saxhandler.cpp

/*
 Copyright (C) 2003-2004 Ronald C Beavis, all rights reserved
 X! tandem 
 This software is a component of the X! proteomics software
 development project

Use of this software governed by the Artistic license, as reproduced here:

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*/

#include "stdafx.h"
#include "saxhandler.h"
#include "base64.h"
#include "mspectrumcondition.h"

#include "zlib.h"  //Pour mzXML 3.0 peak list compression - Brian Pratt for LabKey

#ifdef MSVC
#include <winsock2.h>   ///Pour windows et MinGW
#else


#ifdef GCC
#include <netinet/in.h>  ////Pour linux
#endif

#ifdef GCC4
#include <netinet/in.h>  ////Pour linux gcc v. 4
#endif

#endif // MSVC

#ifdef OSX
#include <sys/types.h>  ////Pour mac
#include <machine/endian.h>
#endif

// Static callback handlers
static void startElementCallback(void *data, const XML_Char *el, const XML_Char **attr)
{
	((SAXHandler*) data)->startElement(el, attr);
}

static void endElementCallback(void *data, const XML_Char *el)
{
	((SAXHandler*) data)->endElement(el);
}

static void charactersCallback(void *data, const XML_Char *s, int len)
{
	((SAXHandler*) data)->characters(s, len);
}

SAXHandler::SAXHandler()
{
	m_parser = XML_ParserCreate(NULL);
	XML_SetUserData(m_parser, this);
	XML_SetElementHandler(m_parser, startElementCallback, endElementCallback);
	XML_SetCharacterDataHandler(m_parser, charactersCallback);
}


SAXHandler::~SAXHandler()
{
	XML_ParserFree(m_parser);
}

void SAXHandler::startElement(const XML_Char *el, const XML_Char **attr)
{
}

void SAXHandler::endElement(const XML_Char *el)
{
}


void SAXHandler::characters(const XML_Char *s, int len)
{
}

bool SAXHandler::parse()
{
	FILE* pfIn = fopen(m_strFileName.data(), "r");
	if (pfIn == NULL)
	{
		cerr << "Failed to open input file '" << m_strFileName << "'.\n";
		return false;
	}
	char buffer[8192];
	int readBytes = 0;
	bool success = true;
	while (success && (readBytes = (int) fread(buffer, 1, sizeof(buffer), pfIn)) > 0)
	{
		success = (XML_Parse(m_parser, buffer, readBytes, false) != 0);
	}
	success = success && (XML_Parse(m_parser, buffer, 0, true) != 0);

	fclose(pfIn);

	if (!success)
	{
		XML_Error error = XML_GetErrorCode(m_parser);

		cerr << m_strFileName
			<< "(line " << XML_GetCurrentLineNumber(m_parser)
		        << " column " << XML_GetCurrentColumnNumber(m_parser)
		        << ")"
			<< " : error " << (int) error << ", "
		     << XML_ErrorString(error) << ": ";

		switch (error)
		{
			case XML_ERROR_SYNTAX:
			case XML_ERROR_INVALID_TOKEN:
			case XML_ERROR_UNCLOSED_TOKEN:
				cerr << "Syntax error parsing XML.";
				break;

			// TODO: Add more descriptive text for interesting errors.

			default:
				cerr << "XML Parsing error.";
				break;
		}
		cerr << "\n";
		return false;
	}
	return true;
}

/*******************************************************
 * SAXSpectraHandler class
 *
 * Inspired by DtaSAX2Handler.cpp
 * copyright            : (C) 2002 by Pedrioli Patrick, ISB, Proteomics
 * email                : ppatrick@systemsbiology.org
 * Artistic License granted 3/11/2005
 *******************************************************/

