/**
* Factory for command line tools to call different functions
*
* @author Muhammad Shamim
* @since 1/30/2015
*/
public class CLTFactory {
// Commenting some out because we're not going to release all these when we release CLT
private static final String[] commandLineToolUsages = {
// "addGWNorm", "addGWNorm <input_HiC_file> <min resolution>",
// "addNorm", "addNorm <input_HiC_file> [0 for no frag, 1 for no single frag]",
// "bigWig", "bigWig <bigWig path or URL> <window size in bp> [chr] [start base]
// [end base]",
// "binToPairs", "binToPairs <input_HiC_file> <output_HiC_file>",
// "bpToFrag", "bpToFrag <fragmentFile> <inputBedFile> <outputFile>",
// "calcKR", "calcKR <input_HiC_file>",
// "fragmentToBed","fragmentToBed <fragmentFile>",
// "pairsToBin", "pairsToBin <input_HiC_file> <output_HiC_file> <genomeID>",
// "db", "db <frag|annot|update> [items]",
Dump.getUsage(),
PreProcessing.getBasicUsage(),
APA.getBasicUsage(),
Arrowhead.getBasicUsage(),
HiCCUPS.getBasicUsage(),
HiCCUPSDiff.getBasicUsage(),
ValidateFile.getUsage()
};
public static void generalUsage() {
System.out.println("Juicebox and Juicer Command Line Tools Usage:");
for (String usage : commandLineToolUsages) {
System.out.println("\t\t" + usage);
}
System.out.println("Type juicebox <commandName> for more detailed usage instructions");
}
public static JuiceboxCLT getCLTCommand(String cmd) {
cmd = cmd.toLowerCase();
if (cmd.equals("pre")) {
return new PreProcessing();
} else if (cmd.equals("dump")) {
return new Dump();
} else if (cmd.equals("validate")) {
return new ValidateFile();
} else if (cmd.equals("addGWNorm".toLowerCase())) {
return new AddGWNorm();
} else if (cmd.equals("addNorm".toLowerCase())) {
return new AddNorm();
} else if (cmd.equals("apa")) {
return new APA();
} else if (cmd.equals("compare")) {
return new CompareLists();
} else if (cmd.equals("arrowhead")) {
return new Arrowhead();
} else if (cmd.equals("bigWig".toLowerCase())) {
return new BigWig();
} else if (cmd.equals("binToPairs".toLowerCase())) {
return new BinToPairs();
} else if (cmd.equals("bpToFrag".toLowerCase())) {
return new BPToFragment();
} else if (cmd.equals("calcKR".toLowerCase())) {
return new CalcKR();
} else if (cmd.equals("fragmentToBed".toLowerCase())) {
return new FragmentToBed();
} else if (cmd.equals("hiccups")) {
return new HiCCUPS();
} else if (cmd.equals("motifs")) {
return new MotifFinder();
} else if (cmd.equals("pairsToBin".toLowerCase())) {
return new PairsToBin();
} else if (cmd.equals("db")) {
return new SQLDatabase();
} else if (cmd.equals("hiccupsdiff")) {
return new HiCCUPSDiff();
} else if (cmd.equals("ab_compdiff")) {
return new ABCompartmentsDiff();
}
return null;
}
}
