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[proteowizard-commit] SF.net SVN: proteowizard: [133] trunk/pwiz/pwiz/data
|
From: <ch...@us...> - 2008-04-24 14:37:44
|
Revision: 133
http://proteowizard.svn.sourceforge.net/proteowizard/?rev=133&view=rev
Author: chambm
Date: 2008-04-24 07:37:48 -0700 (Thu, 24 Apr 2008)
Log Message:
-----------
- added and made use of some necessary terms for chromatogram handling to the CV (the ones I suggested to psidev-ms)
- added chromatogram building to Reader_Thermo
- TODO: make chromatogram building smarter and move it outside the Reader :)
- separated Reader_Thermo into 4 separate translation units:
* Reader_Thermo.cpp/hpp
* SpectrumList_Thermo.cpp/hpp
* ChromatogramList_Thermo.cpp/hpp
* Reader_Thermo_Detail.cpp/hpp (translates pwiz::raw enums to CVIDs)
- added chromatogram checking (only for "TIC") to Reader_Thermo_Test
* TODO: expand chromatogram test to include testing binary data?
* TODO: we need a small example SRM file for Reader_Thermo_Test
- changed from using anonymous namespace to "detail" namespace, like boost
* TODO: discuss doing this for all anonymous namespaces (which are very ugly in MSVC :( )
Modified Paths:
--------------
trunk/pwiz/pwiz/data/msdata/cv.cpp
trunk/pwiz/pwiz/data/msdata/cv.hpp
trunk/pwiz/pwiz/data/vendor_readers/Jamfile
trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo.cpp
trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp
Added Paths:
-----------
trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.cpp
trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.hpp
trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.cpp
trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.hpp
Modified: trunk/pwiz/pwiz/data/msdata/cv.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/cv.cpp 2008-04-24 13:50:25 UTC (rev 132)
+++ trunk/pwiz/pwiz/data/msdata/cv.cpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -646,6 +646,10 @@
{MS_ProteinLynx_Global_Server_mass_spectrum_XML_file, "MS:1000614", "ProteinLynx Global Server mass spectrum XML file", "Peak list file format used by ProteinLynx Global Server."},
{MS_ProteoWizard, "MS:1000615", "ProteoWizard", "ProteoWizard software for data analysis. Currently developed and maintained by Darren Kessner at Parag Mallick's lab SFCAP at Cedars-Sinai."},
{MS_preset_scan_configuration, "MS:1000616", "preset scan configuration", "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time."},
+ {MS_selected_ion_chromatogram, "MS:1000999", "selected ion chromatogram", "blah"},
+ {MS_precursor_m_z, "MS:1000998", "precursor m/z", "blah"},
+ {MS_product_m_z, "MS:1000997", "product m/z", "blah"},
+ {MS_total_ion_chromatogram, "MS:1000996", "total ion chromatogram", "blah"}
}; // termInfos_
Modified: trunk/pwiz/pwiz/data/msdata/cv.hpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/cv.hpp 2008-04-24 13:50:25 UTC (rev 132)
+++ trunk/pwiz/pwiz/data/msdata/cv.hpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -747,7 +747,11 @@
MS_ProteinLynx_Global_Server_mass_spectrum_XML_file = 1000614,
MS_ProteoWizard = 1000615,
MS_pwiz = MS_ProteoWizard,
- MS_preset_scan_configuration = 1000616
+ MS_preset_scan_configuration = 1000616,
+ MS_selected_ion_chromatogram = 1000999,
+ MS_precursor_m_z = 1000998,
+ MS_product_m_z = 1000997,
+ MS_total_ion_chromatogram = 1000996
}; // enum CVID
Added: trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.cpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.cpp (rev 0)
+++ trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.cpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -0,0 +1,66 @@
+#include "data/msdata/CVTranslator.hpp"
+#include "utility/vendor_api/thermo/RawFile.h"
+#include "utility/misc/SHA1Calculator.hpp"
+#include "boost/shared_ptr.hpp"
+#include "boost/lexical_cast.hpp"
+#include "boost/algorithm/string.hpp"
