/**
* Constructor
*
* @throws IOException
*/
public JustAnotherPackageManager(Reporter reporter, Platform platform, File homeDir, File binDir)
throws IOException {
this.platform = platform;
this.reporter = reporter;
this.homeDir = homeDir;
if (!homeDir.exists() && !homeDir.mkdirs())
throw new IllegalArgumentException("Could not create directory " + homeDir);
repoDir = IO.getFile(homeDir, "repo");
if (!repoDir.exists() && !repoDir.mkdirs())
throw new IllegalArgumentException("Could not create directory " + repoDir);
commandDir = new File(homeDir, COMMANDS);
serviceDir = new File(homeDir, SERVICE);
commandDir.mkdir();
serviceDir.mkdir();
service = new File(repoDir, SERVICE_JAR_FILE);
if (!service.isFile()) init();
this.binDir = binDir;
if (!binDir.exists() && !binDir.mkdirs())
throw new IllegalArgumentException("Could not create bin directory " + binDir);
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'f':
fastas = IO.extractFiles(args[i + 1], "fasta");
i++;
break;
case 'n':
numberOfBases = Integer.parseInt(args[i + 1]);
i++;
break;
case 'i':
indexDirectory = new File(args[i + 1]);
i++;
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError: unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
// make index directory?
if (indexDirectory == null) {
indexDirectory = new File(fastas[0].getParentFile(), "IndexedSequences");
indexDirectory.mkdir();
}
}