int CoreBioComponent :: AnalyzeGridSM (SampleData& fileData, GridDataStruct* gridData) {
//
// This is ladder stage 1
//
Endl endLine;
RGString Notice;
smTestForColorCorrectionMatrixPreset testForColorCorrectionMatrixPreset;
int status = InitializeSM (fileData, gridData->mCollection, gridData->mMarkerSetName, TRUE);
if (status < 0) {
Notice << "BioComponent could not initialize:";
cout << Notice << endl;
gridData->mExcelText << CLevel (1) << Notice << "\n" << ErrorString << "Skipping...\n" << PLevel ();
gridData->mText << Notice << "\n" << ErrorString << "Skipping\n";
return -1;
}
if (CoreBioComponent::UseRawData) {
if (GetMessageValue (testForColorCorrectionMatrixPreset))
status = SetAllRawDataWithMatrixSM (fileData, gridData->mTestControlPeak, gridData->mTestControlPeak);
else
status = SetAllRawDataSM (fileData, gridData->mTestControlPeak, gridData->mTestControlPeak);
}
else
status = SetAllDataSM (fileData, gridData->mTestControlPeak, gridData->mTestControlPeak);
if (status < 0) {
Notice << "BioComponent could not set data:";
cout << Notice << endl;
gridData->mExcelText << CLevel (1) << Notice << "\n" << ErrorString << "Skipping...\n" << PLevel ();
gridData->mText << Notice << "\n" << ErrorString << "Skipping...\n";
return -2;
}
if (CoreBioComponent::UseRawData)
FindAndRemoveFixedOffsets ();
status = AnalyzeGridSM (gridData->mText, gridData->mExcelText, gridData->mMsg);
if (status < 0) {
Notice << "BioComponent could not analyze grid. Skipping...";
cout << Notice << endl;
Notice << "\n";
gridData->mExcelText.Write (1, Notice);
gridData->mText << Notice;
return -3;
}
return 0;
}
void DataSignal :: WriteSmartTableArtifactInfoToXML (RGTextOutput& text, RGTextOutput& tempText, const RGString& indent, const RGString& bracketTag, const RGString& locationTag) {
int peak;
Endl endLine;
RGString suffix;
RGString label;
SmartMessageReporter* notice;
int i;
RGString virtualAllele;
SmartMessageReporter* nextNotice;
text.SetOutputLevel (1);
int msgNum;
smAcceptedOLLeft acceptedOLLeft;
smAcceptedOLRight acceptedOLRight;
int reportedMessageLevel = GetHighestMessageLevelWithRestrictionSM ();
//bool hasThreeLoci;
//bool needLocus0;
if ((!DontLook ()) && (NumberOfSmartNoticeObjects () != 0)) {
bool firstNotice = true;
peak = (int) floor (Peak () + 0.5);
virtualAllele = GetVirtualAlleleName ();
text << indent << "<" << bracketTag << ">" << endLine; // Should be <Artifact>
text << indent << "\t<Id>" << GetSignalID () << "</Id>" << endLine;
text << indent << "\t<Level>" << reportedMessageLevel << "</Level>" << endLine;
text << indent << "\t<RFU>" << peak << "</RFU>" << endLine;
text << indent << "\t<" << locationTag << ">" << GetApproximateBioID () << "</" << locationTag << ">" << endLine;
text << indent << "\t<PeakArea>" << TheoreticalArea () << "</PeakArea>" << endLine;
text << indent << "\t<Time>" << GetMean () << "</Time>" << endLine;
text << indent << "\t<Fit>" << GetCurveFit () << "</Fit>" << endLine;
if (!mAllowPeakEdit)
text << indent << "\t<AllowPeakEdit>false</AllowPeakEdit>" << endLine;
RGDListIterator it (*mSmartMessageReporters);
i = 0;
while (notice = (SmartMessageReporter*) it ()) {
if (!notice->GetDisplayOsirisInfo ())
continue;
if (firstNotice) {
label = indent + "\t<Label>";
firstNotice = false;
}
if (i > 0)
label << " ";
label += notice->GetMessage ();
label += notice->GetMessageData ();
i++;
}
if (i > 0) {
label << "</Label>";
text << label << endLine;
}
// Now add list of notices...