+#include "boost/filesystem/path.hpp"
+#include "Reader_Thermo_Detail.hpp"
+#include "ChromatogramList_Thermo.hpp"
+#include <iostream>
+#include <stdexcept>
+
+
+namespace pwiz {
+namespace msdata {
+namespace detail {
+
+ChromatogramList_Thermo::ChromatogramList_Thermo()
+{
+}
+
+
+size_t ChromatogramList_Thermo::size() const
+{
+ return index_.size();
+}
+
+
+const ChromatogramIdentity& ChromatogramList_Thermo::chromatogramIdentity(size_t index) const
+{
+ if (index>size())
+ throw runtime_error(("[ChromatogramList_Thermo::chromatogramIdentity()] Bad index: "
+ + lexical_cast<string>(index)).c_str());
+ return reinterpret_cast<const ChromatogramIdentity&>(index_[index]);
+}
+
+
+size_t ChromatogramList_Thermo::find(const string& id) const
+{
+ map<string, size_t>::const_iterator itr = idMap_.find(id);
+ if (itr != idMap_.end())
+ return itr->second;
+
+ return size();
+}
+
+
+size_t ChromatogramList_Thermo::findNative(const string& nativeID) const
+{
+ return find(nativeID);
+}
+
+
+ChromatogramPtr ChromatogramList_Thermo::chromatogram(size_t index, bool getBinaryData) const
+{
+ if (index>size())
+ throw runtime_error(("[ChromatogramList_Thermo::chromatogram()] Bad index: "
+ + lexical_cast<string>(index)).c_str());
+
+ // chromatogram is created in memory, so it always has binary data
+ return index_[index];
+}
+
+} // detail
+} // msdata
+} // pwiz
Added: trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.hpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.hpp (rev 0)
+++ trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.hpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -0,0 +1,37 @@
+#ifndef _CHROMATOGRAMLIST_THERMO_
+#define _CHROMATOGRAMLIST_THERMO_
+#include "data/msdata/MSData.hpp"
+#include "utility/vendor_api/thermo/RawFile.h"
+#include <map>
+#include <vector>
+
+using namespace std;
+using boost::shared_ptr;
+using boost::lexical_cast;
+using boost::bad_lexical_cast;
+using namespace pwiz::raw;
+
+namespace pwiz {
+namespace msdata {
+namespace detail {
+
+class ChromatogramList_Thermo : public ChromatogramList
+{
+public:
+
+ ChromatogramList_Thermo();
+ virtual size_t size() const;
+ virtual const ChromatogramIdentity& chromatogramIdentity(size_t index) const;
+ virtual size_t find(const string& id) const;
+ virtual size_t findNative(const string& nativeID) const;
+ virtual ChromatogramPtr chromatogram(size_t index, bool getBinaryData) const;
+
+ map<string, size_t> idMap_;
+ vector<ChromatogramPtr> index_;
+};
+
+} // detail
+} // msdata
+} // pwiz
+
+#endif // _CHROMATOGRAMLIST_THERMO_
Modified: trunk/pwiz/pwiz/data/vendor_readers/Jamfile
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/Jamfile 2008-04-24 13:50:25 UTC (rev 132)
+++ trunk/pwiz/pwiz/data/vendor_readers/Jamfile 2008-04-24 14:37:48 UTC (rev 133)
@@ -33,7 +33,7 @@
lib pwiz_data_vendor_readers
: ExtendedReaderList.cpp
- Reader_Thermo.cpp
+ [ glob *_Thermo*.cpp ]
../../utility/vendor_api/thermo
../msdata//pwiz_data_msdata
;
Modified: trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo.cpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo.cpp 2008-04-24 13:50:25 UTC (rev 132)
+++ trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo.cpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -23,7 +23,6 @@
#include "Reader_Thermo.hpp"
-
namespace {
// helper function used by both forms (real and stubbed) of Reader_Thermo
bool _hasRAWHeader(const std::string& head)
@@ -52,6 +51,9 @@
#include "boost/lexical_cast.hpp"
#include "boost/algorithm/string.hpp"
#include "boost/filesystem/path.hpp"
+#include "Reader_Thermo_Detail.hpp"
+#include "SpectrumList_Thermo.hpp"
+#include "ChromatogramList_Thermo.hpp"
#include <iostream>
#include <stdexcept>
@@ -67,333 +69,10 @@
using namespace pwiz::raw;
using namespace pwiz::util;
namespace bfs = boost::filesystem;
