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Add optional stdout print flags

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efischer
2022-03-01 15:27:04 -06:00
parent 3fc39302c7
commit 4c872ed48e
1 changed files with 46 additions and 15 deletions
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61
src/main/java/CommandLineInterface.java
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@@ -194,6 +194,27 @@ public class CommandLineInterface {
System.out.println(k + ": " + result.getMetadata().get(k));
}
}
if(line.hasOption("print-error")) {
System.out.println("pairing error rate: " + result.getPairingErrorRate());
}
if(line.hasOption("print-attempt")) {
System.out.println("pairing attempt rate: " +result.getPairingAttemptRate());
}
if(line.hasOption("print-correct")) {
System.out.println("correct pairings: " + result.getCorrectPairingCount());
}
if(line.hasOption("print-incorrect")) {
System.out.println("incorrect pairings: " + result.getIncorrectPairingCount());
}
if(line.hasOption("print-alphas")) {
System.out.println("total alphas found: " + result.getAlphaCount());
}
if(line.hasOption("print-betas")) {
System.out.println("total betas found: " + result.getBetaCount());
}
if(line.hasOption("print-time")) {
System.out.println("simulation time (seconds): " + result.getSimulationTime());
}
}
}
catch (ParseException exp) {
@@ -413,22 +434,32 @@ public class CommandLineInterface {
.addOption(outputFile);
//options for output to System.out
// Option printErrorRate = Option.builder().longOpt("print-error")
// .desc("(Optional) Print the pairing error rate to stdout").build();
// Option printAttempt = Option.builder().longOpt("print-attempt")
// .desc("(Optional) Print the pairing attempt rate to stdout").build();
// Option printCorrect = Option.builder().longOpt("print-correct")
// .desc("(Optional) Print the number of correct pairs to stdout").build();
// Option printIncorrect = Option.builder().longOpt("print-incorrect")
// .desc("(Optional) Print the number of incorrect pairs to stdout").build();
Option printMetadata = Option.builder().longOpt("print-metadata")
.desc("(Optional) Print summary of matching results to stdout.").build();
Option printAlphaCount = Option.builder().longOpt("print-alphas")
.desc("(Optional) Print the number of distinct alpha sequences to stdout.").build();
Option printBetaCount = Option.builder().longOpt("print-betas")
.desc("(Optional) Print the number of distinct beta sequences to stdout.").build();
Option printTime = Option.builder().longOpt("print-time")
.desc("(Optional) Print the total simulation time to stdout.").build();
Option printErrorRate = Option.builder().longOpt("print-error")
.desc("(Optional) Print the pairing error rate to stdout").build();
Option printAttempt = Option.builder().longOpt("print-attempt")
.desc("(Optional) Print the pairing attempt rate to stdout").build();
Option printCorrect = Option.builder().longOpt("print-correct")
.desc("(Optional) Print the number of correct pairs to stdout").build();
Option printIncorrect = Option.builder().longOpt("print-incorrect")
.desc("(Optional) Print the number of incorrect pairs to stdout").build();
Option printMetadata = Option.builder().longOpt("print-metadata")
.desc("(Optional) Print a full summary of the matching results to stdout.").build();
matchCDR3options
// .addOption(printErrorRate)
// .addOption(printAttempt)
// .addOption(printCorrect)
// .addOption(printIncorrect)
.addOption(printMetadata);
.addOption(printErrorRate)
.addOption(printAttempt)
.addOption(printCorrect)
.addOption(printIncorrect)
.addOption(printMetadata)
.addOption(printAlphaCount)
.addOption(printBetaCount)
.addOption(printTime);
return matchCDR3options;
}