ms1quant.MS1TargetQuantThread.java Source code

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Here is the source code for ms1quant.MS1TargetQuantThread.java

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package ms1quant;

import MSUmpire.BaseDataStructure.InstrumentParameter;
import MSUmpire.LCMSPeakStructure.LCMSPeakMS1;
import MSUmpire.PSMDataStructure.LCMSID;
import java.io.File;
import java.util.concurrent.TimeUnit;
import org.apache.commons.lang.exception.ExceptionUtils;
import org.apache.log4j.Logger;

/**
 *
 * @author Chih-Chiang Tsou
 */
public class MS1TargetQuantThread implements Runnable {

    InstrumentParameter param = null;
    File mzxmlfile = null;
    int NoCPUs = 5;
    LCMSID id = null;
    String outputfolder = "";

    public MS1TargetQuantThread(File mzxmlfile, LCMSID id, int NoCPUs, String outputfolder,
            InstrumentParameter param) {
        this.param = param;
        this.mzxmlfile = mzxmlfile;
        this.NoCPUs = NoCPUs;
        this.id = id;
        this.outputfolder = outputfolder;
    }

    @Override
    public void run() {
        try {

            Logger.getRootLogger().info("Processing file " + mzxmlfile.getAbsolutePath() + "....");

            long time = System.currentTimeMillis();
            LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzxmlfile.getAbsolutePath(), NoCPUs);
            LCMS1.SetParameter(param);

            LCMS1.Resume = false;
            if (!param.TargetIDOnly) {
                LCMS1.CreatePeakFolder();
            }
            LCMS1.ExportPeakClusterTable = false;

            if (id.PSMList.isEmpty()) {
                Logger.getRootLogger()
                        .warn("There is no PSM mapped to the file:" + mzxmlfile.getName() + ", skipping the file.");
                return;
            }
            LCMS1.IDsummary = id;
            LCMS1.IDsummary.mzXMLFileName = mzxmlfile.getAbsolutePath();

            if (param.TargetIDOnly) {
                LCMS1.SaveSerializationFile = false;
            }

            if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) {
                LCMS1.PeakClusterDetection();
            }

            LCMS1.AssignQuant(false);
            LCMS1.IDsummary.ExportPepID(outputfolder);

            time = System.currentTimeMillis() - time;
            //logger.info(LCMS1.ParentmzXMLName + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time))));
            Logger.getRootLogger()
                    .info(LCMS1.ParentmzXMLName + " processed time:"
                            + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time),
                                    TimeUnit.MILLISECONDS.toMinutes(time)
                                            - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)),
                                    TimeUnit.MILLISECONDS.toSeconds(time)
                                            - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time))));
            LCMS1.BaseClearAllPeaks();
            LCMS1.SetSpectrumParser(null);
            LCMS1.IDsummary = null;
            LCMS1 = null;
            id.ReleaseIDs();
            id = null;
            System.gc();
        } catch (Exception ex) {
            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        }
    }

}