massbank.QueryFileUtil.java Source code

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Here is the source code for massbank.QueryFileUtil.java

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/*******************************************************************************
 *
 * Copyright (C) 2010 JST-BIRD MassBank
 *
 * This program 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.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 *
 *******************************************************************************
 *
 * NGt@C?[eBeBNX
 *
 * ver 1.0.0 2012.02.15
 *
 ******************************************************************************/
package massbank;

import java.util.ArrayList;
import java.text.DecimalFormat;
import java.io.File;
import java.io.FileReader;
import java.io.BufferedReader;
import org.apache.commons.lang.NumberUtils;

public class QueryFileUtil {

    private ArrayList<String> nameList = null;
    private ArrayList<String[]> mzList = null;
    private ArrayList<String[]> intensityList = null;
    private String filePath = "";

    /**
     * RXgN^
     */
    public QueryFileUtil(String filePath) {
        this.nameList = new ArrayList<String>();
        this.mzList = new ArrayList<String[]>();
        this.intensityList = new ArrayList<String[]>();
        this.filePath = filePath;

        String line = "";
        String name = "";
        String peak = "";
        int lineNo = 0;
        int cnt = 1;

        ArrayList<String[]> queryList = new ArrayList();
        try {
            File f = new File(filePath);
            BufferedReader in = new BufferedReader(new FileReader(f));
            while ((line = in.readLine()) != null) {
                line = line.trim();

                // R?g?sXLbv
                if (line.startsWith("//")) {
                    continue;
                }
                // NAME^O
                else if (line.matches("^Name:.*")) {
                    name = line.replaceFirst("^Name: *", "").trim();
                } else if (line.matches(".*:.*")) {
                } else if (line.equals("")) {
                    if (lineNo > 0) {
                        addList(name, peak);
                        cnt++;
                        name = "";
                        peak = "";
                        lineNo = 0;
                    }
                } else {
                    peak += line;
                    if (!line.substring(line.length() - 1).equals(";")) {
                        peak += ";";
                    }
                    lineNo++;
                }
            }
            in.close();
            if (lineNo > 0) {
                addList(name, peak);
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    /**
     * OXg
     */
    public String[] getNameList() {
        return this.nameList.toArray(new String[0]);
    }

    /**
     * m/zXg
     */
    public String[] getMzs(int index) {
        return this.mzList.get(index);
    }

    /**
     * xXg
     */
    public String[] getAbsIntensities(int index) {
        return this.intensityList.get(index);
    }

    /**
     * xXg
     */
    public String[] getRelIntensities(int index) {

        double max = 0;
        double absInte = 0;
        String[] relIntes = intensityList.get(index);
        int num = relIntes.length;
        for (int i = 0; i < num; i++) {
            absInte = Double.parseDouble(relIntes[i]);
            if (absInte > max) {
                max = absInte;
            }
        }

        String[] vals = new String[num];
        for (int i = 0; i < num; i++) {
            absInte = Double.parseDouble(relIntes[i]);
            int relInte = new Double(absInte / max * 999).intValue();
            vals[i] = String.valueOf(relInte);
        }
        return vals;
    }

    /**
     * e|t@C??
     */
    public void delete() {
        File f = new File(this.filePath);
        f.delete();
    }

    /**
     * NG?Xg
     */
    private void addList(String name, String peak) {
        DecimalFormat df = new DecimalFormat("000000");
        int no = this.nameList.size() + 1;
        if (name.equals("")) {
            name = "Compound_" + df.format(no);
        }
        this.nameList.add(name);

        String[] items = peak.split(";");
        int num = items.length;
        String[] mzs = new String[num];
        String[] intes = new String[num];
        for (int i = 0; i < items.length; i++) {
            String pair = items[i].trim();
            pair = pair.replaceAll(" +", ",");
            pair = pair.replaceAll("\t+", ",");
            String[] vals = pair.split(",");
            if (vals.length < 2 || !NumberUtils.isNumber(vals[0]) || !NumberUtils.isNumber(vals[1])) {
                mzs[i] = ("-1");
                intes[i] = ("-1");
            } else {
                mzs[i] = vals[0];
                intes[i] = vals[1];
            }

        }
        mzList.add(mzs);
        intensityList.add(intes);
    }
}