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.cli.ResultInfo;
import ru.autosome.commons.importer.DiPWMImporter;
import ru.autosome.commons.importer.PWMImporter;
import ru.autosome.commons.motifModel.di.DiPWM;
import ru.autosome.commons.motifModel.mono.PWM;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class ScanCollection extends ru.autosome.macroape.cli.generalized.ScanCollection<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.ScanCollection";
}
@Override
protected String DOC_additional_options() {
return " [--query-from-mono] - obtain query DiPWM from mono PWM/PCM/PPM.\n" +
" [--collection-from-mono] - obtain collection DiPWMs from mono PWM/PCM/PPMs.\n";
}
boolean queryFromMononucleotide, collectionFromMononucleotide;
@Override
protected void initialize_defaults() {
super.initialize_defaults();
queryFromMononucleotide = false;
collectionFromMononucleotide = false;
}
@Override
protected boolean failed_to_recognize_additional_options(String opt, List<String> argv) {
if (opt.equals("--query-from-mono")) {
queryFromMononucleotide = true;
return false;
} else if (opt.equals("--collection-from-mono")) {
collectionFromMononucleotide = true;
return false;
} else {
return true;
}
}
@Override
protected DiBackgroundModel extractBackground(String str) {
return DiBackground.fromString(str);
}
@Override
protected void initialize_default_background() {
queryBackground = new DiWordwiseBackground();
collectionBackground = new DiWordwiseBackground();
}
private ScanCollection() {
initialize_defaults();
}
private static ScanCollection from_arglist(ArrayList<String> argv) {
ScanCollection result = new ScanCollection();
Helper.print_help_if_requested(argv, new ScanCollection().documentString());
result.setup_from_arglist(argv);
return result;
}
private static ScanCollection from_arglist(String[] args) {
ArrayList<String> argv = new ArrayList<String>();
Collections.addAll(argv, args);
return from_arglist(argv);
}
@Override
protected List<DiPWM> loadMotifCollection() {
if (collectionFromMononucleotide) {
BackgroundModel collectionBackgroundMononucleotide = Background.fromDiBackground(collectionBackground);
PWMImporter importer = new PWMImporter(collectionBackgroundMononucleotide, dataModel, effectiveCount, collectionTranspose);
List<PWM> monoCollection = importer.loadMotifCollection(pathToCollectionOfPWMs);
List<DiPWM> diCollection = new ArrayList<DiPWM>(monoCollection.size());
for(PWM monoPWM: monoCollection) {
diCollection.add(DiPWM.fromPWM(monoPWM));
}
return diCollection;
} else {
DiPWMImporter importer = new DiPWMImporter(collectionBackground, dataModel, effectiveCount, collectionTranspose);
return importer.loadMotifCollection(pathToCollectionOfPWMs);
}
}
@Override
protected DiPWM loadQueryMotif() {
if (queryFromMononucleotide) {
BackgroundModel queryBackgroundMononucleotide = Background.fromDiBackground(queryBackground);
PWMImporter importer = new PWMImporter(queryBackgroundMononucleotide, dataModel, effectiveCount, queryTranspose);
return DiPWM.fromPWM(importer.loadMotif(queryPMFilename));
} else {
DiPWMImporter importer = new DiPWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
return importer.loadMotif(queryPMFilename);
}
}
protected ru.autosome.macroape.calculation.di.ScanCollection calculator() {
ru.autosome.macroape.calculation.di.ScanCollection calculator;
calculator = new ru.autosome.macroape.calculation.di.ScanCollection(pwmCollection, queryPWM);
calculator.pvalue = pvalue;
calculator.queryPredefinedThreshold = queryPredefinedThreshold;
calculator.roughDiscretizer = roughDiscretizer;
calculator.preciseDiscretizer = preciseDiscretizer;
calculator.queryBackground = queryBackground;
calculator.collectionBackground = collectionBackground;
calculator.pvalueBoundaryType = pvalueBoundaryType;
calculator.maxHashSize = maxHashSize;
calculator.maxPairHashSize = maxPairHashSize;
calculator.similarityCutoff = similarityCutoff;
calculator.preciseRecalculationCutoff = preciseRecalculationCutoff;
return calculator;
}
public static void main(String[] args) {
try {
ScanCollection calculation = ScanCollection.from_arglist(args);
List<? extends ResultInfo> infos = calculation.process();
System.out.println(calculation.report_table(infos).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 ScanCollection().documentString());
System.exit(1);
}
}
}