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The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.
package org.jcamp.parser;
import org.jcamp.spectrum.Multiplicity;
/**
* tokenizer (parser) that handles data in peak tables and peak assignments.
* @author Thomas Weber
*/
public class DatatableTokenizer 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 DatatableTokenizer(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 DatatableTokenizer(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 {
DataType dataType = null;
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"))
dataType = DataType.XY;
} else if (varSymbols.length == 3) {
if (varSymbols[0].equalsIgnoreCase("X")
&& varSymbols[1].equalsIgnoreCase("Y")
&& varSymbols[2].equalsIgnoreCase("W"))
dataType = DataType.XYW;
else if (
varSymbols[0].equalsIgnoreCase("X")
&& varSymbols[1].equalsIgnoreCase("Y")
&& varSymbols[2].equalsIgnoreCase("M"))
dataType = DataType.XYM;
else if (
varSymbols[0].equalsIgnoreCase("X")
&& varSymbols[1].equalsIgnoreCase("Y")
&& varSymbols[2].equalsIgnoreCase("A"))
dataType = DataType.XYA;
} else if (varSymbols.length == 4) {
if (varSymbols[0].equalsIgnoreCase("X")
&& varSymbols[1].equalsIgnoreCase("Y")
&& varSymbols[2].equalsIgnoreCase("W")
&& varSymbols[3].equalsIgnoreCase("A"))
dataType = DataType.XYWA;
else if (
varSymbols[0].equalsIgnoreCase("X")
&& varSymbols[1].equalsIgnoreCase("Y")
&& varSymbols[2].equalsIgnoreCase("M")
&& varSymbols[3].equalsIgnoreCase("A"))
dataType = DataType.XYMA;
} else if (varSymbols.length == 5) {
if (varSymbols[0].equalsIgnoreCase("X")
&& varSymbols[1].equalsIgnoreCase("Y")
&& varSymbols[2].equalsIgnoreCase("M")
&& varSymbols[3].equalsIgnoreCase("W")
&& varSymbols[4].equalsIgnoreCase("A"))
dataType = DataType.XYMWA;
}
return dataType;
}
/**
* 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)
return true;
return false;
}
/**
* parse next double
*
* @return double
*/
private Double nextDouble(char delimiter) throws JCAMPException {
Double x = null;
String s = nextString(delimiter);
try {
x = new Double(s);
} catch (NumberFormatException e) {
throw new JCAMPException("bad number format");
}
return x;
}
/**
* 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.DataGroup
*/
public DataGroup nextGroup() throws JCAMPException {
if (pos >= length)
throw new JCAMPException("parsed beyond end of data block");
if (type.equals(DataType.XY))
return nextXYGroup();
if (type.equals(DataType.XYW))
return nextXYWGroup();
if (type.equals(DataType.XYM))
return nextXYMGroup();
if (type.equals(DataType.XYA))
return nextXYAGroup();
if (type.equals(DataType.XYWA))
return nextXYWAGroup();
if (type.equals(DataType.XYMA))
return nextXYMAGroup();
if (type.equals(DataType.XYMWA))
return nextXYMWAGroup();
int n = varSymbols.length;
Object[] values = new Object[n];
for (int i = 0; i < n - 1; i++) {
try {
values[i] = nextQString(',');
} catch (JCAMPException e) {
//try numeric data
String s = nextString(',');
try {
values[i] = new Double(s);
} catch (NumberFormatException ex) {
values[i] = s;
}
}
}
try {
values[n - 1] = nextQString(';');
} catch (JCAMPException e) {
//try numeric data
String s = nextString(';');
try {
values[n - 1] = new Double(s);
} catch (NumberFormatException ex) {
values[n - 1] = s;
}
}
return new DataGroup(varSymbols, values);
}
/**
* parse next multiplet char.
*
* @return char
* @param delimiter char
*/
private char nextMulti(char delimiter) throws JCAMPException {
char m;
String s = nextString(delimiter);
if (s.length() == 1) {
m = s.charAt(0);
if (!(m == 'S' || m == 'D' || m == 'T' || m == 'Q' || m == 'M' || m == 'U'))
throw new JCAMPException("bad multiplet data: \"" + s + "\"");
} else {
throw new JCAMPException("bad multiplet data: \"" + s + "\"");
}
return m;
}
/**
* parse next quoted string.
*
* @return java.lang.String
* @param delimiter char
* @exception com.creon.chem.jcamp.JCAMPException The exception description.