+using namespace pwiz::msdata::detail;
//
-// SpectrumList_Thermo
-//
-
-
-namespace {
-
-
-class SpectrumList_Thermo : public SpectrumList
-{
- public:
-
- SpectrumList_Thermo(const MSData& msd, shared_ptr<RawFile> rawfile);
- virtual size_t size() const;
- virtual const SpectrumIdentity& spectrumIdentity(size_t index) const;
- virtual size_t find(const string& id) const;
- virtual size_t findNative(const string& nativeID) const;
- virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const;
-
- private:
-
- const MSData& msd_;
- shared_ptr<RawFile> rawfile_;
- size_t size_;
- mutable vector<SpectrumPtr> spectrumCache_;
- vector<SpectrumIdentity> index_;
-
- void createIndex();
- string findPrecursorID(int precursorMsLevel, size_t index) const;
-};
-
-
-SpectrumList_Thermo::SpectrumList_Thermo(const MSData& msd, shared_ptr<RawFile> rawfile)
-: msd_(msd), rawfile_(rawfile),
- size_(rawfile->value(NumSpectra)),
- spectrumCache_(size_), index_(size_)
-{
- createIndex();
-}
-
-
-size_t SpectrumList_Thermo::size() const
-{
- return size_;
-}
-
-
-const SpectrumIdentity& SpectrumList_Thermo::spectrumIdentity(size_t index) const
-{
- if (index>size_)
- throw runtime_error(("[SpectrumList_Thermo::spectrumIdentity()] Bad index: "
- + lexical_cast<string>(index)).c_str());
- return index_[index];
-}
-
-
-size_t SpectrumList_Thermo::find(const string& id) const
-{
- try
- {
- size_t scanNumber = lexical_cast<size_t>(id);
- if (scanNumber>=1 && scanNumber<=size())
- return scanNumber-1;
- }
- catch (bad_lexical_cast&) {}
-
- return size();
-}
-
-
-size_t SpectrumList_Thermo::findNative(const string& nativeID) const
-{
- return find(nativeID);
-}
-
-
-CVParam translateAsScanningMethod(ScanType scanType)
-{
- switch (scanType)
- {
- case ScanType_Full:
- return MS_full_scan;
- case ScanType_Zoom:
- return MS_zoom_scan;
- case ScanType_SIM:
- return MS_SIM;
- case ScanType_SRM:
- return MS_SRM;
- case ScanType_CRM:
- return MS_CRM;
- case ScanType_Unknown:
- default:
- return CVParam();
- }
-}
-
-
-CVParam translateAsSpectrumType(ScanType scanType)
-{
- switch (scanType)
- {
- case ScanType_Full:
- case ScanType_Zoom:
- return MS_MSn_spectrum;
- case ScanType_SIM:
- return MS_SIM_spectrum;
- case ScanType_SRM:
- return MS_SRM_spectrum;
- case ScanType_CRM:
- return MS_CRM_spectrum;
- case ScanType_Unknown:
- default:
- return CVParam();
- }
-}
-
-
-CVParam translate(MassAnalyzerType type)
-{
- switch (type)
- {
- case MassAnalyzerType_ITMS: return MS_ion_trap;
- case MassAnalyzerType_FTMS: return MS_FT_ICR;
- case MassAnalyzerType_TOFMS: return MS_time_of_flight;
- case MassAnalyzerType_TQMS: return MS_quadrupole;
- case MassAnalyzerType_SQMS: return MS_quadrupole;
- case MassAnalyzerType_Sector: return MS_magnetic_sector;
- case MassAnalyzerType_Unknown:
- default:
- return CVParam();
- }
-}
-
-
-CVParam translateAsIonizationType(IonizationType ionizationType)
-{
- switch (ionizationType)
- {
- case IonizationType_EI: return MS_electron_ionization;
- case IonizationType_CI: return MS_chemical_ionization;
- case IonizationType_FAB: return MS_fast_atom_bombardment_ionization;
- case IonizationType_ESI: return MS_electrospray_ionization;
- case IonizationType_NSI: return MS_nanoelectrospray;
- case IonizationType_APCI: return MS_atmospheric_pressure_chemical_ionization;
- //case IonizationType_TSP: return MS_thermospray_ionization;
- case IonizationType_FD: return MS_field_desorption;
- case IonizationType_MALDI: return MS_matrix_assisted_laser_desorption_ionization;
- case IonizationType_GD: return MS_glow_discharge_ionization;
- case IonizationType_Unknown:
- default:
- return CVParam();
- }
-}
-
-
-CVParam translateAsInletType(IonizationType ionizationType)
-{
- switch (ionizationType)
- {
- //case IonizationType_EI: return MS_electron_ionization;
- //case IonizationType_CI: return MS_chemical_ionization;
