ScanSelection.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.parameters.parametertypes.selectors;

import java.util.ArrayList;
import java.util.List;

import javax.annotation.concurrent.Immutable;

import com.google.common.base.Strings;
import com.google.common.collect.Range;

import io.github.msdk.datamodel.msspectra.MsSpectrumType;
import io.github.msdk.datamodel.rawdata.MsScan;
import io.github.msdk.datamodel.rawdata.PolarityType;
import io.github.msdk.datamodel.rawdata.RawDataFile;
import io.github.mzmine.util.TextUtils;

@Immutable
public class ScanSelection {

  private final Range<Integer> scanNumberRange;
  private final Range<Double> scanRTRange;
  private final PolarityType polarity;
  private final MsSpectrumType spectrumType;
  private final Integer msLevel;
  private String scanDefinition;

  public ScanSelection() {
    this(1);
  }

  public ScanSelection(int msLevel) {
    this(null, null, null, null, msLevel, null);
  }

  public ScanSelection(Range<Double> scanRTRange, int msLevel) {
    this(null, scanRTRange, null, null, msLevel, null);
  }

  public ScanSelection(Range<Integer> scanNumberRange, Range<Double> scanRTRange,
      PolarityType polarity, MsSpectrumType spectrumType, Integer msLevel, String scanDefinition) {
    this.scanNumberRange = scanNumberRange;
    this.scanRTRange = scanRTRange;
    this.polarity = polarity;
    this.spectrumType = spectrumType;
    this.msLevel = msLevel;
    this.scanDefinition = scanDefinition;
  }

  public Range<Integer> getScanNumberRange() {
    return scanNumberRange;
  }

  public Range<Double> getScanRTRange() {
    return scanRTRange;
  }

  public PolarityType getPolarity() {
    return polarity;
  }

  public MsSpectrumType getSpectrumType() {
    return spectrumType;
  }

  public Integer getMsLevel() {
    return msLevel;
  }

  public String getScanDefinition() {
    return scanDefinition;
  }

  public List<MsScan> getMatchingScans(RawDataFile dataFile) {

    final List<MsScan> matchingScans = new ArrayList<>();

    for (MsScan scan : dataFile.getScans()) {

      if ((msLevel != null) && (!msLevel.equals(scan.getMsFunction().getMsLevel())))
        continue;

      if ((polarity != null) && (!polarity.equals(scan.getPolarity())))
        continue;

      if ((spectrumType != null) && (!spectrumType.equals(scan.getSpectrumType())))
        continue;

      if ((scanNumberRange != null) && (!scanNumberRange.contains(scan.getScanNumber())))
        continue;

      if ((scanRTRange != null)
          && (!scanRTRange.contains(scan.getChromatographyInfo().getRetentionTime().doubleValue())))
        continue;

      if (!Strings.isNullOrEmpty(scanDefinition)) {

        final String actualScanDefition = scan.getScanDefinition();

        if (Strings.isNullOrEmpty(actualScanDefition))
          continue;

        final String regex = TextUtils.createRegexFromWildcards(scanDefinition);

        if (!actualScanDefition.matches(regex))
          continue;

      }

      matchingScans.add(scan);
    }

    return matchingScans;

  }
}