package ru.autosome.ape.di;
import ru.autosome.commons.backgroundModel.di.DiBackground;
import ru.autosome.commons.backgroundModel.di.DiBackgroundModel;
import ru.autosome.commons.backgroundModel.di.DiWordwiseBackground;
import ru.autosome.ape.calculation.findThreshold.CanFindThreshold;
import ru.autosome.ape.calculation.findThreshold.FindThresholdAPE;
import ru.autosome.ape.calculation.findThreshold.FindThresholdBsearchBuilder;
import ru.autosome.commons.backgroundModel.mono.Background;
import ru.autosome.commons.backgroundModel.mono.BackgroundModel;
import ru.autosome.commons.backgroundModel.mono.WordwiseBackground;
import ru.autosome.commons.cli.Helper;
import ru.autosome.commons.importer.DiPWMImporter;
import ru.autosome.commons.importer.MotifImporter;
import ru.autosome.commons.importer.PWMImporter;
import ru.autosome.commons.motifModel.di.DiPWM;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class FindThreshold extends ru.autosome.ape.cli.generalized.FindThreshold<DiPWM, DiBackgroundModel> {
@Override
protected String DOC_background_option() {
return "ACGT - 16 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.02,0.03,0.03,0.02,0.08,0.12,0.12,0.08,0.08,0.12,0.12,0.08,0.02,0.03,0.03,0.02";
}
@Override
protected String DOC_run_string() {
return "java ru.autosome.ape.di.FindThreshold";
}
@Override
protected String DOC_additional_options() {
return " [--from-mono] - obtain DiPWM from mono PWM/PCM/PPM.\n";
}
boolean fromMononucleotide;
@Override
protected void initialize_defaults() {
super.initialize_defaults();
fromMononucleotide = false;
}
@Override
protected void initialize_default_background() {
background = new DiWordwiseBackground();
}
@Override
protected DiPWM loadMotif(String filename) {
if (fromMononucleotide) {
BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
PWMImporter importer = new PWMImporter(backgroundMononucleotide, data_model, effective_count, transpose);
return DiPWM.fromPWM( importer.loadMotif(filename) );
} else {
DiPWMImporter importer = new DiPWMImporter(background, data_model, effective_count, transpose);
return importer.loadMotif(filename);
}
}
@Override
protected void extract_background(String str) {
background = DiBackground.fromString(str);
}
@Override
protected boolean failed_to_recognize_additional_options(String opt, List<String> argv) {
if (opt.equals("--from-mono")) {
fromMononucleotide = true;
return false;
} else {
return true;
}
}
@Override
protected CanFindThreshold calculator() {
if (cache_calculator == null) {
if (thresholds_folder == null) {
cache_calculator = new FindThresholdAPE<DiPWM, DiBackgroundModel>(motif, background, discretizer, max_hash_size);
} else {
cache_calculator = new FindThresholdBsearchBuilder(thresholds_folder).thresholdCalculator(motif);
}
}
return cache_calculator;
}
public FindThreshold() {
initialize_defaults();
}
protected static FindThreshold from_arglist(ArrayList<String> argv) {
FindThreshold result = new FindThreshold();
Helper.print_help_if_requested(argv, result.documentString());
result.setup_from_arglist(argv);
return result;
}
protected static FindThreshold from_arglist(String[] args) {
ArrayList<String> argv = new ArrayList<String>();
Collections.addAll(argv, args);
return from_arglist(argv);
}
public static void main(String args[]) {
try {
FindThreshold cli = ru.autosome.ape.di.FindThreshold.from_arglist(args);
System.out.println(cli.report_table().report());
} catch (Exception err) {
System.err.println("\n" + err.getMessage() + "\n--------------------------------------\n");
err.printStackTrace();
System.err.println("\n--------------------------------------\nUse --help option for help\n\n" + new FindPvalue().documentString());
System.exit(1);
}
}
}