ScanSelectionParameter.java

/*
 * Copyright 2006-2015 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 javax.annotation.Nonnull;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;

import com.google.common.collect.Range;

import io.github.msdk.datamodel.msspectra.MsSpectrumType;
import io.github.msdk.datamodel.rawdata.PolarityType;
import io.github.mzmine.parameters.parametertypes.AbstractParameter;

public class ScanSelectionParameter extends AbstractParameter<ScanSelection> {

  public ScanSelectionParameter() {
    this("Scans", "Select scans that should be included.", null, null);
  }

  public ScanSelectionParameter(ScanSelection defaultValue) {
    this("Scans", "Select scans that should be included.", null, defaultValue);
  }

  public ScanSelectionParameter(String name, String description, String category,
      ScanSelection defaultValue) {
    super(name, description, category, ScanSelectionEditor.class, null);
  }

  @Override
  public @Nonnull ScanSelectionParameter clone() {
    ScanSelectionParameter copy =
        new ScanSelectionParameter(getName(), getDescription(), getCategory(), getValue());
    return copy;
  }

  @Override
  public void loadValueFromXML(Element xmlElement) {

    Range<Integer> scanNumberRange = null;
    Range<Double> scanRTRange = null;
    PolarityType polarity = null;
    MsSpectrumType spectrumType = null;
    Integer msLevel = null;
    String scanDefinition = null;

    NodeList items = xmlElement.getElementsByTagName("scan_numbers");
    for (int i = 0; i < items.getLength(); i++) {
      if (items.item(i).getChildNodes().getLength() != 2)
        continue;
      String minText = items.item(i).getChildNodes().item(0).getTextContent();
      String maxText = items.item(i).getChildNodes().item(1).getTextContent();
      scanNumberRange = Range.closed(Integer.valueOf(minText), Integer.valueOf(maxText));
    }

    items = xmlElement.getElementsByTagName("retention_time");
    for (int i = 0; i < items.getLength(); i++) {
      if (items.item(i).getChildNodes().getLength() != 2)
        continue;
      String minText = items.item(i).getChildNodes().item(0).getTextContent();
      String maxText = items.item(i).getChildNodes().item(1).getTextContent();
      scanRTRange = Range.closed(Double.valueOf(minText), Double.valueOf(maxText));
    }

    items = xmlElement.getElementsByTagName("ms_level");
    for (int i = 0; i < items.getLength(); i++) {
      msLevel = Integer.valueOf(items.item(i).getTextContent());
    }

    items = xmlElement.getElementsByTagName("polarity");
    for (int i = 0; i < items.getLength(); i++) {
      try {
        polarity = PolarityType.valueOf(items.item(i).getTextContent());
      } catch (Exception e) {
        polarity = null;
      }
    }

    items = xmlElement.getElementsByTagName("spectrum_type");
    for (int i = 0; i < items.getLength(); i++) {
      spectrumType = MsSpectrumType.valueOf(items.item(i).getTextContent());
    }

    items = xmlElement.getElementsByTagName("scan_definition");
    for (int i = 0; i < items.getLength(); i++) {
      scanDefinition = items.item(i).getTextContent();
    }

    ScanSelection newValue = new ScanSelection(scanNumberRange, scanRTRange, polarity, spectrumType,
        msLevel, scanDefinition);
    setValue(newValue);
  }

  @Override
  public void saveValueToXML(Element xmlElement) {
    ScanSelection value = getValue();
    if (value == null)
      return;
    Document parentDocument = xmlElement.getOwnerDocument();

    final Range<Integer> scanNumberRange = value.getScanNumberRange();
    final Range<Double> scanRetentionTimeRange = value.getScanRTRange();
    final PolarityType polarity = value.getPolarity();
    final MsSpectrumType spectrumType = value.getSpectrumType();
    final Integer msLevel = value.getMsLevel();
    final String scanDefinition = value.getScanDefinition();

    if (scanNumberRange != null) {
      Element scanNumElement = parentDocument.createElement("scan_numbers");
      xmlElement.appendChild(scanNumElement);
      Element newElement = parentDocument.createElement("min");
      newElement.setTextContent(String.valueOf(scanNumberRange.lowerEndpoint()));
      scanNumElement.appendChild(newElement);
      newElement = parentDocument.createElement("max");
      newElement.setTextContent(String.valueOf(scanNumberRange.upperEndpoint()));
      scanNumElement.appendChild(newElement);
    }

    if (scanRetentionTimeRange != null) {
      Element scanRtElement = parentDocument.createElement("retention_time");
      xmlElement.appendChild(scanRtElement);
      Element newElement = parentDocument.createElement("min");
      newElement.setTextContent(String.valueOf(scanRetentionTimeRange.lowerEndpoint()));
      scanRtElement.appendChild(newElement);
      newElement = parentDocument.createElement("max");
      newElement.setTextContent(String.valueOf(scanRetentionTimeRange.upperEndpoint()));
      scanRtElement.appendChild(newElement);
    }

    if (polarity != null) {
      Element newElement = parentDocument.createElement("polarity");
      newElement.setTextContent(polarity.toString());
      xmlElement.appendChild(newElement);
    }

    if (spectrumType != null) {
      Element newElement = parentDocument.createElement("spectrum_type");
      newElement.setTextContent(spectrumType.toString());
      xmlElement.appendChild(newElement);
    }

    if (msLevel != null) {
      Element newElement = parentDocument.createElement("ms_level");
      newElement.setTextContent(String.valueOf(msLevel));
      xmlElement.appendChild(newElement);
    }

    if (scanDefinition != null) {
      Element newElement = parentDocument.createElement("scan_definition");
      newElement.setTextContent(scanDefinition);
      xmlElement.appendChild(newElement);
    }

  }

}