/**
* Initialises the list of Spectra with the next Set of Spectra
*
* @throws JSpecViewException
*/
public void initNextSetOfSpectra() throws JSpecViewException {
Vector<JDXSpectrum> jdxSpectra = this.getSpectra();
jdxSpectra.clear();
jdxSpectra.ensureCapacity(MAX_NUMBER_SPECTRA);
String tabularSpecData = null;
JDXSpectrum spectrum;
HashMap<String, String> LDRTable;
double offset = Graph.ERROR;
double obFreq = Graph.ERROR;
double firstX, lastX, xFactor = 1;
double deltaX = 0, yFactor = 1;
boolean continuous = true;
int nPoints;
String xUnits = "", title = "", yUnits = "";
String page = "";
int dataPointNum = -1;
int shiftRefType = -1;
String[] plotSymbols = new String[2];
Coordinate[] xyCoords;
JDXSourceStringTokenizer t = new JDXSourceStringTokenizer(sourceContents);
String label = "";
if (!hasMoreSpectra()) return;
int setIndex = currentSpectraSetIndex;
int spectrumIndex = 0;
boolean found = false;
while (t.hasMoreTokens()) {
if (found) break;
if (label.equals("##PAGE")) {
if ((spectrumIndex % numberOfSets) != setIndex) {
spectrumIndex++;
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
continue;
}
} else {
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
}
}
spectrum = new JDXSpectrum();
while (t.hasMoreTokens()) {
if (label.equals("##ENDNTUPLES")) {
break;
}
if (label.equals("##PAGE")) {
page = t.value;
t.nextToken(); // ignore ##PAGE
label = JSpecViewUtils.cleanLabel(t.label);
continue;
}
LDRTable = new HashMap<String, String>();
while (!label.equals("##DATATABLE")) {
LDRTable.put(t.label, t.value);
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
}
if (label.equals("##DATATABLE")) {
// determine if continuous
String dtblStr = t.value;
try {
BufferedReader reader = new BufferedReader(new StringReader(dtblStr));
String line = reader.readLine();
if (line.trim().indexOf("PEAKS") > 0) {
continuous = false;
}
// parse variable list
int index1 = line.indexOf('(');
int index2 = line.lastIndexOf(')');
if (index1 == -1 || index2 == -1) throw new JDXSourceException("Variable List not Found");
String varList = line.substring(index1, index2 + 1);
ArrayList<String> symbols = (ArrayList<String>) nTupleTable.get("##SYMBOL");
int countSyms = 0;
for (int i = 0; i < symbols.size(); i++) {
String sym = ((String) symbols.get(i)).trim();
if (varList.indexOf(sym) != -1) {
plotSymbols[countSyms++] = sym;
}
if (countSyms == 2) break;
}
} catch (IOException ioe) {
}
if (continuous) {
spectrum.setContinuous(true);
spectrum.setDataClass("XYDATA");
} else {
spectrum.setContinuous(false);
spectrum.setDataClass("PEAKTABLE");
}
}
// Get Tabular Spectral Data
tabularSpecData = t.value;
if (tabularSpecData == null) throw new JSpecViewException("Error Reading Data Set");
String tmp = tabularSpecData;
try {
char chr;
do {
tmp = tmp.substring(tmp.indexOf("\n") + 1);
chr = tmp.trim().charAt(0);
} while (!Character.isDigit(chr) && chr != '+' && chr != '-' && chr != '.');
} catch (IndexOutOfBoundsException iobe) {
throw new JSpecViewException("Error Reading Data Set");
}
tabularSpecData = tmp;
ArrayList<String> list;
if (spectrum.getDataClass().equals("XYDATA")) {
// Get Label Values
list = (ArrayList<String>) nTupleTable.get("##SYMBOL");
int index1 = list.indexOf(plotSymbols[0]);
int index2 = list.indexOf(plotSymbols[1]);
list = (ArrayList<String>) nTupleTable.get("##FACTOR");
xFactor = Double.parseDouble((String) list.get(index1));
yFactor = Double.parseDouble((String) list.get(index2));
list = (ArrayList<String>) nTupleTable.get("##LAST");
lastX = Double.parseDouble((String) list.get(index1));
// lastY = Double.parseDouble((String)list.get(index1));
list = (ArrayList<String>) nTupleTable.get("##FIRST");
firstX = Double.parseDouble((String) list.get(index1));
// firstY = Double.parseDouble((String)list.get(index2));