- case IonizationType_FAB: return MS_continuous_flow_fast_atom_bombardment;
- case IonizationType_ESI: return MS_electrospray_inlet;
- case IonizationType_NSI: return MS_nanospray_inlet;
- //case IonizationType_APCI: return MS_atmospheric_pressure_chemical_ionization;
- case IonizationType_TSP: return MS_thermospray_inlet;
- //case IonizationType_FD: return MS_field_desorption;
- //case IonizationType_MALDI: return MS_matrix_assisted_laser_desorption_ionization;
- //case IonizationType_GD: return MS_glow_discharge_ionization;
- case IonizationType_Unknown:
- default:
- return CVParam();
- }
-}
-
-
-CVParam translate(PolarityType polarityType)
-{
- switch (polarityType)
- {
- case PolarityType_Positive:
- return MS_positive_scan;
- case PolarityType_Negative:
- return MS_negative_scan;
- case PolarityType_Unknown:
- default:
- return CVParam();
- }
-}
-
-
-SpectrumPtr SpectrumList_Thermo::spectrum(size_t index, bool getBinaryData) const
-{
- if (index>size_)
- throw runtime_error(("[SpectrumList_Thermo::spectrum()] Bad index: "
- + lexical_cast<string>(index)).c_str());
-
- // returned cached Spectrum if possible
-
- if (!getBinaryData && spectrumCache_[index].get())
- return spectrumCache_[index];
-
- // allocate a new Spectrum
-
- SpectrumPtr result(new Spectrum);
- if (!result.get())
- throw runtime_error("[SpectrumList_Thermo::spectrum()] Allocation error.");
-
- // get rawfile::ScanInfo and translate
-
- long scanNumber = static_cast<int>(index) + 1;
- auto_ptr<ScanInfo> scanInfo = rawfile_->getScanInfo(scanNumber);
- if (!scanInfo.get())
- throw runtime_error("[SpectrumList_Thermo::spectrum()] Error retrieving ScanInfo.");
-
- result->index = index;
- result->id = result->nativeID = lexical_cast<string>(scanNumber);
-
- SpectrumDescription& sd = result->spectrumDescription;
- Scan& scan = sd.scan;
-
- if (msd_.instrumentPtrs.empty())
- throw runtime_error("[SpectrumList_Thermo::spectrum()] No instruments defined.");
- scan.instrumentPtr = msd_.instrumentPtrs[0];
-
- string filterString = scanInfo->filter();
-
- scan.cvParams.push_back(CVParam(MS_filter_string, filterString));
-
- string scanEvent = scanInfo->trailerExtraValue("Scan Event:");
- scan.cvParams.push_back(CVParam(MS_preset_scan_configuration, scanEvent));
-
- /* currently non-standard for mzML
- if (scanInfo->massAnalyzerType_ > MassAnalyzerType_Unknown)
- scan.cvParams.push_back(translate(scanInfo->massAnalyzerType_));*/
-
- result->set(MS_ms_level, scanInfo->msLevel());
-
- ScanType scanType = scanInfo->scanType();
- if (scanType!=ScanType_Unknown)
- {
- result->cvParams.push_back(translateAsSpectrumType(scanType));
- scan.cvParams.push_back(translateAsScanningMethod(scanType));
- }
-
- PolarityType polarityType = scanInfo->polarityType();
- if (polarityType!=PolarityType_Unknown) scan.cvParams.push_back(translate(polarityType));
-
- if (scanInfo->isProfileScan()) sd.cvParams.push_back(MS_profile_mass_spectrum);
- else if (scanInfo->isCentroidScan()) sd.cvParams.push_back(MS_centroid_mass_spectrum);
-
- scan.cvParams.push_back(CVParam(MS_scan_time, scanInfo->startTime(), MS_minute));
- sd.cvParams.push_back(CVParam(MS_lowest_m_z_value, scanInfo->lowMass()));
- sd.cvParams.push_back(CVParam(MS_highest_m_z_value, scanInfo->highMass()));
- sd.cvParams.push_back(CVParam(MS_base_peak_m_z, scanInfo->basePeakMass()));
- sd.cvParams.push_back(CVParam(MS_base_peak_intensity, scanInfo->basePeakIntensity()));
- sd.cvParams.push_back(CVParam(MS_total_ion_current, scanInfo->totalIonCurrent()));
-
- for (long i=0, precursorCount=scanInfo->parentCount(); i<precursorCount; i++)
- {
- // Note: we report what RawFile gives us, which comes from the filter string;
- // we can look in the trailer extra values for better (but still unreliable)
- // info. Precursor recalculation should be done outside the Reader.
