efischer/BiGpairSEQ
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efischer
2022-03-01 08:34:35 -06:00
parent f301327693
commit 25acf920c2
3 changed files with 10 additions and 1 deletions
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3
src/main/java/BiGpairSEQ.java
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@@ -16,6 +16,7 @@ public class BiGpairSEQ {
private static String priorityQueueHeapType = "FIBONACCI";
private static boolean outputBinary = true;
private static boolean outputGraphML = false;
private static final String version = "version 2.0";
public static void main(String[] args) {
if (args.length == 0) {
@@ -172,5 +173,5 @@ public class BiGpairSEQ {
public static boolean outputGraphML() {return outputGraphML;}
public static void setOutputGraphML(boolean b) {outputGraphML = b;}
public static String getVersion() { return version; }
}

6
src/main/java/CommandLineInterface.java
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@@ -72,6 +72,9 @@ public class CommandLineInterface {
System.out.println();
formatter.printHelp("BiGpairSEQ_Sim.jar -match", matchOptions);
}
else if (line.hasOption("version")) {
System.out.println("BiGpairSEQ_Sim " + BiGpairSEQ.getVersion());
}
else if (line.hasOption("cells")) {
line = parser.parse(cellOptions, Arrays.copyOfRange(args, 1, args.length));
Integer number = Integer.valueOf(line.getOptionValue("n"));
@@ -230,8 +233,11 @@ public class CommandLineInterface {
.longOpt("match-cdr3")
.desc("Matches CDR3s. Requires a graph/data file.")
.build();
Option printVersion = Option.builder("version")
.desc("Print the version number").build();
OptionGroup mainGroup = new OptionGroup();
mainGroup.addOption(help);
mainGroup.addOption(printVersion);
mainGroup.addOption(makeCells);
mainGroup.addOption(makePlate);
mainGroup.addOption(makeGraph);

2
src/main/java/InteractiveInterface.java
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@@ -570,6 +570,8 @@ public class InteractiveInterface {
}
private static void acknowledge(){
System.out.println("BiGpairSEQ_Sim " + BiGpairSEQ.getVersion());
System.out.println();
System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
System.out.println();