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File decomp.patch of Package xtandem
diff --git a/src/Makefile_ubuntu b/src/Makefile_ubuntu index 27521b5..48c1d5b 100644 --- a/src/Makefile_ubuntu +++ b/src/Makefile_ubuntu @@ -17,7 +17,7 @@ CXXFLAGS = -w -O2 -DGCC4_3 #ubuntu 64 bit version #LDFLAGS = -lpthread -lm -L/usr/lib -static -lexpat -LDFLAGS = -lpthread -L/usr/lib -lm -lexpat +LDFLAGS = -lpthread -lm -lexpat -lz SRCS := $(wildcard *.cpp) OBJS := $(patsubst %.cpp,%.o,$(wildcard *.cpp)) diff --git a/src/base64.cpp b/src/base64.cpp index aa75eba..069864a 100644 --- a/src/base64.cpp +++ b/src/base64.cpp @@ -2,6 +2,7 @@ //#include <math.h> //#include <stdio.h> //#include <string.h> +#include <zlib.h> #include "stdafx.h" #include "base64.h" @@ -90,11 +91,12 @@ inline int getPosition( char buf ) } -// Returns the total number of bytes decoded -int b64_decode_mio ( char *dest, char *src, size_t size ) +// Returns the total number of bytes decoded, or -1 if destination buffer overflows or there is a decompression error +int b64_decode_mio ( char *const dest, const size_t dest_size, char *src, const size_t src_size, bool decomp ) { char *temp = dest; - char *end = dest + size; + char *const dest_end = dest + dest_size; + char *const src_end = src + src_size; for (;;) { @@ -102,11 +104,11 @@ int b64_decode_mio ( char *dest, char *src, size_t size ) int register b; int t1,t2,t3,t4; - if (!(t1 = *src++) || !(t2 = *src++) || !(t3 = *src++) || !(t4 = *src++)) - return (int)(temp-dest); - - if (t1 == 61 || temp >= end) // if == '=' - return(int)(temp-dest); + // Read first and second characters + if (src >= src_end || !(t1 = *src++) || t1 == 61) // if == '=' + break; + if (src >= src_end || !(t2 = *src++)) + break; if( t1 > 96 ) // [a-z] a = (t1 - 71); @@ -119,7 +121,6 @@ int b64_decode_mio ( char *dest, char *src, size_t size ) else // src[0] == '/' a = 63; - if( t2 > 96 ) // [a-z] b = (t2 - 71); else if( t2 > 64 ) // [A-Z] @@ -131,10 +132,14 @@ int b64_decode_mio ( char *dest, char *src, size_t size ) else // src[0] == '/' b = 63; + // Write first byte + if (temp >= dest_end) // destination overflow! + return -1; *temp++ = ( a << 2) | ( b >> 4); - if (t3 == 61 || temp >= end) - return (int)(temp-dest);; + // Read third character (if any) + if (src >= src_end || !(t3 = *src++) || t3 == 61) + break; if( t3 > 96 ) // [a-z] a = (t3 - 71); @@ -147,10 +152,14 @@ int b64_decode_mio ( char *dest, char *src, size_t size ) else // src[0] == '/' a = 63; + // Write second byte + if (temp >= dest_end) // destination overflow! + return -1; *temp++ = ( b << 4) | ( a >> 2); - if (t4 == 61 || temp >= end) - return (int)(temp-dest);; + // Read fourth character (if any) + if (src >= src_end || !(t4 = *src++) || t4 == 61) + break; if( t4 > 96 ) // [a-z] b = (t4 - 71); @@ -163,6 +172,26 @@ int b64_decode_mio ( char *dest, char *src, size_t size ) else // src[0] == '/' b = 63; + // Write third byte + if (temp >= dest_end) // destination overflow! + return -1; *temp++ = ( a << 6) | ( b ); } + + // Decompress if required + if (decomp) { + Bytef *decompBuf = (Bytef*)malloc(dest_size); + uLongf decompLen = dest_size; + int result = uncompress(decompBuf, &decompLen, (Bytef*)dest, (uLong)(temp - dest)); + if (result == Z_OK) { + memcpy(dest, decompBuf, decompLen); + temp = dest + decompLen; + } + free(decompBuf); + if (result != Z_OK) // decompression error + return -1; + } + + // Done + return temp - dest; } diff --git a/src/base64.h b/src/base64.h index e7c1bc5..b529dfa 100644 --- a/src/base64.h +++ b/src/base64.h @@ -1,5 +1,5 @@ #ifndef BASE64_H #define BASE64_H -int b64_decode_mio (char *dest, char *src, size_t size); +int b64_decode_mio (char *dest, size_t dest_size, char *src, size_t src_size, bool