guineu.modules.database.openQualityControlFileDB.SampleInfo.java Source code

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Here is the source code for guineu.modules.database.openQualityControlFileDB.SampleInfo.java

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/*
 * Copyright 2007-2013 VTT Biotechnology
 * This file is part of Guineu.
 *
 * Guineu 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.
 *
 * Guineu 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
 * Guineu; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
 * Fifth Floor, Boston, MA 02110-1301 USA
 */
package guineu.modules.database.openQualityControlFileDB;

import guineu.data.impl.peaklists.SimplePeakListRowOther;
import java.text.DecimalFormat;
import java.text.ParseException;
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;

/**
 *
 * @author scsandra
 */
public class SampleInfo {

    String sampleName;
    String date;
    Data LysoPC, PC_50, TG_50, LPC, PC, TGC;
    DecimalFormat formatter = new DecimalFormat("####.##");

    public void setSampleName(String name, String date) {
        this.sampleName = name;
        this.date = date;
    }

    public void setLysoPC(String[] data) {
        LysoPC = new Data(data);
    }

    public void setPC(String[] data) {
        PC_50 = new Data(data);
    }

    public void setTG(String[] data) {
        TG_50 = new Data(data);
    }

    public void setLPC(String[] data) {
        LPC = new Data(data);
    }

    public void setPCD(String[] data) {
        PC = new Data(data);
    }

    public void setTGC(String[] data) {
        TGC = new Data(data);
    }

    public SimplePeakListRowOther getRow(DescriptiveStatistics Stats[]) {
        SimplePeakListRowOther row = new SimplePeakListRowOther();
        int cont = 1;
        row.setPeak(String.valueOf(cont++), sampleName);
        //Lyso
        row.setPeak(String.valueOf(cont++), String.valueOf(LysoPC.RT));
        Stats[0].addValue(LysoPC.RT);

        row.setPeak(String.valueOf(cont++), String.valueOf(LysoPC.heightArea));
        Stats[1].addValue(LysoPC.heightArea);

        row.setPeak(String.valueOf(cont++), getLysoPCratio());
        Stats[2].addValue(Double.valueOf(getLysoPCratio()));

        //PC
        row.setPeak(String.valueOf(cont++), String.valueOf(PC_50.RT));
        Stats[3].addValue(PC_50.RT);

        row.setPeak(String.valueOf(cont++), String.valueOf(PC_50.heightArea));
        Stats[4].addValue(PC_50.heightArea);

        row.setPeak(String.valueOf(cont++), getPCratio());
        Stats[5].addValue(Double.valueOf(getPCratio()));

        //TG
        row.setPeak(String.valueOf(cont++), String.valueOf(TG_50.RT));
        Stats[6].addValue(TG_50.RT);

        row.setPeak(String.valueOf(cont++), String.valueOf(TG_50.heightArea));
        Stats[7].addValue(TG_50.heightArea);

        row.setPeak(String.valueOf(cont++), getTGratio());
        Stats[8].addValue(Double.valueOf(getTGratio()));

        row.setPeak(String.valueOf(cont++), date);
        row.setPeak(String.valueOf(cont++), LysoPC.time);
        return row;
    }

    public SimplePeakListRowOther getRow2(DescriptiveStatistics superStats[]) {
        SimplePeakListRowOther row = new SimplePeakListRowOther();
        int cont = 1;
        row.setPeak(String.valueOf(cont++), sampleName);
        row.setPeak(String.valueOf(cont++), getlysoPCHeight());
        superStats[0].addValue(Double.valueOf(getlysoPCHeight()));
        row.setPeak(String.valueOf(cont++), getPC_50Height());
        superStats[1].addValue(Double.valueOf(getPC_50Height()));
        row.setPeak(String.valueOf(cont++), getTG_50Height());
        superStats[2].addValue(Double.valueOf(getTG_50Height()));
        row.setPeak(String.valueOf(cont++), getLPCHeight());
        superStats[3].addValue(Double.valueOf(getLPCHeight()));
        row.setPeak(String.valueOf(cont++), getLPCRT());
        superStats[4].addValue(Double.valueOf(getLPCRT()));
        row.setPeak(String.valueOf(cont++), getPCHeight());
        superStats[5].addValue(Double.valueOf(getPCHeight()));
        row.setPeak(String.valueOf(cont++), getPCRT());
        superStats[6].addValue(Double.valueOf(getPCRT()));
        row.setPeak(String.valueOf(cont++), getTGCHeight());
        superStats[7].addValue(Double.valueOf(getTGCHeight()));
        row.setPeak(String.valueOf(cont++), getTGCRT());
        superStats[8].addValue(Double.valueOf(getTGCRT()));
        return row;
    }

