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 CPlayerLevels::AddLevel( const FData& level, const std::string& levelId, std::list<CLevel>& levelList )
{
FData value;
value = level.get("PlayerId",value);
if(!value.isString())
{
return;
}
std::string playerId(value.asString());
value = level.get("PlayerName",value);
std::string playerName(value.asString());
value = level.get("PlayerSource",value);
std::string playerSource(value.asString());
value = level.get("Name",value);
std::string name(value.asString());
value = level.get("Data",value);
std::string ldata(value.asString());
value = level.get("thumb",value);
std::string lthumb(value.asString());
value = level.get("RDate",value);
std::string relativeDate(value.asString());
value = level.get("SDate",value);
std::string date(value.asString());
value = level.get("Plays",value);
int plays = value.asInt();
value = level.get("Votes",value);
int votes = value.asInt();
value = level.get("Score",value);
int score = value.asInt();
value = level.get("Rating",value);
float rating = value.asFloat();
value = level.get("CustomData",value);
CustomData customData;
Json::ValueIterator it = value.begin();
for(; it != value.end(); it++)
{
customData.insert(std::make_pair(it.key().asString(), (*it).asString()));
}
levelList.push_back( CLevel(name, playerName, playerId,
playerSource, ldata, lthumb, votes, plays,
rating, score, date, relativeDate, customData, levelId));
}
void CoreBioComponent :: ReportXMLSmartSampleTableRowWithLinks (RGTextOutput& text, RGTextOutput& tempText) {
RGString type;
if (mIsNegativeControl)
type = "-Control";
else if (mIsPositiveControl)
type = "+Control";
else
type = "Sample";
RGString pResult;
RGString SimpleFileName (mName);
size_t startPos = 0;
size_t endPos;
size_t length = SimpleFileName.Length ();
if (SimpleFileName.FindLastSubstringCaseIndependent (DirectoryManager::GetDataFileType (), startPos, endPos)) {
if (endPos == length - 1)
SimpleFileName.ExtractAndRemoveLastCharacters (4);
}
SimpleFileName.FindAndReplaceAllSubstrings ("\\", "/");
startPos = endPos = 0;
if (SimpleFileName.FindLastSubstring ("/", startPos, endPos)) {
SimpleFileName.ExtractAndRemoveSubstring (0, startPos);
}
text << CLevel (1) << "\t\t<Sample>\n";
text << "\t\t\t<Name>" << xmlwriter::EscAscii (SimpleFileName, &pResult) << "</Name>\n";
text << "\t\t\t<SampleName>" << xmlwriter::EscAscii (mSampleName, &pResult) << "</SampleName>\n";
text << "\t\t\t<RunStart>" << mRunStart.GetData () << "</RunStart>\n";
text << "\t\t\t<Type>" << type.GetData () << "</Type>\n" << PLevel ();
int trigger = Notice::GetMessageTrigger ();
// int channelHighestLevel;
// bool channelAlerts = false;
int cbcHighestMsgLevel = GetHighestMessageLevelWithRestrictionSM ();
RGDListIterator it (*mSmartMessageReporters);
SmartMessageReporter* nextNotice;
bool includesExportInfo = false;
while (nextNotice = (SmartMessageReporter*) it ()) {
if (nextNotice->HasViableExportInfo ()) {
includesExportInfo = true;
break;
}
}
if (((cbcHighestMsgLevel > 0) && (cbcHighestMsgLevel <= trigger)) || includesExportInfo) {
// text << CLevel (1) << "\t\t\t<SampleAlerts>\n" << PLevel ();
// get message numbers and report
ReportXMLSmartNoticeObjects (text, tempText, " ");
// text << CLevel (1) << "\t\t\t</SampleAlerts>\n" << PLevel ();
}
mDataChannels [mLaneStandardChannel]->ReportXMLILSSmartNoticeObjects (text, tempText, " ");
int i;
//for (i=1; i<=mNumberOfChannels; i++) {
