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convert exit() calls to C++ exceptions #37

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20 changes: 7 additions & 13 deletions src/MSToolkit/MSReader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ limitations under the License.
*/
#include "MSReader.h"
#include <iostream>
#include <stdexcept>
using namespace std;
using namespace MSToolkit;

Expand Down Expand Up @@ -457,9 +458,7 @@ bool MSReader::readMGFFile(const char* c, Spectrum& s){

//Sanity check that we are at next spectrum
if(strstr(strMGF,"BEGIN IONS")==NULL) {
cout << "Malformed MGF spectrum entry. Exiting." << endl;
cout << "line: " << strMGF << endl;
exit(-10);
throw std::runtime_error(std::string("Malformed MGF spectrum entry. Line: ") + std::string(strMGF));
}

//Read [next] spectrum header, modernization from JKE across entire while block
Expand Down Expand Up @@ -498,8 +497,7 @@ bool MSReader::readMGFFile(const char* c, Spectrum& s){

//Process header information
if(s.getMZ()==0) {
cout << "Error in MGF file: no PEPMASS found." << endl;
exit(-12);
throw std::runtime_error("Error in MGF file: no PEPMASS found.");
}
if(ch!=0){
s.addZState(ch,s.getMZ()*ch-1.007276466*(ch-1));
Expand Down Expand Up @@ -530,14 +528,12 @@ bool MSReader::readMGFFile(const char* c, Spectrum& s){

tok=strtok_r(strMGF," \t\n\r", &nextTok);
if(tok==NULL){
cout << "Error in MGF file: bad m/z or intensity value." << endl;
exit(-13);
throw std::runtime_error("Error in MGF file: bad m/z or intensity value.");
}
mz=atof(tok);
tok=strtok_r(NULL," \t\n\r", &nextTok);
if(tok==NULL){
cout << "Error in MGF file: bad m/z or intensity value." << endl;
exit(-13);
throw std::runtime_error("Error in MGF file: bad m/z or intensity value.");
}
intensity=(float)atof(tok);
if(!mgfOnePlus){
Expand Down Expand Up @@ -660,8 +656,7 @@ bool MSReader::readMGFFile2(const char* c, Spectrum& s){
if (tokens[0].find("END IONS") != string::npos) {
//convert any header information to MST spectrum information
if (s.getMZ() == 0) {
cout << "Error in MGF file: no PEPMASS found." << endl;
exit(-12);
throw std::runtime_error("Error in MGF file: no PEPMASS found.");
}
if (ch != 0){
s.addZState(ch, s.getMZ()*ch - 1.007276466*(ch - 1));
Expand Down Expand Up @@ -793,8 +788,7 @@ bool MSReader::readMSTFile(const char *c, bool text, Spectrum& s, int scNum){
readSpecHeader(fileIn,ms);

if(scNum<0) {
cerr << "ERROR: readMSTFile(): Cannot request previous scan. Function not supported. " << flush;
exit(1);
throw std::runtime_error("ERROR: readMSTFile(): Cannot request previous scan. Function not supported.");
}
if(scNum!=0){

Expand Down
42 changes: 20 additions & 22 deletions src/mzParser/saxhandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,8 @@ The End
*/

#include "mzParser.h"
#include <stdexcept>
#include <string>
using namespace std;
using namespace mzParser;

Expand Down Expand Up @@ -305,33 +307,29 @@ bool mzpSAXHandler::parseOffset(f_off offset){
if(m_bStopParse) break;
}
}
if (!success && !m_bStopParse)
{
XML_Error error = XML_GetErrorCode(m_parser);

if (!success && !m_bStopParse)
{
XML_Error error = XML_GetErrorCode(m_parser);
std::string msg = std::string(m_strFileName) + "(" + std::to_string(XML_GetCurrentLineNumber(m_parser)) + ") : parseOffset() " + std::to_string((int)error) + ": ";

cerr << m_strFileName
<< "(" << XML_GetCurrentLineNumber(m_parser) << ")"
<< " : parseOffset() " << (int) error << ": ";
switch (error)
{
case XML_ERROR_SYNTAX:
case XML_ERROR_INVALID_TOKEN:
case XML_ERROR_UNCLOSED_TOKEN:
msg += "Syntax error parsing XML.";
break;

switch (error)
{
case XML_ERROR_SYNTAX:
case XML_ERROR_INVALID_TOKEN:
case XML_ERROR_UNCLOSED_TOKEN:
cerr << "Syntax error parsing XML." << endl;
break;
// TODO: Add more descriptive text for interesting errors.

