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[Sashimi-commit] SF.net SVN: sashimi: [3148] trunk/trans_proteomic_pipeline/src/mzXML/ converters/trapper/MassHunterInterface.cpp
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From: <spa...@us...> - 2008-04-25 00:44:12
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Revision: 3148
http://sashimi.svn.sourceforge.net/sashimi/?rev=3148&view=rev
Author: spacepod
Date: 2008-04-24 17:44:04 -0700 (Thu, 24 Apr 2008)
Log Message:
-----------
[trapper] improved error reporting
Modified Paths:
--------------
trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/MassHunterInterface.cpp
Modified: trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/MassHunterInterface.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/MassHunterInterface.cpp 2008-04-25 00:05:46 UTC (rev 3147)
+++ trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/MassHunterInterface.cpp 2008-04-25 00:44:04 UTC (rev 3148)
@@ -40,6 +40,7 @@
hr = comcall; \
if (hr != S_OK) { \
cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << ":" << endl; \
+ cerr << "HR = " << hr << endl; \
cerr << errMsg << endl; \
action; \
} \
@@ -169,24 +170,25 @@
try {
//IMsdrDataReaderPtr pMSDataReader;
- hr = CoCreateInstance(
+ COMCHECK(CoCreateInstance(
MH::CLSID_MassSpecDataReader,
NULL,
CLSCTX_INPROC_SERVER ,
MH::IID_IMsdrDataReader,
- (void**)&pMSDataReader_);
- if (hr != S_OK) {
- cerr << "ERROR - CoCreateInstance failed." << endl;
- return false;
- }
+ (void**)&pMSDataReader_),
+ "ERROR - CoCreateInstance failed.",
+ return false);
VARIANT_BOOL pRetVal = VARIANT_TRUE;
CComBSTR fileName(inputFileName_.c_str());
- hr = pMSDataReader_->OpenDataFile(
- fileName,
- &pRetVal);
+ COMCHECK(pMSDataReader_->OpenDataFile(
+ fileName,
+ &pRetVal),
+ "OpenDataFile",
+ return false);
//SysFreeString(fileName);
- if (FAILED(hr) || pRetVal == VARIANT_FALSE) {
+ // also check return value
+ if (pRetVal == VARIANT_FALSE) {
cerr << "Failed to open data folder" << endl;
return false;
}
@@ -196,11 +198,10 @@
// get scan file information
MH::BDA::IBDAFileInformationPtr pFileInfo;
- hr = pMSDataReader_->get_FileInformation(&pFileInfo);
- if (hr != S_OK) {
- cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << endl;
- return false;
- }
+ COMCHECK(pMSDataReader_->get_FileInformation(&pFileInfo),
+ "error getting file information",
+ return false);
+
DATE date;
pFileInfo->get_AcquisitionTime(&date);
COleDateTime dateTime(date);
@@ -218,19 +219,15 @@
// Get MS scan file information
MH::BDA::IBDAMSScanFileInformationPtr pScanInfo;
- hr = pMSDataReader_->get_MSScanFileInformation(&pScanInfo);
- if (hr != S_OK) {
- cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << endl;
- return false;
- }
+ COMCHECK(pMSDataReader_->get_MSScanFileInformation(&pScanInfo),
+ "get_MSScanFileInformation",
+ return false);
// get total number of scans
__int64 totalNumScans = 0;
- hr = pScanInfo->get_TotalScansPresent(&totalNumScans);
- if (hr != S_OK) {
- cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << endl;
- return false;
- }
+ COMCHECK(pScanInfo->get_TotalScansPresent(&totalNumScans),
+ "get_TotalScansPresent",
+ return false);
totalNumScans_ = (long)totalNumScans;
if (verbose_) {
@@ -241,7 +238,7 @@
// dual-mode detection
VARIANT_BOOL bDualMode = VARIANT_FALSE;
COMCHECK(pScanInfo->IsMultipleSpectraPerScanPresent(&bDualMode),
- cerr << "error checking if dual-mode" << endl,
+ "error in checking if file is dual-mode",
return false);
if (bDualMode == VARIANT_FALSE) {
cout << "single mode file" << endl;
@@ -252,7 +249,7 @@
// specifically record and detect if peak and/or profile data is present
MH::MSStorageMode storageMode;