SAXSpectraHandler::SAXSpectraHandler(vector<mspectrum>& _vS, mspectrumcondition& _sC, mscore& _m)
{
	m_pvSpec = &_vS;
	m_pSpecCond = &_sC;
	m_pScore = &_m;

	m_tId = 1;
	m_lLoaded = 0;
	m_bNetworkData = true;
	m_bLowPrecision = true;
	m_bGaml=false;
	m_dProton = 1.007276;

	reset();
}

SAXSpectraHandler::~SAXSpectraHandler()
{
}

void SAXSpectraHandler::pushSpectrum()
{
	int i=0;
	if(m_precursorCharge > 0)	// Known charge
	{
		pushSpectrum(m_precursorCharge);
	}
	else 	// Not sure about the charge state
	{
		// Guess charge state
		m_precursorCharge = guessCharge();

		if( m_precursorCharge == 1)
		{
			pushSpectrum(1);
		}
		else	// Multiple charge, most likely 2 or 3
		{
			pushSpectrum(2);
			m_tId += 100000000;
			pushSpectrum(3);
			m_tId -= 100000000;
		}
	}
}

void SAXSpectraHandler::pushPeaks(bool bM /*= true*/, bool bI /*= true*/)
{
	if(bM)
		m_vfM.clear();
	if(bI)
		m_vfI.clear();

	if(m_bGaml){
		int a=0;
		char *pLine = new char[m_strData.size()+1];
		char *pValue = NULL;
		strcpy(pLine,m_strData.c_str());
		pValue = pLine;
		if(bM){
			while(*pValue != '\0' && a < m_peaksCount)	{
				while(*pValue != '\0' && isspace(*pValue))
					pValue++;
				if(pValue == '\0')
					break;
				m_vfM.push_back((float)atof(pValue));
				while(*pValue != '\0' && !isspace(*pValue))
					pValue++;
				a++;
			}
		}
		else{
			while(*pValue != '\0' && a < m_peaksCount)	{
				while(*pValue != '\0' && isspace(*pValue))
					pValue++;
				if(pValue == '\0')
					break;
				m_vfI.push_back((float)atof(pValue));
				while(*pValue != '\0' && !isspace(*pValue))
					pValue++;
				a++;
			}
		}
		delete pLine;
	}
	else{
		if (m_bLowPrecision)	{
			decode32(bM,bI);
		}
		else	{
			decode64(bM,bI);
		}
	}
}

void SAXSpectraHandler::decode32(bool bM /*= true*/, bool bI /*= true*/)
{
// This code block was revised so that it packs floats correctly
// on both 64 and 32 bit machines, by making use of the uint32_t
// data type. -S. Wiley
	const char* pData = m_strData.data();
	size_t stringSize = m_strData.size();
	int setCount = 0;
	if(bM == true) {
		setCount++;
	}
	if(bI == true) {
		setCount++;
	}
	size_t size = m_peaksCount * setCount * sizeof(uint32_t);
    size_t sizeDecode = (m_bCompressed ? m_lenCompressed : size);
	char* pDecoded = (char *) new char[sizeDecode];
	memset(pDecoded, 0, sizeDecode);
	if(m_peaksCount > 0) {
		// Base64 decoding
		// By comparing the size of the unpacked data and the expected size
		// an additional check of the data file integrity can be performed
		int length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize );
		if (m_bCompressed) { // handle zlib compression - Brian Pratt for LabKey
			Byte *pUncompr = (Byte *)new char[size];
			unsigned long lsize = (unsigned long)size; 
			int err = uncompress( pUncompr , &lsize , (const Byte *)pDecoded , (unsigned long)length);
			if (err) {
				cout << " zlib data decompression returns error " << err << "\n";
				cout << " Cause: possible corrupted file.\n";
				exit(EXIT_FAILURE);
			}
			delete[] pDecoded;
			pDecoded = (char *)pUncompr; 
			length = lsize;
		}
		if(length != size) {
			cout << " decoded size " << length << " and required size " << (unsigned long)size << " dont match:\n";
			cout << " Cause: possible corrupted file.\n";
			exit(EXIT_FAILURE);
		}
	}
		// And byte order correction
	union udata {
		float fData;
		uint32_t iData;  
	} uData; 

