MSUmpire.SpectrumParser.DIA_Setting.java Source code

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Here is the source code for MSUmpire.SpectrumParser.DIA_Setting.java

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/* 
 * Author: Chih-Chiang Tsou <chihchiang.tsou@gmail.com>
 *             Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics, 
 *             University of Michigan, Ann Arbor
 *
 * Copyright 2014 University of Michigan, Ann Arbor, MI
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package MSUmpire.SpectrumParser;

import MSUmpire.BaseDataStructure.SpectralDataType;
import MSUmpire.BaseDataStructure.XYData;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.TreeMap;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.exception.ExceptionUtils;
import org.apache.log4j.Logger;

/**
 * Definitions of DIA type and isolation window settings
 * @author Chih-Chiang Tsou <chihchiang.tsou@gmail.com>
 */
public class DIA_Setting implements Serializable {
    private static final long serialVersionUID = 646984181894L;
    public TreeMap<XYData, ArrayList<Integer>> DIAWindows = new TreeMap<XYData, ArrayList<Integer>>();
    public TreeMap<XYData, ArrayList<Integer>> MS1Windows = new TreeMap<XYData, ArrayList<Integer>>();
    public float F_DIA_WindowSize = 25;
    public SpectralDataType.DataType dataType;

    public void WriteDIASettingSerialization(String mzXMLFileName) {
        try {
            Logger.getRootLogger().info("Writing DIA setting to file:" + FilenameUtils.getFullPath(mzXMLFileName)
                    + FilenameUtils.getBaseName(mzXMLFileName) + "_diasetting.ser...");
            FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(mzXMLFileName)
                    + FilenameUtils.getBaseName(mzXMLFileName) + "_diasetting.ser", false);
            ObjectOutputStream oos = new ObjectOutputStream(fout);
            oos.writeObject(this);
            oos.close();
            fout.close();
        } catch (Exception ex) {
            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        }
    }

    public static DIA_Setting ReadDIASettingSerialization(String filepath) {
        if (!new File(FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + "_diasetting.ser")
                .exists()) {
            return null;
        }
        try {
            Logger.getRootLogger().debug("Reading DIA setting from file:" + FilenameUtils.getFullPath(filepath)
                    + FilenameUtils.getBaseName(filepath) + "_diasetting.ser...");

            FileInputStream fileIn = new FileInputStream(
                    FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + "_diasetting.ser");
            ObjectInputStream in = new ObjectInputStream(fileIn);
            DIA_Setting setting = (DIA_Setting) in.readObject();
            in.close();
            fileIn.close();
            return setting;

        } catch (Exception ex) {
            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
            return null;
        }
    }

}