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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;

/**
 * tokenizer (parser) that handles numeric data tables in AFFN format.
 * @author Thomas Weber
 */
public class AFFNTokenizer implements java.util.Enumeration {
	private final DataType type;
	private String data;
	private final String[] varSymbols;
	private int pos;
	private int length;
/**
 * AFFNTokenizer constructor comment.
 */
public AFFNTokenizer(String[] symbols, String data) throws JCAMPException {
    super();
    this.type = checkSymbols(symbols);
    if (this.type == null)
        this.varSymbols = symbols;
    else
        this.varSymbols = this.type.getSymbols();
    this.data = normalizeData(varSymbols.length, data);
    this.length = this.data.length();
}
/**
 * AFFNTokenizer constructor comment.
 */
public AFFNTokenizer(JCAMPDataRecord ldr) throws JCAMPException {
	super();
	DataVariableInfo varInfo = new DataVariableInfo(ldr);
	this.type = checkSymbols(varInfo.getSymbols());
 	if (this.type == null)
		this.varSymbols = varInfo.getSymbols();
	else
		this.varSymbols = this.type.getSymbols();
	String ldrData = ldr.getContent();
	LineTokenizer lt = new LineTokenizer(ldrData);
	lt.nextLine(); // skip variable declaration
	this.data =
		normalizeData(varSymbols.length, ldrData.substring(lt.getPosition()));
	this.length = this.data.length();
}
/**
 * check for errornous symbols or standard symbols.
 * 
 */
private static DataType checkSymbols(String[] varSymbols) throws JCAMPException {
	if (varSymbols == null || varSymbols.length == 0)
		throw new JCAMPException("bad variable declaration");
	if (varSymbols.length == 2) {
		if (varSymbols[0].equalsIgnoreCase("X") && varSymbols[1].equalsIgnoreCase("Y"))
			return DataType.XY;
	} else if (varSymbols.length == 3) {
		if (varSymbols[0].equalsIgnoreCase("X")
			&& varSymbols[1].equalsIgnoreCase("Y")
			&& varSymbols[2].equalsIgnoreCase("W"))
			return DataType.XYW;
	}
	return null;
}
/**
 * get variable symbols.
 * 
 * @return java.lang.String[]
 */
public final java.lang.String[] getSymbols() {
	return varSymbols;
}
/**
 * Insert the method's description here.
 * 
 * @return com.creon.chem.jcamp.DataType
 */
public final DataType getType() {
	return type;
}
/**
 * returns true if more data is available.
 * 
 * @return boolean
 */
public boolean hasMoreElements() {
	return hasMoreGroups();
}
/**
 * returns true if more data is available.
 * 
 * @return boolean
 */
public boolean hasMoreGroups() {
    if (pos < length-1)
        return true;
    return false;
}
/**
 * gets next data group.
 * 
 * @return Object
 */
public Object nextElement() {
	try {
		return nextGroup();
	} catch (JCAMPException e) {
		throw new java.util.NoSuchElementException(e.getMessage());
	}
}
/**
 * gets next data group.
 * 
 * @return com.creon.chem.jcamp.AFFNGroup
 */
public AFFNGroup nextGroup() throws JCAMPException {
    if (pos >= length)
        throw new JCAMPException("parsed beyond end of AFFN block");
    if (DataType.XY.equals(type))
        return nextXYGroup();
    if (DataType.XYW.equals(type))
        return nextXYWGroup();
    int n = varSymbols.length;
    double[] values = new double[n];
    for (int i = 0; i < n - 1; i++) {
        int p = data.indexOf(",", pos);
        if (p < 0)
            throw new JCAMPException("missing data in AFFN block");
        values[i] = Double.parseDouble(data.substring(pos, p));
        pos = p + 1;
    }

    int p = data.indexOf(";", pos);
    if (p < 0)
        throw new JCAMPException("extra data in AFFN block");
    values[n - 1] = Double.parseDouble(data.substring(pos, p));
    pos = p + 1;
    return new AFFNGroup(varSymbols, values);

}
/**
 * gets next data group.
 * 
 * @return com.creon.chem.jcamp.AFFNGroup
 */
private AFFNGroup nextXYGroup() throws JCAMPException {
	double x;
	double y;
	int p = data.indexOf(',', pos);
	if (p < 0) {
		throw new JCAMPException("missing x data");
	}
	x = Double.parseDouble(data.substring(pos, p));
	pos = p + 1;
	p = data.indexOf(';', pos);
	if (p < 0)
		throw new JCAMPException("missing y data");
	y = Double.parseDouble(data.substring(pos, p));
	pos = p + 1;
	return new AFFNGroup(x, y);
}
/**
 * gets next data group.
 * 
 * @return com.creon.chem.jcamp.AFFNGroup
 */
private AFFNGroup nextXYWGroup() throws JCAMPException {
	double x;
	double y;
	double w;
	int p = data.indexOf(',', pos);
	if (p < 0)
		throw new JCAMPException("missing x data");
	x = Double.parseDouble(data.substring(pos, p));
	pos = p + 1;
	p = data.indexOf(',', pos);
	if (p < 0)
		throw new JCAMPException("missing y data");
	y = Double.parseDouble(data.substring(pos, p));
	pos = p + 1;
	p = data.indexOf(';', pos);
	if (p < 0)
		throw new JCAMPException("missing w data");
	w = Double.parseDouble(data.substring(pos, p));
	pos = p + 1;
	return new AFFNGroup(x, y, w);
}
/**
 * normalize data block in standard form:
 * values are separated by ',', groups are separated by ';'
 * whitespace is skipped
 * 
 * @return java.lang.String
 * @param orig java.lang.String
 */
private static String normalizeData(int groupLength, String orig)
	throws JCAMPException {
	StringBuffer normal = new StringBuffer();
	boolean inWS = false;
	boolean inNumber = false;
	int j = 0;
	for (int i = 0; i < orig.length(); i++) {
		char c = orig.charAt(i);
		if (Character.isWhitespace(c)) {
			if (inNumber) {
				inNumber = false;
				j++;
				if (jgroupLength)
					throw new JCAMPException("extra numbers in AFFN data");
				normal.append(';');
				j=0;
			}
			continue;
		}
		if (c == ',') {
			if (inNumber) {
				inNumber = false;
				j++;
				if (j>=groupLength)
					throw new  JCAMPException("extra commas in AFFN data");
				normal.append(',');
			}
			continue;
		}
		if (Character.isDigit(c)
			|| c == '.'
			|| c == '+'
			|| c == '-'
			|| c == 'e'
			|| c == 'E') {
			normal.append(c);
			inWS = false;
			inNumber = true;
		} else {
			throw new JCAMPException("unexpected character \'" + c + "\' in AFFN data");
		}
	}
	normal.append(';');
	return normal.toString();
}
}