Well at this stage I'm trying anything/everything. I've been trying for over a week now to use proteowizard's default bjam system and that has not worked out at all.
I only need to read open source file formats: mzXML mzML mzData . All I want to do is to write a function that is passed a file name and a scan number. The function returns a C++ map<double, double> where the key is m/z of the peak and the value is the intensity of the peak. I didn't think this was going to be so hard. Can someone tell me what the minimum set of files are that I need to accomplish my task? What I mean is: which *.cpp and *.hpp files do I need to have in my source directory to enable reading of open source data file formats? I'm happy to use the source code inside the TPP trunk I just don't know what to grab. Thanks Damian On Dec 10, 12:55 pm, Brian Pratt <[email protected]> wrote: > Are you using the TPP build system, and its copy of ProteoWizard, or > are you using the official ProteoWizard build system? If it's the > latter you might be better asking on the proteowizard support list. > > Brian > > On Fri, Dec 10, 2010 at 6:57 AM, GATTACA <[email protected]> wrote: > > Hello. > > > I'm trying to compile a simple C++ program to read in an mzXML file > > and print to the screen the spectrum of a given scan number. I'm using > > proteowizard (revision 2414) to do this but without much luck. > > > There seems to be a problem with linking the files. When I compile my > > program with this command: > > g++ -Wall -I./pwiz_src pwizReader.cpp -o pwizReader.exe > > > I get the following error messages: > > /tmp/cclnMeVZ.o: In function `main': > > pwizReader.cpp:(.text+0x102): undefined reference to > > `pwiz::msdata::MSDataFile::MSDataFile(std::basic_string<char, > > std::char_traits<char>, std::allocator<char> > const&, > > pwiz::msdata::Reader const*, bool)' > > pwizReader.cpp:(.text+0x1bd): undefined reference to > > `pwiz::msdata::id::value(std::basic_string<char, > > std::char_traits<char>, std::allocator<char> > const&, > > std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' > > pwizReader.cpp:(.text+0x299): undefined reference to > > `pwiz::msdata::MSData::~MSData()' > > pwizReader.cpp:(.text+0x30e): undefined reference to > > `pwiz::msdata::Spectrum::getMZIntensityPairs(std::vector<pwiz::msdata::MZIntensityPair, > > std::allocator<pwiz::msdata::MZIntensityPair> >&) const' > > /tmp/cclnMeVZ.o: In function > > `pwiz::msdata::MSDataFile::~MSDataFile()': > > pwizReader.cpp: > > (.text._ZN4pwiz6msdata10MSDataFileD1Ev[pwiz::msdata::MSDataFile::~MSDataFile()] > > +0x8): undefined reference to `pwiz::msdata::MSData::~MSData()' > > /tmp/cclnMeVZ.o: In function > > `pwiz::msdata::MSDataFile::~MSDataFile()': > > pwizReader.cpp: > > (.text._ZN4pwiz6msdata10MSDataFileD0Ev[pwiz::msdata::MSDataFile::~MSDataFile()] > > +0xc): undefined reference to `pwiz::msdata::MSData::~MSData()' > > /tmp/cclnMeVZ.o:(.rodata._ZTIN4pwiz6msdata10MSDataFileE[typeinfo for > > pwiz::msdata::MSDataFile]+0x10): undefined reference to `typeinfo for > > pwiz::msdata::MSData' > > collect2: ld returned 1 exit status > > > These errors tell me that compiling isn't the issue but something is > > going wrong with the linking. > > > Is there something obvious I'm missing here? > > Thanks in advance for any and all help. > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
