void SAXMzxmlHandler::endElement(const XML_Char *el)
{
if(isElement("peaks", el))
{
processData();
m_bInPeaks = false;
}
else if(isElement("precursorMz", el))
{
processData();
m_bInPrecursorMz = false;
}
else if(isElement("scan", el) && m_bInMsLevel2 == true)
{
// only add a spectrum without charge (which will lead
// to internal xtandem charge state guessing) if there
// were no values parsed from *both* "precursorCharge"
// or "possibleCharges"
if ( (m_precursorCharge == 0) && (m_viPossiblePrecursorCharges.size() == 0) ) {
// add spectrum, with precursorMz charge
pushSpectrum();
}
else {
// add the spectrum with the m_precursorCharge value
int originalPrecursorMZ = m_precursorCharge; // do other pushSpectrum calls change this?
pushSpectrum(m_precursorCharge);
// are there any multiple precursor charges from mzXML 3.1's
// possibleCharges?
if (m_viPossiblePrecursorCharges.size() > 0) {
size_t originalId = m_tId;
for (vector<int>::iterator i = m_viPossiblePrecursorCharges.begin();
i != m_viPossiblePrecursorCharges.end();
++i) {
int z = *i;
if (z != originalPrecursorMZ) { // no need to duplicate if already added
m_tId += 100000000;
pushSpectrum(z);
}
}
m_tId = originalId;
}
}
m_bInMsLevel2 = false;
}
}
void SAXMzdataHandler::endElement(const XML_Char *el)
{
if(isElement("mzArrayBinary", el))
m_bInmzArrayBinary = false;
else if(isElement("intenArrayBinary", el))
m_bInintenArrayBinary = false;
else if(isElement("data", el))
{
processData();
m_bInData = false;
}
else if(isElement("spectrum", el) && m_bInMsLevel2)
{
pushSpectrum();
m_bInMsLevel2 = false;
}
}
void SAXMzmlHandler::endElement(const XML_Char *el)
{
if(isElement("binary", el)) {
processData();
m_bInintenArrayBinary = false;
m_bInmzArrayBinary = false;
m_bInData = false;
}
else if(isElement("spectrum", el) && m_bInMsLevel2)
{
pushSpectrum();
m_bInMsLevel2 = false;
}
else if (isElement("referenceableParamGroup", el))
{
m_bInRefGroup = false;
}
}
void SAXMzxmlHandler::endElement(const XML_Char *el)
{
if(isElement("peaks", el))
{
processData();
m_bInPeaks = false;
}
else if(isElement("precursorMz", el))
{
processData();
m_bInPrecursorMz = false;
}
else if(isElement("scan", el) && m_bInMsLevel2 == true)
{
pushSpectrum();
m_bInMsLevel2 = false;
}
}
void SAXGamlHandler::endElement(const XML_Char *el)
{
if(isElement("note", el) && m_bDesc){
m_bDesc=false;
}
else if(isElement("GAML:Xdata", el) && m_bInData){
pushPeaks(m_bMZ, m_bINT);
m_strData.clear();
m_bMZ = false;
}
else if(isElement("GAML:Ydata", el) && m_bInData){
pushPeaks(m_bMZ, m_bINT);
m_strData.clear();
m_bINT = false;
}
else if(isElement("GAML:trace", el) && m_bInData){
pushSpectrum();
reset();
m_bInData=false;
}
}