	int n = 0;
	uint32_t* pDecodedInts = (uint32_t*)pDecoded; // cast to uint_32 for reading int sized chunks
	for(int i = 0; i < m_peaksCount; i++) {
		if(bM){
			uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData);
			m_vfM.push_back(uData.fData);
		}
		if(bI){
			uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData);
			m_vfI.push_back(uData.fData);
		}
	}
	// Free allocated memory
	delete[] pDecoded;
}

void SAXSpectraHandler::decode64(bool bM /*= true*/, bool bI /*= true*/)
{
// This code block was revised so that it packs floats correctly
// on both 64 and 32 bit machines, by making use of the uint32_t
// data type. -S. Wiley
	const char* pData = m_strData.data();
	size_t stringSize = m_strData.size();
	int setCount = 0;
	if(bM == true) {
		setCount++;
	}
	if(bI == true) {
		setCount++;
	}
	size_t size = m_peaksCount * setCount * sizeof(uint64_t);
    size_t sizeDecode = (m_bCompressed ? m_lenCompressed : size);
	char* pDecoded = (char *) new char[sizeDecode];
	memset(pDecoded, 0, sizeDecode);
	if(m_peaksCount > 0) {
		// Base64 decoding
		// By comparing the size of the unpacked data and the expected size
		// an additional check of the data file integrity can be performed
		int length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize );
		if (m_bCompressed) { // handle zlib compression - Brian Pratt for LabKey
			Byte *pUncompr = (Byte *)new char[size];
			unsigned long lsize = (unsigned long)size; 
			int err = uncompress( pUncompr , &lsize , (const Byte *)pDecoded , (unsigned long)length);
			if (err) {
				cout << " zlib data decompression returns error " << err << "\n";
				cout << " Cause: possible corrupted file.\n";
				exit(EXIT_FAILURE);
			}
			delete[] pDecoded;
			pDecoded = (char *)pUncompr; 
			length = lsize;
		}
		if(length != size) {
			cout << " decoded size " << length << " and required size " << (unsigned long)size << " dont match:\n";
			cout << " Cause: possible corrupted file.\n";
			exit(EXIT_FAILURE);
		}
	}
		// And byte order correction
	union udata {
		double fData;
		uint64_t iData;  
	} uData; 

	int n = 0;
	uint64_t* pDecodedInts = (uint64_t*)pDecoded; // cast to uint_64 for reading int sized chunks
	for(int i = 0; i < m_peaksCount; i++) {
		if(bM){
			uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData);
			m_vfM.push_back((float)uData.fData);
		}
		if(bI){
			uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData);
			m_vfI.push_back((float)uData.fData);
		}
	}
	// Free allocated memory
	delete[] pDecoded;
}

unsigned long SAXSpectraHandler::dtohl(uint32_t l, bool bNet)
{
	// mzData allows little-endian data format, so...
	// If it is not network (i.e. big-endian) data, reverse the byte
	// order to make it network format, and then use ntohl (network to host)
	// to get it into the host format.
	//if compiled on OSX the reverse is true
#ifdef OSX
	if (bNet)
	{
		l = (l << 24) | ((l << 8) & 0xFF0000) |
			(l >> 24) | ((l >> 8) & 0x00FF00);
	}
#else
	if (!bNet)
	{
		l = (l << 24) | ((l << 8) & 0xFF0000) |
			(l >> 24) | ((l >> 8) & 0x00FF00);
	}
#endif
	return l;
}

uint64_t SAXSpectraHandler::dtohl(uint64_t l, bool bNet)
{
	// mzData allows little-endian data format, so...
	// If it is not network (i.e. big-endian) data, reverse the byte
	// order to make it network format, and then use ntohl (network to host)
	// to get it into the host format.
	//if compiled on OSX the reverse is true
#ifdef OSX
	if (bNet)
	{
		l = (l << 56) | ((l << 40) & 0xFF000000000000LL) | ((l << 24) & 0x0000FF0000000000LL) | ((l << 8) & 0x000000FF00000000LL) |
			(l >> 56) | ((l >> 40) & 0x0000000000FF00LL) | ((l >> 24) & 0x0000000000FF0000LL) | ((l >> 8) & 0x00000000FF000000LL) ;
	}
#else
	if (!bNet)
	{
		l = (l << 56) | ((l << 40) & 0x00FF000000000000LL) | ((l << 24) & 0x0000FF0000000000LL) | ((l << 8) & 0x000000FF00000000LL) |
			(l >> 56) | ((l >> 40) & 0x000000000000FF00LL) | ((l >> 24) & 0x0000000000FF0000LL) | ((l >> 8) & 0x00000000FF000000LL) ;
	}
#endif
	return l;
}