it.Reset ();
while (nextNotice = (SmartMessageReporter*) it ()) {
msgNum = Notice::GetNextMessageNumber ();
nextNotice->SetMessageCount (msgNum);
text << indent << "\t<MessageNumber>" << msgNum << "</MessageNumber>" << endLine;
tempText << "\t\t<Message>\n";
tempText << "\t\t\t<MessageNumber>" << msgNum << "</MessageNumber>\n";
tempText << "\t\t\t<Text>" << nextNotice->GetMessage () << nextNotice->GetMessageData () << "</Text>\n";
if (nextNotice->HasViableExportInfo ()) {
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Hidden>false</Hidden>\n";
else
tempText << "\t\t\t<Hidden>true</Hidden>\n";
if (!nextNotice->IsCritical ())
tempText << "\t\t\t<Critical>false</Critical>\n";
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Enabled>true</Enabled>\n";
else
tempText << "\t\t\t<Enabled>false</Enabled>\n";
if (!nextNotice->IsEditable ())
tempText << "\t\t\t<Editable>false</Editable>\n";
if (nextNotice->GetDisplayExportInfo ())
tempText << "\t\t\t<DisplayExportInfo>true</DisplayExportInfo>\n";
else
tempText << "\t\t\t<DisplayExportInfo>false</DisplayExportInfo>\n";
if (!nextNotice->GetDisplayOsirisInfo ())
tempText << "\t\t\t<DisplayOsirisInfo>false</DisplayOsirisInfo>\n";
tempText << "\t\t\t<MsgName>" << nextNotice->GetMessageName () << "</MsgName>\n";
//tempText << "\t\t\t<ExportProtocolList>";
//tempText << "\t\t\t" << nextNotice->GetExportProtocolInformation ();
//tempText << "\t\t\t</ExportProtocolList>\n";
}
tempText << "\t\t</Message>\n";
}
// Now add list of alleles
//hasThreeLoci = (mLocus != NULL) && (mLeftLocus != NULL) && (mRightLocus != NULL);
//if (mLocus != NULL) {
// if ((mLeftLocus == NULL) && (mRightLocus == NULL))
// needLocus0 = true;
// else
// needLocus0 = false;
//}
//else
// needLocus0 = false;
//needLocus0 = (!hasThreeLoci) && ((mLocus != mLeftLocus) || (mLocus != mRightLocus));
if (mLocus != NULL) {
//testing
RGString locusName = mLocus->GetLocusName ();
suffix = GetAlleleName (0);
if ((suffix.Length () > 0) || (virtualAllele.Length () > 0)) {
text << indent << "\t<Allele>" << endLine;
if (suffix.Length () > 0)
text << indent << "\t\t<Name>" << suffix << "</Name>" << endLine;
else
text << indent << "\t\t<Name>" << virtualAllele << "</Name>" << endLine;
if (mOffGrid)
suffix = "true";
else if (mAcceptedOffGrid)
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (0) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>0</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
if ((mLeftLocus != NULL) && (mLeftLocus != mLocus)) {
if (mAlleleNameLeft.Length () > 0) {
text << indent << "\t<Allele>" << endLine;
text << indent << "\t\t<Name>" << mAlleleNameLeft << "</Name>" << endLine;
if (mIsOffGridLeft)
suffix = "true";
else if (GetMessageValue (acceptedOLLeft))
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (-1) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mLeftLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>-1</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
if ((mRightLocus != NULL) && (mRightLocus != mLocus)) {
if (mAlleleNameRight.Length () > 0) {
text << indent << "\t<Allele>" << endLine;
text << indent << "\t\t<Name>" << mAlleleNameRight << "</Name>" << endLine;
if (mIsOffGridRight)
suffix = "true";
else if (GetMessageValue (acceptedOLRight))
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (1) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mRightLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>1</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
text << indent << "</" + bracketTag << ">" << endLine;
}
text.ResetOutputLevel ();
}
bool CoreBioComponent :: GetIgnoreNoiseAboveDetectionInSmoothingFlag () const {
smIgnoreNoiseAnalysisAboveDetectionThresholdInSmoothing ignore;
return GetMessageValue (ignore);
}
int CoreBioComponent :: PreliminarySampleAnalysisSM (RGDList& gridList, SampleDataStruct* sampleData) {
//
// This is sample stage 1
//
smAssociatedLadderIsCritical associatedLadderIsCritical;
// CoreBioComponent* grid = GetBestGridBasedOnTimeForAnalysis (gridList);
const double* characteristicArray;
mLSData->GetCharacteristicArray (characteristicArray);
smUseMaxSecondDerivativesForSampleToLadderFit use2ndDeriv;
bool useSecondDerivative = GetMessageValue (use2ndDeriv);
CSplineTransform* timeMap;
CoreBioComponent* grid;