// TODO: Add more descriptive text for interesting errors.
default:
msg += std::string("Spectrum XML Parsing error: ") + XML_ErrorString(error);
break;
}

default:
cerr << "Spectrum XML Parsing error:\n";
cerr << XML_ErrorString(error) << endl;
break;
}
exit(-7);
return false;
}
throw std::runtime_error(msg);
}
return true;
}

Expand Down
10 changes: 4 additions & 6 deletions src/mzParser/saxmzmlhandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
*******************************************************/

#include "mzParser.h"
#include <stdexcept>
using namespace std;
using namespace mzParser;

Expand Down Expand Up @@ -893,8 +894,7 @@ void mzpSAXMzmlHandler::decode(vector<double>& d){
unzippedLen = m_peaksCount*sizeof(uint64_t);
} else {
if(!m_bNumpressLinear && !m_bNumpressSlof && !m_bNumpressPic){
cout << "Unknown data format to unzip. Stopping file read." << endl;
exit(EXIT_FAILURE);
throw std::runtime_error("Unknown data format to unzip. Stopping file read.");
}
//don't know the unzipped size of numpressed data, so assume it to be no larger than unpressed 64-bit data
unzippedLen = m_peaksCount*sizeof(uint64_t);
Expand Down Expand Up @@ -922,8 +922,7 @@ void mzpSAXMzmlHandler::decode(vector<double>& d){
else ms::numpress::MSNumpress::decodePic((unsigned char*)decoded,decodeLen,unpressed);
}
} catch (const char* ch){
cout << "Exception: " << ch << endl;
exit(EXIT_FAILURE);
throw std::runtime_error(std::string("Exception: ") + ch);
}

if(m_bZlib) delete [] unzipped;
Expand Down Expand Up @@ -1233,8 +1232,7 @@ bool mzpSAXMzmlHandler::generateIndexOffset() {
char *pStr;

if (f==NULL){
cout << "Error cannot open file " << m_strFileName[0] << endl;
exit(EXIT_FAILURE);
throw std::runtime_error(std::string("Error cannot open file ") + m_strFileName);
}

bool bReadingFirstSpectrum = true;
Expand Down
15 changes: 5 additions & 10 deletions src/mzParser/saxmzxmlhandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
*******************************************************/

#include "mzParser.h"
#include <stdexcept>

using namespace std;
using namespace mzParser;
Expand Down Expand Up @@ -100,8 +101,7 @@ void mzpSAXMzxmlHandler::startElement(const XML_Char *el, const XML_Char **attr)
if(!strcmp("zlib",&s[0])) m_bCompressedData=true;
else if(!strcmp("none",&s[0])) m_bCompressedData=false;
else if(s.length()>0) {
cout << "Halting! Unknown compression type: " << &s[0] << endl;
exit(-5);
throw std::runtime_error(std::string("Halting! Unknown compression type: ") + s);
}
s=getAttrValue("compressedLen", attr);
if(s.length()>0) m_compressLen = (uLong)atoi(&s[0]);
Expand Down Expand Up @@ -473,9 +473,7 @@ void mzpSAXMzxmlHandler::decode32(){
// an additional check of the data file integrity can be performed
int length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize );
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);
throw std::runtime_error(std::string("Decoded size ") + std::to_string(length) + " and required size " + std::to_string((unsigned long)size) + " don't match: possible corrupted file.");
}
}

Expand Down Expand Up @@ -518,9 +516,7 @@ void mzpSAXMzxmlHandler::decode64(){
// an additional check of the data file integrity can be performed
int length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize );
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);
throw std::runtime_error(std::string("Decoded size ") + std::to_string(length) + " and required size " + std::to_string((unsigned long)size) + " don't match: possible corrupted file.");
}
}

Expand Down Expand Up @@ -655,8 +651,7 @@ bool mzpSAXMzxmlHandler::generateIndexOffset() {
char *pStr;

if (f==NULL){
cout << "Error cannot open file " << m_strFileName[0] << endl;
exit(EXIT_FAILURE);
throw std::runtime_error(std::string("Error cannot open file ") + m_strFileName);
}

bool bReadingFirstSpectrum = true;
Expand Down