Re: [proteowizard-developer] Looking for an example how to manipulate Spectra in MSData and than serialize it

[Matt C. <mat...@gm...>]

Hi Witold,

Is this pseudocode? A default-constructed MSData document will have a default-constructed 
spectrumListPtr, which get() will always return NULL for. The compile error is because 
SpectrumIterator returns cached spectra by const-reference. If you want a copy of the actual 
SpectrumPtr, you need to use the sl->spectrum() method. But to make changes to a SpectrumList, you 
need to use the in-memory SpectrumListSimple or define your own SpectrumList subclass. Basically 
avoid SpectrumIterator entirely and add new spectra to a SpectrumListSimple instead of trying to 
modify existing spectra. All you need to know is in:
pwiz\data\msdata\examples.cpp (initializeTiny())

BTW MS_Th is not an intensity unit, but pwiz doesn't do semantic validation so it won't throw an 
error on it. :)

Hope this helps,
-Matt

On 11/15/2012 3:41 AM, Witold E Wolski wrote:
> Hi,
>
> I would like to know how to change spectrum content in a MSData object and than to serialise it.
>
> What I have tried is something on this line (but it does not work).
>
> - get spectrumListPtr
> - iterate over spectrumList
> - call setMZIntensityArrays on the iterator
>
> pwiz::msdata::MSData msd;
> pwiz::msdata::SpectrumListPtr sl = msd.run.spectrumListPtr;
> if (sl.get())
>      {
>        std::cout << "# of spectra: " << sl->size() << std::endl;
>        pwiz::msdata::SpectrumIterator it(*sl);
>        pwiz::msdata::SpectrumIterator end;
>        std::vector<double> mz(500,1.),intens(500,10.);
>        int i=0;
>        for(; it !=end ; ++it, ++i){
>            std::cout << i << std::endl;
>            it->setMZIntensityArrays(mz,intens,pwiz::cv::MS_Th); // compilation error: passing ‘const
> pwiz::msdata::Spectrum’ as ‘this’ argument of ‘void pwiz:: ...
>          }
>      }
>    pwiz::msdata::MSDataFile::write(msd, filenameOut, pwiz::msdata::MSDataFile::Format_mzXML); //
> uncomment if you want mzXML
>
>
> Can anyone point me to example code how to do it properly.
>
> Thx
> Witold