list = (ArrayList<String>) nTupleTable.get("##VARDIM");
nPoints = Integer.parseInt((String) list.get(index1));
list = (ArrayList<String>) nTupleTable.get("##UNITS");
xUnits = (String) list.get(index1);
yUnits = (String) list.get(index2);
deltaX = (lastX - firstX) / (nPoints - 1);
JDXDecompressor decompressor =
new JDXDecompressor(tabularSpecData, xFactor, yFactor, deltaX);
xyCoords = decompressor.decompressData();
if (xyCoords == null) xyCoords = JSpecViewUtils.parseDSV(tabularSpecData, xFactor, yFactor);
// apply offset
if (offset != Graph.ERROR && obFreq != Graph.ERROR) {
JSpecViewUtils.applyShiftReference(
xyCoords, dataPointNum, firstX, lastX, offset, obFreq, shiftRefType);
}
if (obFreq != Graph.ERROR && xUnits.toUpperCase().equals("HZ")) {
double xScale = obFreq;
JSpecViewUtils.applyScale(xyCoords, (1 / xScale), 1);
xUnits = "PPM";
spectrum.setHZtoPPM(true);
spectrum.setObservedFreq(obFreq);
}
} else if (spectrum.getDataClass().equals("PEAKTABLE")
|| spectrum.getDataClass().equals("XYPOINTS")) {
list = (ArrayList<String>) nTupleTable.get("##SYMBOL");
int index1 = list.indexOf(plotSymbols[0]);
int index2 = list.indexOf(plotSymbols[1]);
list = (ArrayList<String>) nTupleTable.get("##UNITS");
xUnits = (String) list.get(index1);
yUnits = (String) list.get(index2);
xyCoords = JSpecViewUtils.parseDSV(tabularSpecData, xFactor, yFactor);
} else throw new JDXSourceException("Unable to read Ntuple Source");
spectrum.setXUnits(xUnits);
spectrum.setYUnits(yUnits);
spectrum.setTitle(
title.substring(0, (title.length() >= 20 ? 21 : title.length())) + "..." + " : " + page);
for (Iterator<String> iter = sourceLDRTable.keySet().iterator(); iter.hasNext(); ) {
String key = (String) iter.next();
if (!JSpecViewUtils.cleanLabel(key).equals("##TITLE")
&& !JSpecViewUtils.cleanLabel(key).equals("##DATACLASS")
&& !JSpecViewUtils.cleanLabel(key).equals("##NTUPLES"))
LDRTable.put(key, sourceLDRTable.get(key));
}
spectrum.setHeaderTable(LDRTable);
spectrum.setXYCoords(xyCoords);
addJDXSpectrum(spectrum);
found = false;
while (t.hasMoreTokens()) {
if (found) break;
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
if (label.equals("##PAGE")) {
spectrumIndex++;
if ((spectrumIndex % numberOfSets) != setIndex) continue;
}
}
spectrum = new JDXSpectrum();
}
currentSpectraSetIndex++;
}
/**
* Returns an instance of an RestrictedNTupleSource with the first MAX_NUMBER_SPECTRUMS
* instanciated
*
* @param sourceContents the contents of the source
* @param numberOfSpectra the number of spectra
* @return Returns an instance of an RestrictedNTupleSource
* @throws JSpecViewException
*/
public static RestrictedNTupleSource getInstance(String sourceContents, int numberOfSpectra)
throws JSpecViewException {
RestrictedNTupleSource ns = new RestrictedNTupleSource(sourceContents);
ns.numberOfSets = (int) Math.ceil(numberOfSpectra / MAX_NUMBER_SPECTRA);
String tabularSpecData = null;
JDXSpectrum spectrum;
HashMap<String, String> LDRTable;
ns.sourceLDRTable = new HashMap<String, String>();
ns.nTupleTable = new HashMap<String, ArrayList<String>>();
double offset = Graph.ERROR;
double obFreq = Graph.ERROR;
double firstX, lastX, xFactor = 1;
double deltaX = 0, yFactor = 1;
boolean continuous = true;
int nPoints;
String xUnits = "", title = "", yUnits = "";
String page = "";
int dataPointNum = -1;
int shiftRefType = -1;
// True if we have a long date
String[] plotSymbols = new String[2];
Coordinate[] xyCoords;
JDXSourceStringTokenizer t = new JDXSourceStringTokenizer(sourceContents);
// Read Source Specific Header
String label = "";
while (t.hasMoreTokens() && !label.equals("##NTUPLES")) {
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
if (label.equals("##TITLE")) {
title = t.value;
ns.setTitle(title);
continue;
}
if (label.equals("##JCAMPDX")) {
