public IsotopicDistribution clone() {
IsotopicDistribution distribution = null;
try {
distribution = (IsotopicDistribution) super.clone();
} catch (CloneNotSupportedException e) {
throw new MprcException("Cannot clone " + IsotopicDistribution.class.getSimpleName(), e);
}
distribution.set(this);
return distribution;
}
/**
* Returns a new copy of this IsotopicDistribution, with monoisotopic m/z set to <code>therMonoMZ
* </code>, with <code>mzShift</code> added to all mzs, and all intensities scaled by <code>
* intenScale</code>.
*/
public IsotopicDistribution copy(
final double therMonoMZ, final double mzShift, final double intenScale) {
final IsotopicDistribution ret = new IsotopicDistribution(this, false);
ret.therMonoMZ = therMonoMZ;
for (int i = 0; i < ret.dist.size(); ++i) {
ret.dist.setMass(i, ret.dist.getMass(i) + mzShift);
ret.dist.setIntensity(i, ret.dist.getIntensity(i) * intenScale);
}
ret.doInit();
return ret;
}
/**
* Combines isotopic distributions. Adds the given isotopic distribution, scaled by fracOther, to
* this IsotopicDistribution, scaled by 1 - fracOther. Matches peaks to within the given error
* tolerance (peaks which don't match are simply scaled and passed through).
*
* @return New isotopic distribution representing <code>(1-fracOther)*this + fracOther*other
* </code>
*/
public IsotopicDistribution add(
final IsotopicDistribution other, final double fracOther, double errorTolPPM) {
// TODO: which Chemical?
errorTolPPM /= 1000000.;
double maxinten = 0.;
int thisi = 0;
int otheri = 0;
final MassIntensityArray dist = new MassIntensityArray();
while (otheri < other.getNumIsotopes() && thisi < getNumIsotopes()) {
final double othermass = other.getMassOfIsotope(otheri);
final double thismass = getMassOfIsotope(thisi);
final double inten;
if (Math.abs(thismass - othermass) <= thismass * errorTolPPM) {
inten =
fracOther * other.getIntensityOfIsotope(otheri)
+ (1. - fracOther) * getIntensityOfIsotope(thisi);
final double mass = (thismass + othermass) / 2.;
dist.add(mass, inten);
++thisi;
++otheri;
} else if (thismass < othermass) {
dist.add(thismass, inten = (1. - fracOther) * getIntensityOfIsotope(thisi));
++thisi;
} else {
dist.add(othermass, inten = fracOther * other.getIntensityOfIsotope(otheri));
++otheri;
}
if (inten > maxinten) {
maxinten = inten;
}
}
// only one of the two loops below will run
while (otheri < other.getNumIsotopes()) {
final double inten = fracOther * other.getIntensityOfIsotope(otheri);
dist.add(other.getMassOfIsotope(otheri), inten);
++otheri;
if (inten > maxinten) {
maxinten = inten;
}
}
while (thisi < getNumIsotopes()) {
final double inten = (1. - fracOther) * getIntensityOfIsotope(thisi);
dist.add(getMassOfIsotope(thisi), inten);
++thisi;
if (inten > maxinten) {
maxinten = inten;
}
}
return new IsotopicDistribution(
(therMonoMZ + other.therMonoMZ) / 2., chem, name, thresh, extra, dist, true);
}