// CoreBioComponent* grid = GetBestGridBasedOnMaxDelta3DerivForAnalysis (gridList, timeMap);
if (useSecondDerivative) {
cout << "Using 2nd derivative criterion for ladder fit..." << endl;
grid = GetBestGridBasedOnMax2DerivForAnalysis (gridList, timeMap);
}
else {
cout << "Using minimum error criterion for ladder fit..." << endl;
grid = GetBestGridBasedOnLeastTransformError (gridList, timeMap, characteristicArray);
}
if (grid == NULL)
return -1;
//
// Get other fit data from timeMap
//
timeMap->OutputHighDerivativesAndErrors (characteristicArray);
//smTempUseNaturalCubicSplineForTimeTransform useNaturalCubicSpline;
//smTempUseChordalDerivApproxHermiteSplinesForTimeTransform useChordalDerivsForHermiteSpline;
//bool useHermite = !GetMessageValue (useNaturalCubicSpline);
//bool useChords = GetMessageValue (useChordalDerivsForHermiteSpline);
bool useHermite = !UseNaturalCubicSplineTimeTransform;
bool useChords = false;
int gridArtifactLevel = grid->GetHighestMessageLevelWithRestrictionSM ();
if ((gridArtifactLevel > 0) && (gridArtifactLevel <= Notice::GetSeverityTrigger ()))
SetMessageValue (associatedLadderIsCritical, true);
// CSplineTransform* timeMap = TimeTransform (*this, *grid);
CSplineTransform* InverseTimeMap = TimeTransform (*grid, *this, useHermite, useChords); // Could augment calling sequence to use Hermite Cubic Spline transform 04/10/2014
if (InverseTimeMap != NULL) {
mAssociatedGrid = grid->CreateNewTransformedBioComponent (*grid, InverseTimeMap);
// if (!ComputeExtendedLocusTimes (grid, InverseTimeMap))
// cout << "Could not compute extended locus times..." << endl;
delete InverseTimeMap;
}
Endl endLine;
RGString Notice;
Notice << "ANALYSIS WILL USE GRID NAMED " << grid->GetSampleName () << "\n";
sampleData->mExcelText.Write (1, Notice);
RemoveAllSignalsOutsideLaneStandardSM ();
// ValidateAndCorrectCrossChannelAnalysesSM ();
int status = AssignSampleCharacteristicsToLociSM (grid, timeMap);
delete timeMap; // Added 09/26/2014 to prevent memory leak
return status;
}
int CoreBioComponent :: PrepareSampleForAnalysisSM (SampleData& fileData, SampleDataStruct* sampleData) {
//
// This is sample stage 1
//
Endl endLine;
smTestForColorCorrectionMatrixPreset testForColorCorrectionMatrixPreset;
RGString notice;
notice << "Analyzing sample named " << GetSampleName () << "\n";
sampleData->mExcelText.Write (1, notice);
sampleData->mText << notice;
notice = "";
// Notice* newNotice;
// BlobFound newNotice;
smILSFailed ilsRequiresReview;
smNormalizeRawDataRelativeToBaselinePreset normalizeRawData;
smEnableRawDataFilterForNormalizationPreset enableFilteringForNormalization;
Progress = 0;
int j;
int status = InitializeSM (fileData, sampleData->mCollection, sampleData->mMarkerSetName, FALSE);
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT INITIALIZE:";
cout << notice << endl;
sampleData->mExcelText.Write (1, notice);
sampleData->mExcelText << CLevel (1) << notice << "\n" << ErrorString << "Skipping...\n" << PLevel ();
sampleData->mText << notice << "\n" << ErrorString << "Skipping...\n";
return -1;
}
Progress = 1;
if (CoreBioComponent::UseRawData) {
if (GetMessageValue (testForColorCorrectionMatrixPreset))
status = SetAllRawDataWithMatrixSM (fileData, sampleData->mTestControlPeak, sampleData->mTestSamplePeak);
else
status = SetAllRawDataSM (fileData, sampleData->mTestControlPeak, sampleData->mTestSamplePeak);
}
else
status = SetAllDataSM (fileData, sampleData->mTestControlPeak, sampleData->mTestSamplePeak);
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT SET DATA:";
cout << notice << endl;
sampleData->mExcelText << CLevel (1) << notice << "\n" << ErrorString << "Skipping...\n" << PLevel ();
sampleData->mText << notice << "\n" << ErrorString << "Skipping...\n";
return -2;
}
CoreBioComponent::InitializeOffScaleData (fileData);
Progress = 2;
if (CoreBioComponent::UseRawData) {
status = FindAndRemoveFixedOffsets ();
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT COMPUTE OFFSETS ACCURATELY. Skipping...";
cout << notice << endl;
sampleData->mExcelText.Write (1, notice);
sampleData->mText << notice << "\n" << ErrorString << " Skipping...\n";
return -5;
}
}
if (GetMessageValue (enableFilteringForNormalization))
ChannelData::SetUseNormalizationFilter (true);
else
ChannelData::SetUseNormalizationFilter (false);