ns.setJcampdx(t.value);
continue;
}
if (label.equals("##ORIGIN")) {
ns.setOrigin(t.value);
continue;
}
if (label.equals("##OWNER")) {
ns.setOwner(t.value);
continue;
}
if (label.equals("##LONGDATE")) {
ns.setLongDate(t.value);
continue;
}
if (label.equals("##DATE")) {
// notesLDRTable.put(label, t.value);
ns.setDate(t.value);
continue;
}
if (label.equals("##TIME")) {
// notesLDRTable.put(label, t.value);
ns.setTime(t.value);
continue;
}
if (label.equals("##PATHLENGTH")) {
ns.setPathlength(t.value);
continue;
}
if (label.equals("##DATATYPE")) {
ns.setDataType(t.value);
continue;
}
if ((label.equals("##$OFFSET")) && (shiftRefType != 0)) {
offset = Double.parseDouble(t.value);
// bruker doesn't need dataPointNum
dataPointNum = 1;
// bruker type
shiftRefType = 1;
continue;
}
if ((label.equals("##$REFERENCEPOINT")) && (shiftRefType != 0)) {
offset = Double.parseDouble(t.value);
// varian doesn't need dataPointNum
dataPointNum = 1;
// varian type
shiftRefType = 2;
continue;
}
if (label.equals("##.SHIFTREFERENCE")) {
StringTokenizer srt = new StringTokenizer(t.value, ",");
if (srt.countTokens() != 4) continue;
try {
srt.nextToken();
srt.nextToken();
dataPointNum = Integer.parseInt(srt.nextToken().trim());
offset = Double.parseDouble(srt.nextToken().trim());
} catch (NumberFormatException nfe) {
continue;
} catch (NoSuchElementException nsee) {
continue;
}
if (dataPointNum <= 0) dataPointNum = 1;
shiftRefType = 0;
continue;
}
if (label.equals("##.OBSERVEFREQUENCY")) {
obFreq = Double.parseDouble(t.value);
continue;
}
ns.sourceLDRTable.put(label, t.value);
} // Finished Pulling out the LDR Table Data
ns.setHeaderTable(ns.sourceLDRTable);
/*--------------------------------------------*/
/*------------- Fetch Page Data --------------*/
if (!label.equals("##NTUPLES")) throw new JSpecViewException("Invalid NTuple Source");
// Read NTuple Table
StringTokenizer st;
while (t.hasMoreTokens()) {
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
if (label.equals("##PAGE")) {
break;
}
st = new StringTokenizer(t.value, ",");
ns.attrList = new ArrayList<String>();
while (st.hasMoreTokens()) {
ns.attrList.add(st.nextToken().trim());
}
ns.nTupleTable.put(label, ns.attrList);
} // Finised With Page Data
/*--------------------------------------------*/
if (!label.equals("##PAGE")) throw new JSpecViewException("Error Reading NTuple Source");
/*--------------------------------------------*/
/*-------- Gather Spectra Data From File -----*/
// Create and add Spectra
spectrum = new JDXSpectrum();
int setIndex = 0;
int spectrumIndex = 0;
while (t.hasMoreTokens()) {
if (label.equals("##ENDNTUPLES")) {
break;
}
if (label.equals("##PAGE")) {
page = t.value;
t.nextToken(); // ignore ##PAGE
label = JSpecViewUtils.cleanLabel(t.label);
continue;
}
LDRTable = new HashMap<String, String>();
while (!label.equals("##DATATABLE")) {
LDRTable.put(t.label, t.value);
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
}
if (label.equals("##DATATABLE")) {
// determine if continuous
String dtblStr = t.value;
try {
BufferedReader reader = new BufferedReader(new StringReader(dtblStr));
String line = reader.readLine();
if (line.trim().indexOf("PEAKS") > 0) {
continuous = false;
}
// parse variable list
int index1 = line.indexOf('(');
int index2 = line.lastIndexOf(')');
if (index1 == -1 || index2 == -1) throw new JDXSourceException("Variable List not Found");
String varList = line.substring(index1, index2 + 1);
ArrayList<String> symbols = (ArrayList<String>) ns.nTupleTable.get("##SYMBOL");
int countSyms = 0;
for (int i = 0; i < symbols.size(); i++) {
String sym = ((String) symbols.get(i)).trim();
if (varList.indexOf(sym) != -1) {
plotSymbols[countSyms++] = sym;
}
if (countSyms == 2) break;
}
} catch (IOException ioe) {
}
if (continuous) {
