org.jcamp.parser.ChromatogramJCAMPReader Maven / Gradle / Ivy
package org.jcamp.parser;
import org.jcamp.spectrum.ArrayData;
import org.jcamp.spectrum.Assignment;
import org.jcamp.spectrum.Chromatogram;
import org.jcamp.spectrum.EquidistantData;
import org.jcamp.spectrum.IDataArray1D;
import org.jcamp.spectrum.IOrderedDataArray1D;
import org.jcamp.spectrum.ISpectrumIdentifier;
import org.jcamp.spectrum.OrderedArrayData;
import org.jcamp.spectrum.Pattern;
import org.jcamp.spectrum.Peak1D;
import org.jcamp.spectrum.Spectrum;
import org.jcamp.units.CommonUnit;
import org.jcamp.units.Unit;
/**
* adapter between chromatography class and JCAMPReader.
*
* @author Thomas Weber
*/
public class ChromatogramJCAMPReader
extends CommonSpectrumJCAMPReader
implements ISpectrumJCAMPReader {
protected ChromatogramJCAMPReader() {
super();
}
/**
* read chromatogram full spectrum.
*
* @return Chromatogram
* @param block JCAMPBlock
*/
private Chromatogram createFS(JCAMPBlock block) throws JCAMPException {
Chromatogram spectrum;
Unit xUnit = getXUnits(block);
if (xUnit == null)
xUnit = CommonUnit.second;
Unit yUnit = getYUnits(block);
if (yUnit == null)
yUnit = CommonUnit.intensity;
double xFactor = getXFactor(block);
double yFactor = getYFactor(block);
double firstX = getFirstX(block);
double lastX = getLastX(block);
int nPoints = getNPoints(block);
double[] intensities = getXYData(block, firstX, lastX, nPoints, xFactor, yFactor);
if (intensities.length != nPoints) {
block.getErrorHandler().error(
"incorrect ##NPOINTS=: expected "
+ Integer.toString(nPoints)
+ " but got "
+ Integer.toString(intensities.length));
nPoints = intensities.length;
}
IOrderedDataArray1D x = new EquidistantData(firstX, lastX, nPoints, xUnit);
IDataArray1D y = new ArrayData(intensities, yUnit);
spectrum = new Chromatogram(x, y, true);
return spectrum;
}
/**
* create chromatogram peak table (peak spectrum) from JCAMPBlock.
*
* @return chromatogram
* @param block JCAMPBlock
* @exception JCAMPException exception thrown if parsing fails.
*/
private Chromatogram createPeakTable(JCAMPBlock block) throws JCAMPException {
Chromatogram spectrum = null;
Unit xUnit = getXUnits(block);
if (xUnit == null)
xUnit = CommonUnit.second;
Unit yUnit = getYUnits(block);
if (yUnit == null)
yUnit = CommonUnit.intensity;
double xFactor = getXFactor(block);
double yFactor = getYFactor(block);
int nPoints = getNPoints(block);
Object[] tables = getPeaktable(block, nPoints, xFactor, yFactor);
Peak1D[] peaks = (Peak1D[]) tables[0];
if (peaks.length != nPoints) {
block.getErrorHandler().error(
"incorrect ##NPOINTS=: expected "
+ Integer.toString(nPoints)
+ " but got "
+ Integer.toString(peaks.length));
nPoints = peaks.length;
}
double[][] xy = peakTableToPeakSpectrum(peaks);
IOrderedDataArray1D x = new OrderedArrayData(xy[0], xUnit);
IDataArray1D y = new ArrayData(xy[1], yUnit);
spectrum = new Chromatogram(x, y, false);
spectrum.setPeakTable(peaks);
if (tables.length > 1) {
spectrum.setPatternTable((Pattern[]) tables[1]);
if (tables.length > 2)
spectrum.setAssignments((Assignment[]) tables[2]);
}
return spectrum;
}
/**
* createSpectrum method comment.
*/
@Override
public Spectrum createSpectrum(JCAMPBlock block) throws JCAMPException {
if (block.getSpectrumID() != ISpectrumIdentifier.CHROMATOGRAM)
block.getErrorHandler().fatal("JCAMP reader adapter missmatch");
Chromatogram spectrum = null;
JCAMPBlock.Type type = block.getType();
if (type.equals(JCAMPBlock.Type.FULLSPECTRUM))
spectrum = createFS(block);
else if (type.equals(JCAMPBlock.Type.PEAKTABLE))
spectrum = createPeakTable(block);
else if (type.equals(JCAMPBlock.Type.ASSIGNMENT))
spectrum = createPeakTable(block);
else // never reached
block.getErrorHandler().fatal("illegal block type");
setNotes(block, spectrum);
return spectrum;
}
}