if (GetMessageValue (normalizeRawData) && GetMessageValue (enableFilteringForNormalization))
CreateAndSubstituteFilteredDataSignalForRawDataNonILS ();
// status = FitAllCharacteristicsSM (sampleData->mText, sampleData->mExcelText, sampleData->mMsg, FALSE); // ->FALSE
status = FitAllSampleCharacteristicsSM (sampleData->mText, sampleData->mExcelText, sampleData->mMsg, FALSE); // ->FALSE
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT FIT ALL CHARACTERISTICS. Skipping...";
cout << notice << endl;
sampleData->mExcelText.Write (1, notice);
sampleData->mText << notice << "\n" << ErrorString << "Skipping...\n";
return -3;
}
Progress = 3;
// mLSData->ClearAllPeaksBelowAnalysisThreshold ();
if (!GetMessageValue (normalizeRawData)) {
//AnalyzeCrossChannelSM (); // Moved below - 07/31/2013
//status = AnalyzeLaneStandardChannelSM (sampleData->mText, sampleData->mExcelText, sampleData->mMsg, sampleData->mPrint);
//if (status < 0) {
// notice << "BIOCOMPONENT COULD NOT ANALYZE INTERNAL LANE STANDARD. Skipping...";
// cout << notice << endl;
// sampleData->mExcelText << CLevel (1) << notice << "\n" << ErrorString << "Skipping...\n" << PLevel ();
// sampleData->mText << notice << "\n" << ErrorString << "Skipping...\n";
// SetMessageValue (ilsRequiresReview, true);
// return -4;
//}
status = 0;
for (j=1; j<=mNumberOfChannels; j++) {
if (mDataChannels [j]->SetAllApproximateIDs (mLSData) < 0)
status = -1;
}
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT UTILIZE INTERNAL LANE STANDARD. Skipping...";
cout << notice << endl;
SetMessageValue (ilsRequiresReview, true);
notice = "Could not create ILS time to base pairs transform";
SetDataForSmartMessage (ilsRequiresReview, notice);
return -5;
}
//AnalyzeCrossChannelSM (); // Moved here 07/31/2013...happy birthday, Mom. You'd be 99 today.
AnalyzeCrossChannelWithNegativePeaksSM ();
// TestSignalsForLaserOffScaleSM (); // Moved inside AnalyzeCrossChannelWithNegativePeaksSM 09/09/2014
cout << "Analyzed cross channel links with negative peaks" << endl;
Progress = 4;
return 0;
}
//
// In this branch, we normalize the raw data with respect to the dynamic baseline. First, analyze the lane standard, then find
// the baseline and subtract it from the raw data. Finally, refit all non-lane standard channels and continue as before.
//
/*status = AnalyzeLaneStandardChannelSM (sampleData->mText, sampleData->mExcelText, sampleData->mMsg, sampleData->mPrint);
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT ANALYZE INTERNAL LANE STANDARD. Skipping...";
cout << notice << endl;
sampleData->mExcelText << CLevel (1) << notice << "\n" << ErrorString << "Skipping...\n" << PLevel ();
sampleData->mText << notice << "\n" << ErrorString << "Skipping...\n";
SetMessageValue (ilsRequiresReview, true);
return -4;
}*/
status = 0;
for (j=1; j<=mNumberOfChannels; j++) {
if (mDataChannels [j]->SetAllApproximateIDs (mLSData) < 0)
status = -1;
}
if (NormalizeBaselineForNonILSChannelsSM () < 0) {
notice << "BIOCOMPONENT COULD NOT ANALYZE BASELINE. OMITTING BASELINE ANALYSIS...";
cout << notice << endl;
status = -1;
}
//RestoreRawDataAndDeleteFilteredSignalNonILS (); // 02/02/2014: This is now done at the channel level within normalization function.
status = FitNonLaneStandardCharacteristicsSM (sampleData->mText, sampleData->mExcelText, sampleData->mMsg, FALSE); // ->FALSE
FitNonLaneStandardNegativeCharacteristicsSM (sampleData->mText, sampleData->mExcelText, sampleData->mMsg, FALSE);
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT FIT ALL NON ILS CHARACTERISTICS. Skipping...";
cout << notice << endl;
sampleData->mExcelText.Write (1, notice);
sampleData->mText << notice << "\n" << ErrorString << "Skipping...\n";
return -3;
}
for (j=1; j<=mNumberOfChannels; j++) {
if (mDataChannels [j]->SetAllApproximateIDs (mLSData) < 0)
status = -1;
}
if (status < 0) {
notice << "BIOCOMPONENT COULD NOT UTILIZE INTERNAL LANE STANDARD. Skipping...";
cout << notice << endl;
SetMessageValue (ilsRequiresReview, true);
notice = "Could not create ILS time to base pairs transform";
SetDataForSmartMessage (ilsRequiresReview, notice);
return -5;
}
//AnalyzeCrossChannelSM ();
AnalyzeCrossChannelWithNegativePeaksSM ();
// TestSignalsForLaserOffScaleSM (); // Moved inside AnalyzeCrossChannelWithNegativePeaksSM 09/09/2014
Progress = 4;
return 0;
}
