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The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.
There is a newer version: 0.9.2
package org.jcamp.parser;

import java.util.Iterator;

import org.jcamp.spectrum.ISpectrumIdentifier;
import org.jcamp.spectrum.MassSpectrum;
import org.jcamp.spectrum.Peak1D;
import org.jcamp.spectrum.Spectrum;
import org.jcamp.spectrum.notes.Note;
import org.jcamp.spectrum.notes.NoteDescriptor;
import org.jcamp.units.CommonUnit;
import org.jcamp.units.Unit;
/**
 * adapter between MS spectrum class and JCAMPWriter.
 * @author Thomas Weber
 */
public class MSJCAMPWriter extends CommonSpectrumJCAMPWriter implements ISpectrumJCAMPWriter {
    private final static String CRLF = "\r\n";
    /**
     * MSJCAMPAdapter constructor comment.
     */
    protected MSJCAMPWriter() {
        super();
    }
    /**
     * build a peak table.
     * 
     * @return java.lang.String
     * @param ms MassSpectrum
     */
    private String buildPeakTable(int block, MassSpectrum ms) {
	StringBuffer jcamp = new StringBuffer();
        String title = ms.getTitle();
        String origin = ms.getOrigin();
        String owner = ms.getOwner();
        jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
        jcamp.append("##JCAMP-DX=5.00").append(CRLF);
        jcamp.append("##DATATYPE=MASS SPECTRUM").append(CRLF);
        jcamp.append("##DATACLASS=PEAK TABLE").append(CRLF);
        if (block != 0) {
            jcamp.append("##BLOCKID=").append(block).append(CRLF);
        }
	jcamp.append(getJCAMPNotes(ms));
	jcamp.append(getXUnitLDR(ms));
	jcamp.append(getYUnitLDR(ms));
	if (ms.hasPeakTable()) {
            Peak1D[] peaks = ms.getPeakTable();
            int n = peaks.length;
            jcamp.append("##NPOINTS=").append(n).append(CRLF);
            jcamp.append("##PEAKTABLE=(XY..XY)").append(CRLF);
            for (int i = 0; i < n; i++) {
                double x = peaks[i].getPosition()[0];
                double y = peaks[i].getPosition()[1];
                jcamp.append(x).append(',').append(y).append(CRLF);
            }
        } else {
            if (!ms.isFullSpectrum()) {
                int n = ms.getXData().getLength();
                jcamp.append("##NPOINTS=").append(n).append(CRLF);
                jcamp.append("##PEAKTABLE=(XY..XY)").append(CRLF);
                for (int i = 0; i < n; i++) {
                    double x = ms.getXData().pointAt(i);
                    double y = ms.getYData().pointAt(i);
                    jcamp.append(x).append(',').append(y).append(CRLF);
                }
            }
        }
        jcamp.append("##END=").append(CRLF);
        return jcamp.toString();
    }
    /**
     * gets spectrum notes in JCAMP form.
     * title note is ignored, it is handled directly
     * @return java.lang.String
     */
    protected String getJCAMPNotes(Spectrum spectrum) {
	StringBuffer notesStr = new StringBuffer();
        Iterator notesIt = spectrum.getNotes().iterator();
        while (notesIt.hasNext()) {
	    Note note = (Note) notesIt.next();
            NoteDescriptor descr = note.getDescriptor();
	    if ("title".equals(descr.getKey()))
                continue;
            if (!descr.isAllowedForSpectrumID(ISpectrumIdentifier.MS))
                continue;
            Object value = note.getValue();
	    IJCAMPNoteMarshaller marshaller = NoteMarshallerFactory.getInstance().findByDescriptor(descr);
	    if (marshaller != null) {
		    notesStr.append(marshaller.toJCAMP(value));
	    }
        }
        return notesStr.toString();
    }
    /**
     * returns  standard JCAMP unit name.
     * 
     * @return java.lang.String
     * @param ms MassSpectrum
     */
    private static String getXUnitLDR(MassSpectrum ms) {
        String name;
        Unit unit = ms.getXData().getUnit();
        if (unit.equals(CommonUnit.mz))
            name = "##XUNITS=M/Z" + CRLF;
        else
            name = "##XUNITS=ARBITRARY UNITS" + CRLF;
        return name;
    }
    /**
     * return standard JCAMP unit name.
     * 
     * @return java.lang.String
     * @param ms MassSpectrum
     */
    private static String getYUnitLDR(MassSpectrum ms) {
        String name;
        Unit unit = ms.getYData().getUnit();
        if (unit.equals(CommonUnit.relativeAbundance) || unit.equals(CommonUnit.abundance))
            name = "##YUNITS=RELATIVE ABUNDANCE" + CRLF;
        else
            name = "##YUNITS=ARBITRARY UNITS" + CRLF;
        return name;
    }
    /**
     * writes spectrum as compound JCAMP.
     */
    public String toJCAMP(Spectrum spectrum) throws JCAMPException {
	if (!(spectrum instanceof MassSpectrum))
            throw new JCAMPException("JCAMP adapter missmatch");
        MassSpectrum ms = (MassSpectrum) spectrum;
        StringBuffer jcamp = new StringBuffer();
        // mass spectra are always peak spectra
        jcamp.append(buildPeakTable(0, ms));
        return jcamp.toString();
    }
    /**
     * writes spectrum as simple JCAMP.
     */
    public String toSimpleJCAMP(Spectrum spectrum) throws JCAMPException {
        // mass spectra are always simple JCAMPs
        return toJCAMP(spectrum);
    }
}