MZToleranceParameter.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.tolerances;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

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

import io.github.msdk.util.tolerances.MaximumMzTolerance;
import io.github.mzmine.parameters.ParameterValidator;
import io.github.mzmine.parameters.parametertypes.AbstractParameter;

public class MZToleranceParameter extends AbstractParameter<MaximumMzTolerance> {

  public MZToleranceParameter(@Nonnull String name, @Nonnull String description,
      @Nonnull String category) {
    this(name, description, category, null, null);
  }

  public MZToleranceParameter(@Nonnull String name, @Nonnull String description,
      @Nonnull String category, MaximumMzTolerance defaultValue) {
    this(name, description, category, null, defaultValue);
  }

  public MZToleranceParameter(@Nonnull String name, @Nonnull String description,
      @Nonnull String category, @Nullable ParameterValidator<MaximumMzTolerance> validator) {
    this(name, description, category, validator, null);
  }

  public MZToleranceParameter(@Nonnull String name, @Nonnull String description,
      @Nonnull String category, @Nullable ParameterValidator<MaximumMzTolerance> validator,
      @Nullable MaximumMzTolerance defaultValue) {
    super(name, description, category, MZToleranceEditor.class, validator);
    setValue(defaultValue);
  }

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

  @Override
  public void loadValueFromXML(@Nonnull Element xmlElement) {
    // Set some default values
    double MaximumMzTolerance = 0.005;
    double ppmTolerance = 5;
    NodeList items = xmlElement.getElementsByTagName("absolutetolerance");
    for (int i = 0; i < items.getLength(); i++) {
      String itemString = items.item(i).getTextContent();
      MaximumMzTolerance = Double.parseDouble(itemString);
    }
    items = xmlElement.getElementsByTagName("ppmtolerance");
    for (int i = 0; i < items.getLength(); i++) {
      String itemString = items.item(i).getTextContent();
      ppmTolerance = Double.parseDouble(itemString);
    }
    setValue(new MaximumMzTolerance(MaximumMzTolerance, ppmTolerance));
  }

  @SuppressWarnings("null")
  @Override
  public void saveValueToXML(@Nonnull Element xmlElement) {
    if (getValue() == null)
      return;
    Document parentDocument = xmlElement.getOwnerDocument();
    Element newElement = parentDocument.createElement("absolutetolerance");
    newElement.setTextContent(String.valueOf(getValue().getMzTolerance()));
    xmlElement.appendChild(newElement);
    newElement = parentDocument.createElement("ppmtolerance");
    newElement.setTextContent(String.valueOf(getValue().getPpmTolerance()));
    xmlElement.appendChild(newElement);
  }
}