decomp); #endif /* BASE64_H */ diff --git a/src/saxhandler.cpp b/src/saxhandler.cpp index 7afcebf..16a92e9 100644 --- a/src/saxhandler.cpp +++ b/src/saxhandler.cpp @@ -299,7 +299,7 @@ void SAXSpectraHandler::pushSpectrum() } } -void SAXSpectraHandler::pushPeaks(bool bM /*= true*/, bool bI /*= true*/) +void SAXSpectraHandler::pushPeaks(bool bM /*= true*/, bool bI /*= true*/, bool decomp /*= false*/) { if(bM) m_vfM.clear(); @@ -340,10 +340,10 @@ void SAXSpectraHandler::pushPeaks(bool bM /*= true*/, bool bI /*= true*/) } else{ if (m_bLowPrecision) { - decode32(bM,bI); + decode32(bM,bI,decomp); } else { - decode64(bM,bI); + decode64(bM,bI,decomp); } } } @@ -393,7 +393,7 @@ void SAXSpectraHandler::numDepress(char* indata, size_t indataLength, bool bM /* } -void SAXSpectraHandler::decode32(bool bM /*= true*/, bool bI /*= true*/) +void SAXSpectraHandler::decode32(bool bM /*= true*/, bool bI /*= true*/, bool decomp /*= false*/) { // 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 @@ -407,15 +407,15 @@ void SAXSpectraHandler::decode32(bool bM /*= true*/, bool bI /*= true*/) if(bI == true) { setCount++; } - size_t size = stringSize * setCount * 3 / 4; - char* pDecoded = (char *) new char[size]; - - memset(pDecoded, 0, size); + size_t size = m_peaksCount * setCount * sizeof(uint32_t); + size_t dest_size = size + 32; + char* pDecoded = (char *) new char[dest_size]; + memset(pDecoded, 0, dest_size); 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 ); + int length = b64_decode_mio( (char*) pDecoded, dest_size, (char*) pData, stringSize, decomp ); if (!m_strNumpress.empty()){ numDepress((char*) pDecoded, length, bM, bI); } @@ -451,7 +451,7 @@ void SAXSpectraHandler::decode32(bool bM /*= true*/, bool bI /*= true*/) delete[] pDecoded; } -void SAXSpectraHandler::decode64(bool bM /*= true*/, bool bI /*= true*/) +void SAXSpectraHandler::decode64(bool bM /*= true*/, bool bI /*= true*/, bool decomp /*= false*/) { // 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 @@ -465,14 +465,15 @@ void SAXSpectraHandler::decode64(bool bM /*= true*/, bool bI /*= true*/) if(bI == true) { setCount++; } - size_t size = stringSize * setCount * 3 / 4; - char* pDecoded = (char *) new char[size]; - memset(pDecoded, 0, size); + size_t size = m_peaksCount * setCount * sizeof(uint64_t); + size_t dest_size = size + 32; + char* pDecoded = (char *) new char[dest_size]; + memset(pDecoded, 0, dest_size); 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 ); + int length = b64_decode_mio( (char*) pDecoded, dest_size, (char*) pData, stringSize, decomp ); if (!m_strNumpress.empty()){ numDepress(pDecoded, length, bM, bI); diff --git a/src/saxhandler.h b/src/saxhandler.h index 8a076fd..fc66dcc 100644 --- a/src/saxhandler.h +++ b/src/saxhandler.h @@ -231,7 +231,7 @@ public: protected: void pushSpectrum(); // Load current data into pvSpec, may have to guess charge void pushSpectrum(int charge); // Load current data into pvSpec with specific charge - void pushPeaks(bool bM = true, bool bI = true); // Decode m_strData into a peak list + void pushPeaks(bool bM = true, bool bI = true, bool decomp = false); // Decode m_strData into a peak list inline void reset() { @@ -247,8 +247,8 @@ private: int guessCharge(); // Guess the charge based on spectrum peaks void setDescription(); // Set specCurrent description based on current data void numDepress(char* indata, size_t indataLength, bool bM /*= true*/, bool bI /*= true*/); - void decode32(bool bM /*= true*/, bool bI /*= true*/); - void decode64(bool bM /*= true*/, bool bI /*= true*/); + void decode32(bool bM /*= true*/, bool bI /*= true*/, bool decomp /*= false*/); + void decode64(bool bM /*= true*/, bool bI /*= true*/, bool decomp /*= false*/); unsigned long dtohl(uint32_t