// //if (i == mLaneStandardChannel)
// // continue;
// channelHighestLevel = mDataChannels [i]->GetHighestMessageLevelWithRestrictionSM ();
// if ((channelHighestLevel > 0) && (channelHighestLevel <= trigger)) {
// channelAlerts = true;
// break;
// }
//}
// if (channelAlerts) {
text << CLevel (1) << "\t\t\t<ChannelAlerts>\n" << PLevel ();
for (i=1; i<=mNumberOfChannels; i++) {
if (i == mLaneStandardChannel)
continue;
mDataChannels [i]->ReportXMLSmartNoticeObjects (text, tempText, " ");
}
text << CLevel (1) << "\t\t\t</ChannelAlerts>\n" << PLevel ();
// }
mMarkerSet->ResetLocusList ();
Locus* nextLocus;
while (nextLocus = mMarkerSet->GetNextLocus ()) {
nextLocus->ReportXMLSmartSampleTableRowWithLinks (text, tempText, " ");
}
if (mIsPositiveControl)
text << CLevel (1) << "\t\t\t<PositiveControl>" << mPositiveControlName << "</PositiveControl>\n";
text << CLevel (1) << "\t\t</Sample>\n" << PLevel ();
}
bool CoreBioComponent :: ReportXMLSmartNoticeObjects (RGTextOutput& text, RGTextOutput& tempText, const RGString& delim) {
if (NumberOfSmartNoticeObjects () > 0) {
int msgLevel = GetHighestMessageLevelWithRestrictionSM ();
RGDListIterator it (*mSmartMessageReporters);
SmartMessageReporter* nextNotice;
text.SetOutputLevel (msgLevel);
tempText.SetOutputLevel (1);
int msgNum;
int triggerLevel = Notice::GetMessageTrigger ();
bool includesExportInfo = false;
bool viable;
while (nextNotice = (SmartMessageReporter*) it ()) {
if (nextNotice->HasViableExportInfo ()) {
includesExportInfo = true;
break;
}
}
if (!text.TestCurrentLevel () && !includesExportInfo) {
text.ResetOutputLevel ();
tempText.ResetOutputLevel ();
return FALSE;
}
text.ResetOutputLevel ();
text << CLevel (1) << "\t\t\t<SampleAlerts>\n" << PLevel ();
it.Reset ();
text.SetOutputLevel (1);
while (nextNotice = (SmartMessageReporter*) it ()) {
viable = nextNotice->HasViableExportInfo ();
msgLevel = nextNotice->GetMessagePriority ();
if (((msgLevel > 0) && (msgLevel <= triggerLevel)) || viable) {
msgNum = Notice::GetNextMessageNumber ();
nextNotice->SetMessageCount (msgNum);
text << "\t\t\t\t<MessageNumber>" << msgNum << "</MessageNumber>\n";
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 (viable) {
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";
}
}
text.ResetOutputLevel ();
text << CLevel (1) << "\t\t\t</SampleAlerts>\n" << PLevel ();
tempText.ResetOutputLevel ();
}
else
return false;
return true;
}
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;
}
bool COptions::LoadLevels(std::string dynamicDataFolder, std::string pgmFolder)
{
long FindHandle;
_finddata_t FindData;
#ifndef WIN32
// initialise OUR data structure
FindData.name = NULL;
FindData.suffix = NULL;
#endif
//-------------------------------------------
// Set the path where the level files are stored
// (in the program files folder)
//-------------------------------------------
std::string levelFilePath_pgmFolder;
levelFilePath_pgmFolder = pgmFolder;
if (pgmFolder.length() >= 1)
{
char delim = pgmFolder.c_str()[pgmFolder.length()-1];
if (delim != '\\' && delim != '/')
#ifdef WIN32
levelFilePath_pgmFolder.append("\\");
#else
levelFilePath_pgmFolder.append("/");
#endif
}
#ifdef WIN32
levelFilePath_pgmFolder.append( "Levels\\" );
#else
levelFilePath_pgmFolder.append( "levels/" );
#endif
std::string levelFilePath_pgmFolderMask;
levelFilePath_pgmFolderMask = levelFilePath_pgmFolder;
levelFilePath_pgmFolderMask.append( "*.TXT" );
