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The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.
package org.jcamp.spectrum;
import java.util.Enumeration;
import java.util.Vector;
/**
* peak pattern.
* @author Thomas Weber
*/
public class Pattern implements ISpectrumLabel, Cloneable {
private Multiplicity multiplicity = Multiplicity.UNKNOWN;
private double[] position = new double[2];
{
this.position[0] = 0.0;
this.position[1] = 1.0;
}
private Spectrum1D spectrum = null;
private Peak1D[] peaks = null;
/**
* PeakPattern constructor comment.
*/
public Pattern(double position, Multiplicity multi) {
super();
this.position[0] = position;
this.spectrum = null;
this.multiplicity = multi;
}
/**
* PeakPattern constructor comment.
*/
public Pattern(double position, Multiplicity multi, Peak1D[] peaks) {
this(null, position, multi, peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(double position, String multi) {
this(position, Multiplicity.multiplicityOf(multi));
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Multiplicity multi, Peak1D[] peaks) {
super();
double position = 0.0;
this.spectrum = null;
this.multiplicity = multi;
if (peaks == null || peaks.length == 0)
throw new IllegalArgumentException("pattern without position or peaks");
setPeaks(peaks);
for (int i = 0; i < peaks.length; i++) {
position += this.peaks[i].getPosition()[0];
}
this.position[0] = position / this.peaks.length;
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, Peak1D[] peaks) {
this(spectrum, Multiplicity.multiplicityOf(peaks.length), peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, double position, Multiplicity multi) {
super();
this.position[0] = position;
this.spectrum = spectrum;
this.multiplicity = multi;
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, double position, Multiplicity multi, Peak1D[] peaks) {
super();
this.position[0] = position;
this.spectrum = spectrum;
this.multiplicity = multi;
setPeaks(peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, double position, Multiplicity multi, Vector peaks) {
super();
this.position[0] = position;
this.spectrum = spectrum;
this.multiplicity = multi;
setPeaks(peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, double position, String multi) {
this(spectrum, position, Multiplicity.multiplicityOf(multi));
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, double position, String multi, Peak1D[] peaks) {
this(spectrum, position, Multiplicity.multiplicityOf(multi), peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, double position, String multi, Vector peaks) {
this(spectrum, position, Multiplicity.multiplicityOf(multi), peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, Multiplicity multi, Peak1D[] peaks) {
super();
double position = 0.0;
this.spectrum = spectrum;
this.multiplicity = multi;
if (peaks == null || peaks.length == 0)
throw new IllegalArgumentException("pattern without position or peaks");
setPeaks(peaks);
for (int i = 0; i < peaks.length; i++) {
position += this.peaks[i].getPosition()[0];
}
this.position[0] = position / this.peaks.length;
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, Multiplicity multi, Vector peaks) {
super();
double position = 0.0;
this.spectrum = spectrum;
this.multiplicity = multi;
if (peaks == null || peaks.size() == 0)
throw new IllegalArgumentException("pattern without position or peaks");
this.peaks = new Peak1D[peaks.size()];
for (int i = 0; i < peaks.size(); i++) {
this.peaks[i] = (Peak1D) ((Peak1D) peaks.elementAt(i)).clone();
position += this.peaks[i].getPosition()[0];
}
this.position[0] = position / this.peaks.length;
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, String multi, Peak1D[] peaks) {
this(spectrum, Multiplicity.multiplicityOf(multi), peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, String multi, Vector peaks) {
this(spectrum, Multiplicity.multiplicityOf(multi), peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(Spectrum1D spectrum, Vector peaks) {
this(spectrum, Multiplicity.multiplicityOf(peaks.size()), peaks);
}
/**
* PeakPattern constructor comment.
*/
public Pattern(String multi, Peak1D[] peaks) {
this(Multiplicity.multiplicityOf(multi), peaks);
}
/**
* cloning.
* @return java.lang.Object
*/
public Object clone() {
Pattern pattern = new Pattern(spectrum, position[0], multiplicity, peaks);
return pattern;
}
/**
* compareTo method comment.
*/
public int compareTo(java.lang.Object obj) {
double p0 = getPosition()[0];
double p1 = ((ISpectrumLabel) obj).getPosition()[0];
if (p0 < p1)
return -1;
if (p0 > p1)
return 1;
return 0;
}
/**
* gets the label (multiplicity).
*/
public java.lang.String getLabel() {
return multiplicity.getSymbol();
}
/**
* gets multiplicity.
* @return int
*/
public Multiplicity getMultiplicity() {
return multiplicity;
}
/**
* returns array of peaks.
* @return Peak1D[]
*/
public Peak1D[] getPeaks() {
return peaks;
}
/**
* gets position of pattern (center of pattern).
* @return double[]
*/
public double[] getPosition() {
return position;
}
/**
* gets the spectrum the pattern belongs to.
* @return Spectrum1D
*/
public Spectrum1D getSpectrum() {
return spectrum;
}
/**
* gets peaks of the pattern as an enumeration
* @return Vector
*/
public Enumeration peaks() {
return new Enumeration() {
int i = 0;
public Object nextElement() {
if (peaks != null && i < peaks.length) {
Peak1D peak = peaks[i];
i++;
return peak;
}
return null;
}
public boolean hasMoreElements() {
if (peaks != null && i < peaks.length - 1)
return true;
return false;
}
};
}
/**
* sets the multiplicity.
* @param newMultiplicity int
*/
public void setMultiplicity(Multiplicity newMultiplicity) {
multiplicity = newMultiplicity;
}
/**
* sets peaks by copying a peak array.
*/
public void setPeaks(Peak1D[] peaks) {
this.peaks = null;
if (peaks != null) {
this.peaks = new Peak1D[peaks.length];
for (int i = 0; i < peaks.length; i++)
this.peaks[i] = (Peak1D) peaks[i].clone();
}
}
/**
* sets peaks by copying from a vector of peaks.
*/
public void setPeaks(Vector peaks) {
this.peaks = null;
if (peaks != null) {
this.peaks = new Peak1D[peaks.size()];
for (int i = 0; i < peaks.size(); i++) {
this.peaks[i] = (Peak1D) ((Peak1D) peaks.elementAt(i)).clone();
}
}
}
/**
* sets pattern to new position.
* @param newPosition double[]
*/
public void setPosition(double[] newPosition) {
position[0] = newPosition[0];
position[1] = newPosition[1];
}
/**
* assign spectrum to pattern.
* @param newSpectrum Spectrum1D
*/
public void setSpectrum(Spectrum1D newSpectrum) {
if (this.spectrum != newSpectrum) {
this.spectrum = newSpectrum;
if (peaks != null) {
for (int i = 0; i < this.peaks.length; i++) {
peaks[i].setSpectrum(this.spectrum);
}
}
}
}
/**
* write debug info for label.
* @return java.lang.String
*/
public String toString() {
StringBuffer label = new StringBuffer("Pattern[");
for (int i = 0; i < position.length; i++) {
label.append(position[i]);
if (i < position.length - 1)
label.append(",");
}
label.append("]: ").append(getLabel());
return label.toString();
}
/**
* translate the pattern with all its peaks by amount.
*/
public void translate(double[] amount) {
position[0] += amount[0];
position[1] += amount[1];
for (int i = 0; i < this.peaks.length; i++)
this.peaks[i].translate(amount);
}
}
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