void SAXSpectraHandler::pushSpectrum(int charge)
{
	int lLimit = 2000;

	/*
	* create a temporary mspectrum object
	*/
	m_specCurrent.m_tId = m_tId;
	m_specCurrent.m_strRt = m_strRt;
	if(m_bGaml){
		m_specCurrent.m_dMH = m_precursorMz;
		m_specCurrent.m_vdStats.clear();
		m_specCurrent.m_vdStats.push_back(m_dSum);
		m_specCurrent.m_vdStats.push_back(m_dMax);
		m_specCurrent.m_vdStats.push_back(m_dFactor);
	}
	else{
		m_specCurrent.m_dMH = (m_precursorMz - m_dProton)*(float)charge + m_dProton;
	}
	m_specCurrent.m_fZ = (float) charge;

	mi miCurrent;
	m_specCurrent.clear_intensity_values();
	for(size_t i = 0; i < m_vfM.size(); i++)
	{
		miCurrent.m_fM = m_vfM[i];
		miCurrent.m_fI = m_vfI[i];
		// Only push if both mass and intensity are non-zero.
		if (miCurrent.m_fM && miCurrent.m_fI )
			m_specCurrent.m_vMI.push_back(miCurrent);
	}
	if(m_bGaml && m_strDesc != ""){
		m_specCurrent.m_strDescription = m_strDesc;
	}
	else{
		setDescription();
	}

	//Ajout du spectre a m_vSpectra
	if(m_pSpecCond->condition(m_specCurrent, *m_pScore) ){ // || true to force
		m_pvSpec->push_back(m_specCurrent);
		m_lLoaded++;
		if(m_lLoaded == lLimit)	{
			cout << ".";
			cout.flush();
			m_lLoaded = 0;
		}
	}
}

int SAXSpectraHandler::guessCharge()
{
	// All this small routine does is trying to guess the charge state of the precursor
	// from the ratio of the integrals of the intensities below and above m_precursorMz
	float intBelow = 0;
	float intTotal = 0;

	size_t length = m_vfM.size();
	for(size_t i = 0 ; i < length ; i++)
	{
		intTotal += m_vfI[i];
		if(m_vfM[i] < m_precursorMz)
			intBelow += m_vfI[i];   
	}

	// There is no particular reason for the 0.95. It's there just
	// to compensate for the noise.... 
	if(intTotal == 0.0 || intBelow/intTotal > 0.95)
		return 1;
	else
		return 2;
}

void SAXSpectraHandler::setDescription()
{
	m_specCurrent.m_strDescription.clear();
	size_t iPos = 0;
	size_t iSlash = m_strFileName.rfind('/');
	if (iSlash != string::npos && iSlash > iPos)
		iPos = iSlash + 1;
	size_t iBack = m_strFileName.rfind('\\');
	if (iBack != string::npos && iBack > iPos)
		iPos = iBack + 1;
	m_specCurrent.m_strDescription += m_strFileName.substr(iPos);
	m_specCurrent.m_strDescription += " scan ";
	char buffer[20];
	sprintf(buffer, "%d", m_scanNum);
	m_specCurrent.m_strDescription += buffer;
	m_specCurrent.m_strDescription += " (charge ";
	sprintf(buffer, "%d", (int)m_specCurrent.m_fZ);
	m_specCurrent.m_strDescription += buffer;
	m_specCurrent.m_strDescription += ")";
}