//-------------------------------------------
// Determine number of level files available
// (in the program files folder)
//-------------------------------------------
theLog.WriteLine( "Options => Loading level files '%s'.", levelFilePath_pgmFolderMask.c_str() );
std::vector<SFileInfo> files;
FindHandle = _findfirst( levelFilePath_pgmFolderMask.c_str(), &FindData );
if (FindHandle != -1)
{
do
{
SFileInfo file;
file.fileNameWithoutPath = FindData.name;
file.fileNameWithPath = levelFilePath_pgmFolder;
file.fileNameWithPath.append(FindData.name);
files.push_back(file);
}
while (_findnext(FindHandle, &FindData) != -1);
}
_findclose(FindHandle);
// If a dynamic folder is set, load level files from there, too
if ( dynamicDataFolder != "" ) {
//-------------------------------------------
// Set the path where the level files are stored
// (in the user's application data folder)
//-------------------------------------------
std::string levelFilePath_dynamicDataFolder;
levelFilePath_dynamicDataFolder = dynamicDataFolder;
#ifdef WIN32
levelFilePath_dynamicDataFolder.append( "levels\\" );
#else
levelFilePath_dynamicDataFolder.append( "levels/" );
#endif
std::string levelFilePath_dynamicDataFolderMask;
levelFilePath_dynamicDataFolderMask = levelFilePath_dynamicDataFolder;
levelFilePath_dynamicDataFolderMask.append( "*.TXT" );
//-------------------------------------------
// Determine number of level files available
// (in the dynamic data folder)
//-------------------------------------------
theLog.WriteLine( "Options => Loading level files '%s'.", levelFilePath_dynamicDataFolderMask.c_str() );
FindHandle = _findfirst( levelFilePath_dynamicDataFolderMask.c_str(), &FindData );
if (FindHandle != -1)
{
do
{
SFileInfo file;
file.fileNameWithoutPath = FindData.name;
file.fileNameWithPath = levelFilePath_dynamicDataFolder;
file.fileNameWithPath.append(FindData.name);
files.push_back(file);
}
while (_findnext(FindHandle, &FindData) != -1);
}
_findclose(FindHandle);
}
//---------------------
// Sort
//---------------------
#ifdef WIN32
sort(files.begin(), files.end(),
[&](const SFileInfo& a, const SFileInfo& b) {return (a.fileNameWithoutPath < b.fileNameWithoutPath);}
);
#endif
for (std::vector<SFileInfo>::iterator it = files.begin(); it != files.end(); ++it)
{
// Create a new CLevel element and add it to the level container
m_Levels.push_back(CLevel(it->fileNameWithPath, it->fileNameWithoutPath));
}
//---------------------
// Check for a problem
//---------------------
// If there is no level
if (m_Levels.size() == 0)
{
// Log failure
theLog.WriteLine ("Options => !!! There should be at least 1 level.");
return false;
}
// If the level number we read in the cfg file is invalid compared to the number of existing levels
if (m_Level >= (int)m_Levels.size()) // #3078839
{
// Select the first level
m_Level = 0;
}
//------------------------------------------------------
// Load all the level files detected earlier
//------------------------------------------------------
bool ErrorOccurred = false;
for( unsigned int CurrentLevel = 0; CurrentLevel < m_Levels.size(); CurrentLevel++ )
{
//theLog.WriteLine ("Options => Loading level file %s...", levelFileNames_full.at(CurrentLevel).c_str() );
if ( !m_Levels.at( CurrentLevel ).LoadFromFile() )
{
ErrorOccurred = true;
break;
}
}
// If we had to stop then there is a problem.
if (ErrorOccurred)
return false;
// Everything went right
return true;
}