-
- Precursor precursor;
-
- // TODO: better test here for data dependent modes
- if ((scanType==ScanType_Full || scanType==ScanType_Zoom ) && scanInfo->msLevel() > 1)
- precursor.spectrumID = findPrecursorID(scanInfo->msLevel()-1, index);
-
- precursor.ionSelection.cvParams.push_back(CVParam(MS_m_z, scanInfo->parentMass(i)));
- // TODO: determine precursor intensity? (parentEnergy is not precursor intensity!)
- precursor.activation.cvParams.push_back(CVParam(MS_collision_energy, scanInfo->parentEnergy(i)));
- sd.precursors.push_back(precursor);
- }
-
- if (getBinaryData)
- {
- auto_ptr<raw::MassList> massList =
- rawfile_->getMassList(scanNumber, "", raw::Cutoff_None, 0, 0, false);
-
- result->setMZIntensityPairs(reinterpret_cast<MZIntensityPair*>(massList->data()),
- massList->size());
- }
-
- // save to cache if no binary data
-
- if (!getBinaryData && !spectrumCache_[index].get())
- spectrumCache_[index] = result;
-
- return result;
-}
-
-
-void SpectrumList_Thermo::createIndex()
-{
- for (size_t i=0; i<size_; i++)
- {
- SpectrumIdentity& si = index_[i];
- si.index = i;
- si.id = si.nativeID = lexical_cast<string>(i+1);
- }
-}
-
-
-string SpectrumList_Thermo::findPrecursorID(int precursorMsLevel, size_t index) const
-{
- // for MSn spectra (n > 1): return first scan with MSn-1
-
- while (index>0)
- {
- --index;
- SpectrumPtr candidate = spectrum(index, false);
- if (candidate->cvParam(MS_ms_level).valueAs<int>() == precursorMsLevel)
- return candidate->id;
- }
-
- return "";
-}
-
-
-} // namespace
-
-
-//
// Reader_Thermo
//
@@ -526,8 +205,11 @@
shared_ptr<RawFile> rawfile(RawFile::create(filename).release());
rawfile->setCurrentController(Controller_MS, 1);
- result.run.spectrumListPtr = SpectrumListPtr(new SpectrumList_Thermo(result, rawfile));
+ SpectrumList_Thermo* sl = new SpectrumList_Thermo(result, rawfile);
+ result.run.spectrumListPtr = SpectrumListPtr(sl);
+ result.run.chromatogramListPtr = sl->Chromatograms();
+
fillInMetadata(filename, *rawfile, result);
}
Added: trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.cpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.cpp (rev 0)
+++ trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.cpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -0,0 +1,123 @@
+#include "Reader_Thermo_Detail.hpp"
+
+namespace pwiz {
+namespace msdata {
+namespace detail {
+
+CVParam translateAsScanningMethod(ScanType scanType)
+{
+ switch (scanType)
+ {
+ case ScanType_Full:
+ return MS_full_scan;
+ case ScanType_Zoom:
+ return MS_zoom_scan;
+ case ScanType_SIM:
+ return MS_SIM;
+ case ScanType_SRM:
+ return MS_SRM;
+ case ScanType_CRM:
+ return MS_CRM;
+ case ScanType_Unknown:
+ default:
+ return CVParam();
+ }
+}
+
+
+CVParam translateAsSpectrumType(ScanType scanType)
+{
+ switch (scanType)
+ {
+ case ScanType_Full:
+ case ScanType_Zoom:
+ return MS_MSn_spectrum;
+ case ScanType_SIM:
+ return MS_SIM_spectrum;
+ case ScanType_SRM:
+ return MS_SRM_spectrum;
+ case ScanType_CRM:
+ return MS_CRM_spectrum;
+ case ScanType_Unknown:
+ default:
+ return CVParam();
+ }
+}
+
+
+CVParam translate(MassAnalyzerType type)
+{
+ switch (type)
+ {
+ case MassAnalyzerType_ITMS: return MS_ion_trap;
+ case MassAnalyzerType_FTMS: return MS_FT_ICR;
+ case MassAnalyzerType_TOFMS: return MS_time_of_flight;
+ case MassAnalyzerType_TQMS: return MS_quadrupole;
+ case MassAnalyzerType_SQMS: return MS_quadrupole;
+ case MassAnalyzerType_Sector: return MS_magnetic_sector;
+ case MassAnalyzerType_Unknown:
+ default:
+ return CVParam();
+ }
+}
+
+
+CVParam translateAsIonizationType(IonizationType ionizationType)
+{
+ switch (ionizationType)