*/
private String nextQString(char delimiter) throws JCAMPException {
String a;
int p;
if (data.charAt(pos) == '<') { // strings are quoted
pos++;
p = data.indexOf('>', pos);
if (p < 0)
throw new JCAMPException("missing closing '>' quote");
a = data.substring(pos, p);
pos = p + 1;
p = data.indexOf(delimiter, pos);
if (p < 0)
throw new JCAMPException("bad data");
pos = p + 1;
} else {
throw new JCAMPException("unquoted string");
}
return a;
}
/**
* parse next unquoted string.
*
* @return java.lang.String
* @param delimiter char
* @exception com.creon.chem.jcamp.JCAMPException The exception description.
*/
private String nextString(char delimiter) throws JCAMPException {
String a;
int p;
p = data.indexOf(delimiter, pos);
if (p < 0)
throw new JCAMPException("missing data");
a = data.substring(pos, p);
pos = p + 1;
return a;
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.DataGroup
*/
private DataGroup nextXYAGroup() throws JCAMPException {
Double x;
Double y;
String a;
x = nextDouble(',');
y = nextDouble(',');
a = nextQString(';');
return new DataGroup(x, y, a);
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.AFFNGroup
*/
private DataGroup nextXYGroup() throws JCAMPException {
Double x;
Double y;
x = nextDouble(',');
y = nextDouble(';');
return new DataGroup(x, y);
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.DataGroup
*/
private DataGroup nextXYMAGroup() throws JCAMPException {
Double x;
Double y;
char m;
String a;
x = nextDouble(',');
y = nextDouble(',');
m = nextMulti(',');
a = nextQString(';');
return new DataGroup(x, y, Multiplicity.multiplicityOf(m), a);
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.DataGroup
*/
private DataGroup nextXYMGroup() throws JCAMPException {
Double x;
Double y;
char m = 'U';
x = nextDouble(',');
y = nextDouble(',');
m = nextMulti(';');
return new DataGroup(x, y, Multiplicity.multiplicityOf(m));
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.DataGroup
*/
private DataGroup nextXYMWAGroup() throws JCAMPException {
Double x;
Double y;
char m;
Double w;
String a;
x = nextDouble(',');
y = nextDouble(',');
m = nextMulti(',');
w = nextDouble(',');
a = nextQString(';');
return new DataGroup(x, y, Multiplicity.multiplicityOf(m), w, a);
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.DataGroup
*/
private DataGroup nextXYWAGroup() throws JCAMPException {
Double x;
Double y;
Double w;
String a;
x = nextDouble(',');
y = nextDouble(',');
w = nextDouble(',');
a = nextQString(';');
return new DataGroup(x, y, w, a);
}
/**
* gets next data group.
*
* @return com.creon.chem.jcamp.AFFNGroup
*/
private DataGroup nextXYWGroup() throws JCAMPException {
Double x;
Double y;
Double w;
x = nextDouble(',');
y = nextDouble(',');
w = nextDouble(';');
return new DataGroup(x, y, w);
}
/**
* normalize data block in standard form:
* values are separated by ',', groups are separated by ';'
* whitespace is skipped outside quotes
* quotes are '<','>' as defined in JCAMP standard
*
* @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 inDataValue = false;
boolean inQuote = false;
int j = 0;
for (int i = 0; i < orig.length(); i++) {
char c = orig.charAt(i);
if (inQuote) {
if (c == '>') {
inQuote = false;
}
normal.append(c);
continue;
}
if (c == '<') {
inWS = false;
inDataValue = true;
inQuote = true;
normal.append(c);
continue;
}
if (c == '(' || c == ')')
continue;
if (Character.isWhitespace(c)) {
if (inDataValue) {
inDataValue = false;
j++;
if (j < groupLength)
normal.append(',');
else {
normal.append(';');
j = 0;
}
}
inWS = true;
continue;
}
if (c == ';') {
if (inDataValue) {
inDataValue = false;
j++;
if (j < groupLength)
throw new JCAMPException("missing numbers in data");
if (j > groupLength)
throw new JCAMPException("extra numbers in data");
normal.append(';');
j = 0;
}
continue;
}
if (c == ',') {
if (inDataValue) {
inDataValue = false;
j++;
if (j >= groupLength)
throw new JCAMPException("extra commas in data");
normal.append(',');
}
continue;
}
if (Character.isLetterOrDigit(c) || c == '.' || c == '+' || c == '-') {
normal.append(c);
inWS = false;
inDataValue = true;
} else {
throw new JCAMPException("unexpected character \'" + c + "\' in data");
}
}
normal.append(';');
return normal.toString();
}
}
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