Hi Matthias,
I looked at an example file and supporting this in pwiz is
straightforward, but I don't have time to work on it today. If you want
to patch it in yourself, look at:
ChromatogramList_Thermo.cpp
There's two member functions of that class that will need updating,
createIndex() and chromatogram().
Look for the line "case 5: // generate "Total Scan" chromatogram for
entire run", which is the PDA case, which is another kind of detector
that Thermo instruments can use. The ECD chromatograms should be handled
very similarly.
The ECD chromatogram is accessed through Controller_Analog and getting a
chromatogram from it would be like:
rawfile_->setCurrentController(Controller_Analog, 1);
auto_ptr<ChromatogramData> cd = rawfile_->getChromatogramData(
Type_TIC, Operator_None, Type_MassRange,
"", "", "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
The only thing that I'm not sure about is whether the NumSpectra
variable still applies when the ECD doesn't collect any spectra. In that
case, there'd have to be some other way to get the maximum retention time.
Modifying pwiz should be much easier than trying to work with the raw XDK.
-Matt
Natalie Tasman wrote:
> Matthias,
>
> I'm glad to hear that there's another enthusiatic developer interested
> in the Thermo converter. In readw, I suggest looking at the
> '#import'-ed Xrawfile2.dll header, which shows which COM calls are
> available. There is a .doc file in the SDK describing all of the
> calls. Unfortunately, it is sometimes incomplete and poorly documents
> some important calls. There are notes in the readw source code where
> we've encountered this.
>
> Also, the thermo reader in the msconvert code does a nice job of
> writing C++ wrapper functions for the rawfile access, so that's
> another great place to start.
>
> -Natalie
>
> On Fri, Apr 17, 2009 at 3:10 AM, brennmat <[email protected]
> <mailto:[email protected]>> wrote:
>
>
>
>
> On Apr 16, 6:29 pm, Natalie Tasman <[email protected]
> <mailto:[email protected]>> wrote:
> > Hi Mattias,
> >
> > To get started with Xcalibur, you might want to look at the
> "XDK" for
> > examples.
>
> That's what I did. I looked at the HTML documentation and the
> examples. However, the HTML stuff does not give detailed information
> on the objects and datatypes available, and the code examples are in
> VisualBasic (I do not speak VisualBasic at all).
>
> > But I do think it will be easier if you can just use and/or
> adapt existing
> > tools.
>
> I agree, but it might still be fun and educational to get my hands
> dirty...
>
> Thanks
> Matthias
>
>
>
>
> >
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