Dear Matt I tried to apply your suggestion to the code. The modified file is here:
http://homepages.eawag.ch/~brennmat/stuff/Xcalibur/pwiz/ChromatogramList_Thermo.cpp However, I have to admit I did not really understand what I was doing. Also, when I opened the project with MS Visual C++ 2008, the project needed to be converted. I did not know what else to do, so I agreed to convert it. If I try to build the project, the build stops with the following: ----------- Build Log Build started: Project: pwiz, Configuration: Debug| Win32 Command Lines Creating temporary file "C: \DOCUME~1\MATTHI~1\LOCALS~1\Temp\BAT00000440802108.bat" with contents [ @echo off cd c:\Documents and Settings\Matthias Brennwald\Desktop\pwiz_1.5.2\ \build bjam debug -q -n if errorlevel 1 goto VCReportError goto VCEnd :VCReportError echo Project : error PRJ0019: A tool returned an error code from "Performing Makefile project actions" exit 1 :VCEnd ] Creating command line "C:\DOCUME~1\MATTHI~1\LOCALS~1\Temp \BAT00000440802108.bat" Output Window Performing Makefile project actions The system cannot find the path specified. 'bjam' is not recognized as an internal or external command, operable program or batch file. Project : error PRJ0019: A tool returned an error code from "Performing Makefile project actions" Results Build log was saved at "file://c:\Documents and Settings \Matthias Brennwald\Desktop\pwiz_1.5.2\Debug\BuildLog.htm" pwiz - 1 error(s), 0 warning(s) ----------- I have no idea how to proceed with this... what do you think? Matthias On Apr 17, 7:47 pm, Matthew Chambers <[email protected]> wrote: > 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 --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
