You could probably just hack up the mzxml2search code from TPP. If you build mzxml2search you'll get a build of pwiz out of it as well. That doesn't quite meet the goal of a tidy little standalone built of proteowizard since you need to have the whole TPP project to get it, but it does build with gnu make which is desireable.
Brian On Sat, Dec 11, 2010 at 1:04 PM, GATTACA <[email protected]> wrote: > 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. > > -- 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.
