package ru.autosome.macroape.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.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.model.BoundaryType;
import ru.autosome.commons.model.Discretizer;
import ru.autosome.commons.motifModel.di.DiPWM;
import ru.autosome.commons.motifModel.mono.PWM;
import ru.autosome.commons.motifModel.types.DataModel;
import ru.autosome.macroape.calculation.di.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<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.macroape.di.CollectDistanceMatrix";
}
@Override
protected String DOC_additional_options() {
return " [--from-mono] - obtain DiPWMs from mononucleotide PWM/PCM/PPMs.\n";
}
protected boolean failed_to_recognize_additional_options(String opt, List<String> argv) {
if (opt.equals("--from-mono")) {
fromMononucleotide= true;
return false;
} else {
return true;
}
}
boolean fromMononucleotide;
@Override
protected List<DiPWM> loadMotifCollection(File path_to_collection) {
if (fromMononucleotide) {
BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
PWMImporter importer = new PWMImporter(backgroundMononucleotide, dataModel, effectiveCount, transpose);
List<PWM> monoCollection = importer.loadMotifCollection(path_to_collection);
pwmCollection = new ArrayList<DiPWM>(monoCollection.size());
for(PWM monoPWM: monoCollection) {
pwmCollection.add(DiPWM.fromPWM(monoPWM));
}
return pwmCollection;
} else {
DiPWMImporter importer = new DiPWMImporter(background, dataModel, effectiveCount, transpose);
return importer.loadMotifCollection(path_to_collection);
}
}
@Override
protected void initialize_defaults() {
super.initialize_defaults();
fromMononucleotide = false;
}
@Override
protected void initialize_default_background() {
background = new DiWordwiseBackground();
}
@Override
protected DiBackgroundModel extract_background(String str) {
return DiBackground.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 CompareModelsCountsGiven calculator(DiPWM firstModel, DiPWM 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);
}
}
}