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Make calculation of p-values optional, defaulting to off

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eugenefischer
2022-09-30 03:17:58 -05:00
parent 593dd6c60f
commit 457d643477
4 changed files with 27 additions and 10 deletions
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8
src/main/java/InteractiveInterface.java
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@@ -422,7 +422,7 @@ public class InteractiveInterface {
}
//simulate matching
MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
minOverlapPercent, true);
minOverlapPercent, true, BiGpairSEQ.calculatePValue());
//write results to file
assert filename != null;
MatchingFileWriter writer = new MatchingFileWriter(filename, results);
@@ -544,7 +544,8 @@ public class InteractiveInterface {
System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
System.out.println("6) Maximum weight matching algorithm options");
System.out.println("6) Turn " + getOnOff(!BiGpairSEQ.calculatePValue()) + " calculation of p-values");
System.out.println("7) Maximum weight matching algorithm options");
System.out.println("0) Return to main menu");
try {
input = sc.nextInt();
@@ -554,7 +555,8 @@ public class InteractiveInterface {
case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
case 6 -> algorithmOptions();
case 6 -> BiGpairSEQ.setCalculatePValue(!BiGpairSEQ.calculatePValue());
case 7 -> algorithmOptions();
case 0 -> backToMain = true;
default -> System.out.println("Invalid input");
}