private static TagsByTaxa newTBT(String filename, String[] taxonNames, TagCountMutable tcm) {
if (TagsByTaxaUtils.format(filename).equals(TagsByTaxa.FilePacking.Byte)) {
return new TagsByTaxaByteFileMap(filename, taxonNames, tcm);
} else {
return null;
}
}
private static TagsByTaxa newTBT(String filename) {
if (TagsByTaxaUtils.format(filename).equals(TagsByTaxa.FilePacking.Byte)) {
return new TagsByTaxaByteFileMap(filename);
} else {
return null;
}
}
public void setParameters(String[] args) {
myLogger.addAppender(new ConsoleAppender(new SimpleLayout()));
if (args.length == 0) {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (myArgsEngine == null) {
myArgsEngine = new ArgsEngine();
myArgsEngine.add("-i", "--input-directory", true);
myArgsEngine.add("-o", "--output_file", true);
myArgsEngine.add("-s", "--max_tags", true);
myArgsEngine.add("-x", "--combine-synonymous-taxa");
myArgsEngine.add("-h", "--write-hapmap", true);
}
myArgsEngine.parse(args);
if (myArgsEngine.getBoolean("-x")) {
combineSynonymousTaxa = true;
}
if (myArgsEngine.getBoolean("-h")) {
hapmapFile = new File(myArgsEngine.getString("-h"));
}
if (myArgsEngine.getBoolean("-s")) {
maxTags = Integer.parseInt(myArgsEngine.getString("-s"));
}
if (myArgsEngine.getBoolean("-o")) {
outfilename = myArgsEngine.getString("-o");
File outfile = new File(outfilename);
if (outfile.isDirectory()) {
printUsage();
throw new IllegalArgumentException(
"The output filename you provided is a directory, not a file.");
}
} else {
printUsage();
throw new IllegalArgumentException("Please specify an output file.");
}
if (myArgsEngine.getBoolean("-i")) {
inputDirectory = new File(myArgsEngine.getString("-i"));
if (!inputDirectory.isDirectory()) {
printUsage();
throw new IllegalArgumentException("The input name you supplied is not a directory.");
} else {
infiles =
DirectoryCrawler.listFileNames(
".*\\.tbt\\.bin|.*\\.tbt\\.byte", inputDirectory.getAbsolutePath());
myLogger.info("Merging the following .tbt.bin or .tbt.byte files...");
for (String filename : infiles) {
if (!TagsByTaxaUtils.format(filename).equals(TagsByTaxaUtils.format(outfilename))) {
myLogger.warn("Input file extension does not match output file extension.");
}
myLogger.info(filename);
}
myLogger.info("...to \"" + outfilename + "\".");
}
} else {
printUsage();
throw new IllegalArgumentException("You forgot to provide an input directory name.");
}
}