COMCHECK(pScanInfo->get_SpectraFormat(&storageMode),
- cerr << "get SpectraFormat error" << endl,
+ "get SpectraFormat error",
return false);
// TODO: record this info in mzXML header;
@@ -301,11 +298,10 @@
// Get analyzer type
MH::DeviceType devType;
- hr = pScanInfo->get_DeviceType(&devType);
- if (hr != S_OK) {
- cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << endl;
- return false;
- }
+ COMCHECK(pScanInfo->get_DeviceType(&devType),
+ "get_DeviceType",
+ return false);
+
if (verbose_) {
cout << "Device Type: " << devType << endl;
}
@@ -331,11 +327,9 @@
// now that we have the device type, we can get the device name
BSTR tempBstr=NULL;
- hr=pFileInfo->GetDeviceName(devType, &tempBstr);
- if (hr != S_OK) {
- cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << endl;
- return false;
- }
+ COMCHECK(pFileInfo->GetDeviceName(devType, &tempBstr),
+ "GetDeviceName",
+ return false);
string modelName = convertBstrToString(tempBstr);
// TODO: waiting for Agilent instrument types in order to fill in MSTypes corrects
instrumentInfo_.instrumentModel_ = AGILENT_TOF;
@@ -347,11 +341,10 @@
// get ionization mode
MH::IonizationMode ionMode;
- hr = pScanInfo->get_IonModes(&ionMode);
- if (hr != S_OK) {
- cerr << "ERROR at " << __FILE__ << ", " << __LINE__ << endl;
- return false;
- }
+ COMCHECK(pScanInfo->get_IonModes(&ionMode),
+ "get_IonModes",
+ return false);
+
// TODO: check with Agilent if correct
MSIonizationType ionization;
switch (ionMode) {
@@ -418,7 +411,7 @@
CLSCTX_INPROC_SERVER ,
MH::BDA::IID_IBDAChromFilter,
(void**)&pChromFilter),
- cerr << "couldn't create chromfilter" << endl,
+ "couldn't create chromfilter",
return (false)
);
@@ -436,18 +429,16 @@
// extract the chromdata obj from the safearray-- I'm expecting only one
COMCHECK(pMSDataReader_->GetChromatogram(pChromFilter, &pSafeArrayChromData_),
- cerr << "Error getting TIC" << endl,
+ "Error getting TIC",
return (false));
// check to make sure that exactly one TIC was returned from the call
long numTIC = 0;
- hr = SafeArrayGetUBound(pSafeArrayChromData_, 1, &numTIC);
- if( S_OK != hr )
- {
- cerr <<"ERROR - SafeArrayGetUBound failed " << hr << endl;
- return false;
- }
+ COMCHECK(SafeArrayGetUBound(pSafeArrayChromData_, 1, &numTIC),
+ "SafeArrayGetUBound failed.",
+ return false);
+
// TODO: check ubonds result for 0 entries
if (numTIC < 0) {
cerr << "ERROR: no TICs found" << endl;
@@ -470,11 +461,10 @@
long dataPoints = 0;
- hr = pChromData_->get_TotalDataPoints(&dataPoints);
- if ( S_OK != hr ) {
- cerr << "Error getting total data points from TIC." << endl;
- return false;
- }
+ COMCHECK(pChromData_->get_TotalDataPoints(&dataPoints),
+ "Error getting total data points from TIC.",
+ return false);
+
int numMSspectra = dataPoints;
if (numMSspectra != totalNumScans_) {
@@ -483,11 +473,9 @@
}
// xArray is double[]
- hr = pChromData_->get_xArray(&pSafeArrayRetentionTimes_);
- if ( S_OK != hr ) {
- cerr << "Error getting XArray of TIC." << endl;
- return false;
- }
+ COMCHECK(pChromData_->get_xArray(&pSafeArrayRetentionTimes_),
+ "Error getting XArray of TIC.",
+ return false);
SafeArrayAccessData(pSafeArrayRetentionTimes_, reinterpret_cast<void**>(&retentionTimeArray_));
// pSafeArrayRetentionTimes_ is unaccessed in destructor
// set start, end time from retention times
@@ -495,27 +483,23 @@
endTimeInSec_ = retentionTimeArray_[totalNumScans_ - 1] * 60;
// yArray is float[]
- hr = pChromData_->get_yArray(&pSafeArrayTotalIonCurrents_);
- if ( S_OK != hr ) {
- cerr << "Error getting YArray of TIC." << endl;
- return false;
- }
+ COMCHECK(pChromData_->get_yArray(&pSafeArrayTotalIonCurrents_),
+ "Error getting YArray of TIC.",
+ return false);