    public String getLysoPCratio() {
        try {
            return formatter.format(LysoPC.height / LPC.height).toString();
        } catch (Exception e) {
            return String.valueOf(LysoPC.height / LPC.height);
        }
    }

    public String getLysoPCRT() {
        return String.valueOf(LysoPC.RT);
    }

    public String getPCratio() {
        try {
            return formatter.format(PC_50.height / PC.height).toString();
        } catch (Exception e) {
            return String.valueOf(PC_50.height / PC.height);
        }
    }

    public String getPC_50RT() {
        return String.valueOf(PC_50.RT);
    }

    public String getTGratio() {
        try {
            return formatter.format(TG_50.height / TGC.height).toString();
        } catch (Exception e) {
            return String.valueOf(TG_50.height / TGC.height);
        }
    }

    public String getTGRT() {
        return String.valueOf(TG_50.RT);
    }

    public String getTGCRT() {
        return String.valueOf(TGC.RT);
    }

    public String getPCRT() {
        return String.valueOf(PC.RT);
    }

    public String getLPCRT() {
        return String.valueOf(LPC.RT);
    }

    public String getPC_50Height() {
        return String.valueOf(PC_50.height);
    }

    public String getlysoPCHeight() {
        return String.valueOf(LysoPC.height);
    }

    public String getTG_50Height() {
        return String.valueOf(TG_50.height);
    }

    public String getLPCHeight() {
        return String.valueOf(LPC.height);
    }

    public String getPCHeight() {
        return String.valueOf(PC.height);
    }

    public String getTGCHeight() {
        return String.valueOf(TGC.height);
    }

    public String getFormat() {
        String format = "<td>" + String.valueOf(LysoPC.RT) + " </td>" + "<td>" + String.valueOf(LysoPC.heightArea)
                + "</td>" + "<td>" + getLysoPCratio() + "</td>" + "<td>" + String.valueOf(PC_50.RT) + "</td>"
                + "<td>" + String.valueOf(PC_50.heightArea) + "</td>" + "<td>" + getPCratio() + "</td>" + "<td>"
                + String.valueOf(TG_50.RT) + "</td>" + "<td>" + String.valueOf(TG_50.heightArea) + "</td>" + "<td>"
                + getTGratio() + "</td>" + "<td>" + date + "</td>" + "<td>" + LysoPC.time + "</td></tr>";

        return format;
    }

    class Data {

        String Name;
        double RT;
        double height;
        double ratio;
        double heightArea;
        double signalToNoise;
        String time;

        public Data(String[] fields) {
            try {
                DecimalFormat formatter = new DecimalFormat("####.##");
                this.Name = fields[0];
                this.RT = formatter.parse(fields[1]).doubleValue();
                this.height = formatter.parse(fields[2]).doubleValue();
                this.ratio = formatter.parse(fields[3]).doubleValue();
                this.heightArea = formatter.parse(fields[4]).doubleValue();
                this.time = fields[5];
            } catch (ParseException ex) {
                this.Name = fields[0];
                this.RT = Double.valueOf(fields[1]).doubleValue();
                this.height = Double.valueOf(fields[2]).doubleValue();
                this.ratio = Double.valueOf(fields[3]).doubleValue();
                this.heightArea = Double.valueOf(fields[4]).doubleValue();
                this.time = fields[5];

                //Logger.getLogger(ReportTask.class.getName()).log(Level.SEVERE, null, ex);
            }
        }
    }
}