package ru.autosome.macroape;
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.MotifImporter;
import ru.autosome.commons.importer.PWMImporter;
import ru.autosome.commons.model.BoundaryType;
import ru.autosome.commons.model.Discretizer;
import ru.autosome.commons.motifModel.mono.PWM;
import ru.autosome.commons.motifModel.types.DataModel;
import ru.autosome.macroape.calculation.mono.CompareModelsCountsGiven;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class CollectDistanceMatrix extends ru.autosome.macroape.cli.generalized.CollectDistanceMatrix<PWM, BackgroundModel> {
@Override
protected String DOC_background_option() {
return "ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25";
}
@Override
protected String DOC_run_string() {
return "java ru.autosome.macroape.CollectDistanceMatrix";
}
@Override
protected void initialize_default_background() {
background = new WordwiseBackground();
}
@Override
protected BackgroundModel extract_background(String str) {
return Background.fromString(str);
}
private CollectDistanceMatrix() {
initialize_defaults();
}
private static CollectDistanceMatrix from_arglist(List<String> argv) {
CollectDistanceMatrix result = new CollectDistanceMatrix();
Helper.print_help_if_requested(argv, new CollectDistanceMatrix().documentString());
result.setup_from_arglist(argv);
return result;
}
private static CollectDistanceMatrix from_arglist(String[] args) {
ArrayList<String> argv = new ArrayList<String>();
Collections.addAll(argv, args);
return from_arglist(argv);
}
@Override
protected List<PWM> loadMotifCollection(File path_to_collection) {
PWMImporter importer = new PWMImporter(background, dataModel, effectiveCount, transpose);
return importer.loadMotifCollection(path_to_collection);
}
@Override
protected CompareModelsCountsGiven calculator(PWM firstModel, PWM secondModel) {
return new CompareModelsCountsGiven(firstModel, secondModel,
background, background,
roughDiscretizer, maxPairHashSize);
}
public static void main(String[] args) {
try {
CollectDistanceMatrix cli = CollectDistanceMatrix.from_arglist(args);
cli.process();
} 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 CollectDistanceMatrix().documentString());
System.exit(1);
}
}
}