l, bool bNet); // Convert from data to host long uint64_t dtohl(uint64_t l, bool bNet); protected: diff --git a/src/saxmzmlhandler.cpp b/src/saxmzmlhandler.cpp index fe9cfd6..9348b62 100644 --- a/src/saxmzmlhandler.cpp +++ b/src/saxmzmlhandler.cpp @@ -44,6 +44,7 @@ SAXMzmlHandler::SAXMzmlHandler( vector<mspectrum>& _vS, mspectrumcondition& _sC, m_bNetworkData = true; m_bLowPrecision = false; m_bGaml = false; + m_bDecomp = false; } SAXMzmlHandler::~SAXMzmlHandler() @@ -130,6 +131,7 @@ void SAXMzmlHandler::startElement(const XML_Char *el, const XML_Char **attr) m_peaksCount = atoi(getAttrValue("arrayLength", attr)); } m_bInData = true; + m_bDecomp = false; // reset flag } } @@ -215,8 +217,7 @@ void SAXMzmlHandler::processCVParam(const char* name, const char* accession, con m_bInmzArrayBinary = false; } else if(!strcmp(name, "zlib compression") || !strcmp(accession,"MS:1000574")) { - cout << "\nFatal error: unsupported CODEC used for mzML peak data (CODEC type=" << name << ").\n"; - exit(-10); + m_bDecomp = true; } else if(!strcmp(accession, "MS:1002312") || !strcmp(accession, "MS:1002313") || !strcmp(accession, "MS:1002314")) { m_strNumpress = string(accession); @@ -227,11 +228,11 @@ void SAXMzmlHandler::processData() { if(m_bInmzArrayBinary && m_bInMsLevel2 && m_bInData) { - pushPeaks(m_bInmzArrayBinary, m_bInintenArrayBinary); + pushPeaks(m_bInmzArrayBinary, m_bInintenArrayBinary, m_bDecomp); } else if(m_bInintenArrayBinary && m_bInMsLevel2 && m_bInData) { - pushPeaks(m_bInmzArrayBinary, m_bInintenArrayBinary); + pushPeaks(m_bInmzArrayBinary, m_bInintenArrayBinary, m_bDecomp); } m_strData.clear(); diff --git a/src/saxmzmlhandler.h b/src/saxmzmlhandler.h index 3c4d121..c11eae9 100644 --- a/src/saxmzmlhandler.h +++ b/src/saxmzmlhandler.h @@ -72,6 +72,7 @@ private: bool m_bInmzArrayBinary; bool m_bInintenArrayBinary; bool m_bInData; + bool m_bDecomp; string m_ccurrentRefGroupName; class cvParam { diff --git a/src/saxmzxmlhandler.cpp b/src/saxmzxmlhandler.cpp index afccebb..fe34ce9 100644 --- a/src/saxmzxmlhandler.cpp +++ b/src/saxmzxmlhandler.cpp @@ -25,6 +25,7 @@ SAXMzxmlHandler::SAXMzxmlHandler( vector<mspectrum>& _vS, mspectrumcondition& _s m_bInMsLevel2 = false; m_bInPrecursorMz = false; m_bInPeaks = false; + m_bDecomp = false; //added this (true by default) m_bNetworkData = false; } @@ -58,9 +59,16 @@ void SAXMzxmlHandler::startElement(const XML_Char *el, const XML_Char **attr) m_bInPeaks = true; m_bLowPrecision = (strcmp("64", getAttrValue("precision", attr)) != 0); const char *pcompressionType = getAttrValue("compressionType", attr); - if(strlen(pcompressionType) != 0 && !strstr(pcompressionType,"none")) { - cout << "\nFatal error: unsupported CODEC used for mzXML peak data (CODEC type=" << pcompressionType << ").\n"; - exit(-10); + m_bDecomp = false; // default to false in case required attribute is missing + if(strlen(pcompressionType) != 0) { + if (!strcmp(pcompressionType,"none")) { + m_bDecomp = false; + } else if (strstr(pcompressionType,"zlib")) { + m_bDecomp = true; + } else { + cout << "Non-standard CODEC used for mzXML peak data (CODEC type=" << pcompressionType << "): file cannot be interpreted.\n"; + exit(-10); + } } } else if(isElement("precursorMz", el)) @@ -106,7 +114,7 @@ void SAXMzxmlHandler::processData() { if( m_bInPeaks && m_cidLevel == 2) { - pushPeaks(); + pushPeaks(true, true, m_bDecomp); } else if (m_bInPrecursorMz) { diff --git a/src/saxmzxmlhandler.h b/src/saxmzxmlhandler.h index e92f441..fb8c857 100644 --- a/src/saxmzxmlhandler.h +++ b/src/saxmzxmlhandler.h @@ -56,6 +56,7 @@ private: bool m_bInMsLevel2; bool m_bInPrecursorMz; bool m_bInPeaks; + bool m_bDecomp; }; #endif //SAXMzxmlHandler_H
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