/**
* make a form suitable to 1) reconstruct the original given access to starting conditions
*
* @param adder !null where to put the data
*/
@Override
public void serializeAsString(IXMLAppender adder) {
String tag = TAG;
adder.openTag(tag);
adder.appendAttribute(
"precursorIntensity", XTandemUtilities.formatDouble(getPrecursorIntensity(), 1));
adder.appendAttribute("precursorCharge", Integer.toString(getPrecursorCharge()));
FragmentationMethod method = getMethod();
if (method == null) method = FragmentationMethod.CID;
adder.appendAttribute("activationMethod", method);
adder.endTag();
adder.appendText(XTandemUtilities.formatDouble(getMassChargeRatio(), 3));
adder.closeTag(tag);
}
@Override
public double getPrecursorMass(int charge) {
double chargeRatio = getMassChargeRatio();
double protonMass = XTandemUtilities.getProtonMass();
final double ret = ((chargeRatio - protonMass) * charge) + protonMass;
return ret;
// return getMassChargeRatio() * getPrecursorCharge();
}
/**
* return true if a mass such as that of a throretical peak is within the range to scpre
*
* @param mass positive testMass
* @return as above
*/
@Override
public boolean isMassWithinRange(double mass, int charge, IScoringAlgorithm alg) {
if (m_PrecursorCharge == 0) {
// try charge 2
double test1 =
(getMassChargeRatio() - XTandemUtilities.getProtonMass()) * 2
+ XTandemUtilities.getProtonMass();
if (alg.isWithinLimits(test1, mass, 0)) return true;
// try charge 3
double test2 =
(getMassChargeRatio() - XTandemUtilities.getProtonMass()) * 3
+ XTandemUtilities.getProtonMass();
if (alg.isWithinLimits(test2, mass, 0)) return true;
// try charge 1 -NOTE THIS IS NEW
double test3 = getMassChargeRatio();
if (alg.isWithinLimits(test3, mass, 0)) return true;
return false; // give up
} else {
double test = getPrecursorMass();
boolean withinLimits = alg.isWithinLimits(test, mass, m_PrecursorCharge);
if (withinLimits) return true;
return false; // give up
}
}
public static double chargeRatioFromMass(double mass, int charge) {
double protonMass = XTandemUtilities.getProtonMass();
return ((mass - protonMass) / charge) + protonMass;
}