuilder(); for(Integer i: wellConcentrations){ - concen.append(i.toString()); - concen.append(" "); + concentrationStringBuilder.append(i.toString()); + concentrationStringBuilder.append(" "); } - String concenString = concen.toString(); + String concentrationString = concentrationStringBuilder.toString(); List comments = new ArrayList<>(); - comments.add("T cell counts in sample plate wells: " + concenString); + 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);