TargetedDetectionModule.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.modules.featuredetection.targeteddetection;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Scanner;

import javax.annotation.Nonnull;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.datastore.DataPointStoreFactory;
import io.github.msdk.datamodel.featuretables.FeatureTable;
import io.github.msdk.datamodel.impl.MSDKObjectBuilder;
import io.github.msdk.datamodel.ionannotations.IonAnnotation;
import io.github.msdk.datamodel.ionannotations.IonType;
import io.github.msdk.datamodel.rawdata.RawDataFile;
import io.github.msdk.datamodel.rawdata.SeparationType;
import io.github.msdk.util.IonTypeUtil;
import io.github.msdk.util.tolerances.MaximumMzTolerance;
import io.github.msdk.util.tolerances.RTTolerance;
import io.github.mzmine.modules.MZmineProcessingModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesSelection;
import io.github.mzmine.project.MZmineProject;
import javafx.concurrent.Task;

/**
 * Targeted detection module
 */
public class TargetedDetectionModule implements MZmineProcessingModule {

  private Logger logger = LoggerFactory.getLogger(this.getClass());

  private static final String MODULE_NAME = "Targeted detection";
  private static final String MODULE_DESCRIPTION =
      "This module searches for specific features in the raw data files.";

  @Override
  public @Nonnull String getName() {
    return MODULE_NAME;
  }

  @Override
  public @Nonnull String getDescription() {
    return MODULE_DESCRIPTION;
  }

  @Override
  public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
      @Nonnull Collection<Task<?>> tasks) {

    final RawDataFilesSelection rawDataFiles =
        parameters.getParameter(TargetedDetectionParameters.rawDataFiles).getValue();

    final String annotations =
        parameters.getParameter(TargetedDetectionParameters.annotations).getValue();

    final String separator =
        parameters.getParameter(TargetedDetectionParameters.separator).getValue();

    final Double intensityTolerance =
        parameters.getParameter(TargetedDetectionParameters.intensityTolerance).getValue();

    final Double minHeight =
        parameters.getParameter(TargetedDetectionParameters.minHeight).getValue();

    final RTTolerance rtTolerance =
        parameters.getParameter(TargetedDetectionParameters.rtTolerance).getValue();

    final MaximumMzTolerance mzTolerance =
        parameters.getParameter(TargetedDetectionParameters.mzTolerance).getValue();

    final String nameSuffix =
        parameters.getParameter(TargetedDetectionParameters.nameSuffix).getValue();

    if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
      logger.warn("Targeted detection module started with no raw data files selected");
      return;
    }

    // Convert the input annotations into ionAnnotations
    List<IonAnnotation> ionAnnotations = new ArrayList<IonAnnotation>();
    Scanner scanner = new Scanner(annotations);
    while (scanner.hasNextLine()) {
      String line = scanner.nextLine();
      if (line != null) {

        // Only process lines which start with an integer
        char firstChar = line.charAt(0);
        if (Character.digit(firstChar, 10) >= 0) {
          String[] lineArray = line.split(separator);

          String annotationId = lineArray[0];
          Double mz = Double.parseDouble(lineArray[1]);
          Float rt = Float.parseFloat(lineArray[2]) * 60;
          String name = lineArray[3];

          // If formula column is present then add chemical structure
          IMolecularFormula formula = null;
          if (lineArray.length > 4) {
            String formulaString = lineArray[4];
            if (formulaString != null && !formulaString.equals(""))
              formula = MolecularFormulaManipulator.getMolecularFormula(formulaString,
                  DefaultChemObjectBuilder.getInstance());
          }

          // If adduct column is present then add ion type
          IonType ionType = null;

          if (lineArray.length > 5) {
            String adductString = lineArray[5];
            if (adductString != null && !adductString.equals(""))
              ionType = IonTypeUtil.createIonType(adductString);
          }

          IonAnnotation ion = MSDKObjectBuilder.getIonAnnotation();
          ion.setAnnotationId(annotationId);
          ion.setExpectedMz(mz);
          ion.setDescription(name);
          ion.setChromatographyInfo(
              MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.LC, (float) rt));
          if (ionType != null)
            ion.setIonType(ionType);
          if (formula != null)
            ion.setFormula(formula);
          ionAnnotations.add(ion);

        }

      }
    }
    scanner.close();

    for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

      // Create the data structures
      DataPointStore dataStore = DataPointStoreFactory.getMemoryDataStore();

      // New targeted detection task which runs the following two methods:
      // 1. TargetedDetectionMethod
      // 2. ChromatogramToFeatureTableMethod
      TargetedDetectionTask newTask = new TargetedDetectionTask("Targeted feature detection",
          rawDataFile.getName(), ionAnnotations, rawDataFile, dataStore, mzTolerance, rtTolerance,
          intensityTolerance, minHeight, nameSuffix);

      // Add the feature table to the project
      newTask.setOnSucceeded(e -> {
        FeatureTable featureTable = newTask.getResult();
        project.addFeatureTable(featureTable);
      });

      // Add the task to the queue
      tasks.add(newTask);

    }

  }

  @Override
  public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
    return TargetedDetectionParameters.class;
  }

}