spectrum.setContinuous(true);
spectrum.setDataClass("XYDATA");
} else {
spectrum.setContinuous(false);
spectrum.setDataClass("PEAKTABLE");
}
}
// Get Tabular Spectral Data
tabularSpecData = t.value;
if (tabularSpecData == null) throw new JSpecViewException("Error Reading Data Set");
String tmp = tabularSpecData;
try {
char chr;
do {
tmp = tmp.substring(tmp.indexOf("\n") + 1);
chr = tmp.trim().charAt(0);
} while (!Character.isDigit(chr) && chr != '+' && chr != '-' && chr != '.');
} catch (IndexOutOfBoundsException iobe) {
throw new JSpecViewException("Error Reading Data Set");
}
tabularSpecData = tmp;
ArrayList<String> list;
if (spectrum.getDataClass().equals("XYDATA")) {
// Get Label Values
list = (ArrayList<String>) ns.nTupleTable.get("##SYMBOL");
int index1 = list.indexOf(plotSymbols[0]);
int index2 = list.indexOf(plotSymbols[1]);
list = (ArrayList<String>) ns.nTupleTable.get("##FACTOR");
xFactor = Double.parseDouble((String) list.get(index1));
yFactor = Double.parseDouble((String) list.get(index2));
list = (ArrayList<String>) ns.nTupleTable.get("##LAST");
lastX = Double.parseDouble((String) list.get(index1));
// lastY = Double.parseDouble((String)list.get(index1));
list = (ArrayList<String>) ns.nTupleTable.get("##FIRST");
firstX = Double.parseDouble((String) list.get(index1));
// firstY = Double.parseDouble((String)list.get(index2));
list = (ArrayList<String>) ns.nTupleTable.get("##VARDIM");
nPoints = Integer.parseInt((String) list.get(index1));
list = (ArrayList<String>) ns.nTupleTable.get("##UNITS");
xUnits = (String) list.get(index1);
yUnits = (String) list.get(index2);
deltaX = (lastX - firstX) / (nPoints - 1);
JDXDecompressor decompressor =
new JDXDecompressor(tabularSpecData, xFactor, yFactor, deltaX);
xyCoords = decompressor.decompressData();
if (xyCoords == null) xyCoords = JSpecViewUtils.parseDSV(tabularSpecData, xFactor, yFactor);
// apply offset
if (offset != Graph.ERROR
&& obFreq != Graph.ERROR
&& ns.getDataType().toUpperCase().contains("SPECTRUM")) {
JSpecViewUtils.applyShiftReference(
xyCoords, dataPointNum, firstX, lastX, offset, obFreq, shiftRefType);
}
if (obFreq != Graph.ERROR && xUnits.toUpperCase().equals("HZ")) {
double xScale = obFreq;
JSpecViewUtils.applyScale(xyCoords, (1 / xScale), 1);
xUnits = "PPM";
spectrum.setHZtoPPM(true);
spectrum.setObservedFreq(obFreq);
}
} else if (spectrum.getDataClass().equals("PEAKTABLE")
|| spectrum.getDataClass().equals("XYPOINTS")) {
list = (ArrayList<String>) ns.nTupleTable.get("##SYMBOL");
int index1 = list.indexOf(plotSymbols[0]);
int index2 = list.indexOf(plotSymbols[1]);
list = (ArrayList<String>) ns.nTupleTable.get("##UNITS");
xUnits = (String) list.get(index1);
yUnits = (String) list.get(index2);
xyCoords = JSpecViewUtils.parseDSV(tabularSpecData, xFactor, yFactor);
} else throw new JDXSourceException("Unable to read Ntuple Source");
spectrum.setXUnits(xUnits);
spectrum.setYUnits(yUnits);
spectrum.setTitle(
title.substring(0, (title.length() >= 20 ? 21 : title.length())) + "..." + " : " + page);
for (Iterator<String> iter = ns.sourceLDRTable.keySet().iterator(); iter.hasNext(); ) {
String key = (String) iter.next();
if (!JSpecViewUtils.cleanLabel(key).equals("##TITLE")
&& !JSpecViewUtils.cleanLabel(key).equals("##DATACLASS")
&& !JSpecViewUtils.cleanLabel(key).equals("##NTUPLES"))
LDRTable.put(key, ns.sourceLDRTable.get(key));
}
spectrum.setHeaderTable(LDRTable);
spectrum.setXYCoords(xyCoords);
ns.addJDXSpectrum(spectrum);
boolean found = false;
while (t.hasMoreTokens()) {
if (found) break;
t.nextToken();
label = JSpecViewUtils.cleanLabel(t.label);
if (label.equals("##PAGE")) {
spectrumIndex++;
if ((spectrumIndex % ns.numberOfSets) != setIndex) continue;
}
}
spectrum = new JDXSpectrum();
}
ns.currentSpectraSetIndex++;
return ns;
}