efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

Add version information

Browse Source
This commit is contained in:
efischer
2022-03-01 08:34:35 -06:00
parent f301327693
commit 25acf920c2
3 changed files with 10 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
src/main/java/BiGpairSEQ.java
View File

@@ -16,6 +16,7 @@ public class BiGpairSEQ {
private static String priorityQueueHeapType = "FIBONACCI"; private static String priorityQueueHeapType = "FIBONACCI";
private static boolean outputBinary = true; private static boolean outputBinary = true;
private static boolean outputGraphML = false; private static boolean outputGraphML = false;
private static final String version = "version 2.0";
public static void main(String[] args) { public static void main(String[] args) {
if (args.length == 0) { if (args.length == 0) {
@@ -172,5 +173,5 @@ public class BiGpairSEQ {
public static boolean outputGraphML() {return outputGraphML;} public static boolean outputGraphML() {return outputGraphML;}
public static void setOutputGraphML(boolean b) {outputGraphML = b;} public static void setOutputGraphML(boolean b) {outputGraphML = b;}
public static String getVersion() { return version; }
} }

6
src/main/java/CommandLineInterface.java
View File

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

2
src/main/java/InteractiveInterface.java
View File

@@ -570,6 +570,8 @@ public class InteractiveInterface {
} }
private static void acknowledge(){ 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("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("of the pairSEQ algorithm for pairing T cell receptor sequences.");
System.out.println(); System.out.println();