+ {
+ case IonizationType_EI: return MS_electron_ionization;
+ case IonizationType_CI: return MS_chemical_ionization;
+ case IonizationType_FAB: return MS_fast_atom_bombardment_ionization;
+ case IonizationType_ESI: return MS_electrospray_ionization;
+ case IonizationType_NSI: return MS_nanoelectrospray;
+ case IonizationType_APCI: return MS_atmospheric_pressure_chemical_ionization;
+ //case IonizationType_TSP: return MS_thermospray_ionization;
+ case IonizationType_FD: return MS_field_desorption;
+ case IonizationType_MALDI: return MS_matrix_assisted_laser_desorption_ionization;
+ case IonizationType_GD: return MS_glow_discharge_ionization;
+ case IonizationType_Unknown:
+ default:
+ return CVParam();
+ }
+}
+
+
+CVParam translateAsInletType(IonizationType ionizationType)
+{
+ switch (ionizationType)
+ {
+ //case IonizationType_EI: return MS_electron_ionization;
+ //case IonizationType_CI: return MS_chemical_ionization;
+ case IonizationType_FAB: return MS_continuous_flow_fast_atom_bombardment;
+ case IonizationType_ESI: return MS_electrospray_inlet;
+ case IonizationType_NSI: return MS_nanospray_inlet;
+ //case IonizationType_APCI: return MS_atmospheric_pressure_chemical_ionization;
+ case IonizationType_TSP: return MS_thermospray_inlet;
+ //case IonizationType_FD: return MS_field_desorption;
+ //case IonizationType_MALDI: return MS_matrix_assisted_laser_desorption_ionization;
+ //case IonizationType_GD: return MS_glow_discharge_ionization;
+ case IonizationType_Unknown:
+ default:
+ return CVParam();
+ }
+}
+
+
+CVParam translate(PolarityType polarityType)
+{
+ switch (polarityType)
+ {
+ case PolarityType_Positive:
+ return MS_positive_scan;
+ case PolarityType_Negative:
+ return MS_negative_scan;
+ case PolarityType_Unknown:
+ default:
+ return CVParam();
+ }
+}
+
+} // detail
+} // msdata
+} // pwiz
Added: trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.hpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.hpp (rev 0)
+++ trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.hpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -0,0 +1,24 @@
+#ifndef _READER_THERMO_DETAIL_HPP_
+#define _READER_THERMO_DETAIL_HPP_
+
+#include "data/msdata/MSData.hpp"
+#include "utility/vendor_api/thermo/ScanFilter.h"
+
+using namespace pwiz::raw;
+
+namespace pwiz {
+namespace msdata {
+namespace detail {
+
+CVParam translateAsScanningMethod(ScanType scanType);
+CVParam translateAsSpectrumType(ScanType scanType);
+CVParam translate(MassAnalyzerType type);
+CVParam translateAsIonizationType(IonizationType ionizationType);
+CVParam translateAsInletType(IonizationType ionizationType);
+CVParam translate(PolarityType polarityType);
+
+} // detail
+} // msdata
+} // pwiz
+
+#endif // _READER_THERMO_DETAIL_HPP_
Modified: trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp 2008-04-24 13:50:25 UTC (rev 132)
+++ trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp 2008-04-24 14:37:48 UTC (rev 133)
@@ -140,8 +140,15 @@
const Precursor& precursor2 = spectrum->spectrumDescription.precursors[0];
unit_assert(precursor2.spectrumID == "2"); // previous ms1 scan
+ // test chromatogram list
+ unit_assert(msd.run.chromatogramListPtr.get());
+ ChromatogramList& cl = *msd.run.chromatogramListPtr;
+ if (os_) *os_ << "chromatogram list size: " << cl.size() << endl;
+ unit_assert(cl.size() == 1);
+ ChromatogramPtr chromatogram = cl.chromatogram(0, true);
+ unit_assert(chromatogram->id == "TIC");
+
// test file-level metadata
-
unit_assert(msd.fileDescription.fileContent.hasCVParam(MS_MSn_spectrum));
}
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