SafeArrayAccessData(pSafeArrayTotalIonCurrents_, reinterpret_cast<void**>(&totalIonCurrentArray_));
// pSafeArrayTotalIonCurrents_ is unaccessed in destructor
// get base peak info
//CComPtr<MH::BDA::IBDAChromData> pChromDataBasePeaks;
- hr = pMSDataReader_->GetTIC(&pChromDataBasePeaks_);
- if ( S_OK != hr ) {
- cerr << "Error getting base peak chromatogram." << endl;
- return false;
- }
+ COMCHECK(pMSDataReader_->GetTIC(&pChromDataBasePeaks_),
+ "Error getting base peak chromatogram.",
+ return false);
+
// yArray is float[]
- hr = pChromDataBasePeaks_->get_yArray(&pSafeArrayBasePeakIntensities_);
- if ( S_OK != hr ) {
- cerr << "Error getting YArray of TIC." << endl;
- return false;
- }
+ COMCHECK(pChromDataBasePeaks_->get_yArray(&pSafeArrayBasePeakIntensities_),
+ "Error getting YArray of TIC.",
+ return false);
+
SafeArrayAccessData(pSafeArrayBasePeakIntensities_, reinterpret_cast<void**>(&basePeakIntensityArray_));
// pSafeArrayBasePeakIntensities_ is unaccessed in destructor
@@ -712,7 +696,7 @@
filter,
filterOnCentroid,
&pSpecData),
- cerr << "error getting spectrum " << curScanNum_ << endl,
+ "error getting spectrum " << curScanNum_,
return NULL);
hr = pSpecData->ConvertDataToMassUnits();
if(S_OK != hr)
@@ -726,7 +710,7 @@
// and record this info
MH::MSStorageMode spectrumMode; // centroid or profile?
COMCHECK(pSpecData->get_MSStorageMode(&spectrumMode),
- cerr << "error getting spec. mode " << curScanNum_ << endl,
+ "error getting spec. mode " << curScanNum_,
return NULL);
// sanity check:
if ((spectrumMode != MH::MSStorageMode_ProfileSpectrum)
@@ -775,7 +759,7 @@
CLSCTX_INPROC_SERVER ,
MH::IID_IMsdrChargeStateAssignmentFilter,
(void**)&pCsaFilter),
- cerr << "CoCreateInstance for charge state assignment filter failed, hr = " << hr,
+ "CoCreateInstance for charge state assignment filter failed.",
exit(1));
if (limitChargeState_) {
@@ -798,7 +782,7 @@
}
COMCHECK(pMSDataReader_->Deisotope(pSpecData, pCsaFilter),
- cerr << "Error in deisotoping, hr = " << hr << endl,
+ "Error in deisotoping, hr = " << hr,
exit(1));
}
@@ -806,7 +790,7 @@
//get scan ID
long scanID;
COMCHECK(pSpecData->get_ScanId(&scanID),
- cerr << "get ScanId error" << endl,
+ "get ScanId error",
return(NULL));
nativeToSequentialScanNums_[scanID] = curScanNum_;
curScan->nativeScanRef_.setCoordinateType(AGILENT);
@@ -816,7 +800,7 @@
// get scan polarity
MH::IonPolarity polarity;
COMCHECK(pSpecData->get_IonPolarity(&polarity),
- cerr << "ionpolarity error" << endl,
+ "ionpolarity error",
return(NULL));
switch(polarity) {
case MH::IonPolarity_Negative:
@@ -905,7 +889,7 @@
VARIANT_BOOL chargeSuccess = VARIANT_TRUE;
long charge = 0;
COMCHECK(pSpecData->GetPrecursorCharge(&charge, &chargeSuccess),
- cerr << "Error getting Precursor Charge for spectrum " << curScanNum_ << endl,
+ "Error getting Precursor Charge for spectrum " << curScanNum_,
return(NULL));
if (chargeSuccess == VARIANT_TRUE ) {
// record in our scan obj
@@ -918,7 +902,7 @@
double intensity = 0;
VARIANT_BOOL intSuccess = VARIANT_TRUE;
COMCHECK(pSpecData ->GetPrecursorIntensity(&intensity, &intSuccess),
- cerr << "error getting Precursor intensity for spectrum " << curScanNum_ << endl,
+ "error getting Precursor intensity for spectrum " << curScanNum_,
return(NULL));
if (intSuccess == VARIANT_TRUE) {
curScan->precursorIntensity_ = intensity;
@@ -927,7 +911,7 @@
// parent scan ID
long parentScanID;
COMCHECK(pSpecData->get_ParentScanId(&parentScanID),
- cerr << "get ParentScanId error" << endl,
+ "get ParentScanId error",
return(NULL));
// TODO: error checking on map
map<long,long>::iterator iter = nativeToSequentialScanNums_.find(parentScanID);
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