RGDirectory :: RGDirectory (const RGString& fullName) : direct (NULL) {
DWORD dwAttr;
#ifdef FILENAME_MAX
if (fullName.Length () > FILENAME_MAX) {
cout << "Full path name too long: name = " << fullName.GetData () << endl;
return;
}
#endif
// Must be a valid name
if( (fullName.Length () == 0) ||
(dwAttr = GetFileAttributes(fullName.GetData ())) == INVALID_FILE_ATTRIBUTES) {
errno = ENOENT;
}
// Must be a directory
else if (!(dwAttr & FILE_ATTRIBUTE_DIRECTORY)) {
errno = ENOTDIR;
}
else {
direct = new DIR; //(DIR*)malloc(sizeof(DIR));
if (direct == NULL) {
errno = ENOMEM;
}
else {
direct->hFind = findfile_directory (fullName.GetData (), &direct->find_data);
if (direct->hFind == INVALID_HANDLE_VALUE) {
//free(directory);
delete direct;
direct = NULL;
}
else {
// Save the directory, in case of rewind.
lstrcpyA(direct->directory, fullName.GetData ());
lstrcpyA(direct->dirent.d_name, direct->find_data.cFileName);
}
}
}
}
LocusData :: LocusData (const RGString& locusName, const RGString& alleleString) : mLocusName (locusName) {
RGStringArray alleles;
RGStringArray delimiters;
if (alleleString.Length () == 0)
return;
RGString alleleStr = alleleString;
RGStringTokenizer alleleJoin (alleleStr);
alleleJoin.AddDelimiter (",");
alleleJoin.Split (alleles, delimiters);
int n = alleles.Length ();
if (n == 0)
return;
int i;
RGString* newAllele;
cout << "Locus Name = " << (char*)mLocusName.GetData () << " with allele(s) ";
for (i=0; i<n; i++) {
newAllele = new RGString (alleles [i]);
cout << (char*)newAllele->GetData () << " ";
mAlleleList.append (newAllele);
}
cout << endl;
}
STRAlleleName :: STRAlleleName (const RGString& name) {
size_t position;
RGString repeats;
RGString variant;
size_t len;
if (name.FindNextSubstring (0, ".", position)) {
repeats = name.ExtractSubstring (0, position - 1);
mRepeats = repeats.ConvertToInteger ();
len = name.Length () - 1;
if (position <= len) {
variant = name.ExtractSubstring (position + 1, len);
mMicroVariant = variant.ConvertToInteger ();
}
else
mMicroVariant = 0;
}
else {
mRepeats = name.ConvertToInteger ();
mMicroVariant = 0;
}
}
Boolean RGDirectory :: MakeDirectory (const RGString& fullName) {
if (fullName.Length () == 0)
return FALSE;
// Must not already exist
if (FileOrDirectoryExists (fullName)) {
cout << "File or directory " << fullName << " already exists" << endl;
return FALSE;
}
return CreateDirectory (fullName, NULL);
}
bool DirectoryManager :: TestForExtension (const RGString& fileName) {
RGString Extension;
int length = fileName.Length ();
// size_t position;
// RGString localFileName (fileName);
// localFileName.ToLower ();
if (length > 4)
Extension = fileName.ExtractSubstring (length-4, length-1);
if ((length > 4) && (Extension == DirectoryManager::DataFileTypeWithDot))
return true;
return false;
}
Boolean DirectoryManager :: TestForPositiveControl (const RGString& fileName) {
int length = (int)fileName.Length ();
RGString Extension;
Boolean FoundPosControl;
Boolean FoundLadder;
if (length > 4)
Extension = fileName.ExtractSubstring (length-4, length-1);
FoundPosControl = mPServer->PosControlDoesTargetStringContainASynonymCaseIndep (fileName);
FoundLadder = mPServer->LadderDoesTargetStringContainASynonymCaseIndep (fileName);
if ((length > 4) && (Extension == DirectoryManager::DataFileTypeWithDot) && FoundPosControl && !FoundLadder) //old = if ((length > 4) && (Extension == ".fsa") && FoundPosControl && !FoundLadder)
return TRUE;
return FALSE;
}
Boolean DirectoryManager :: TestForNonLadder (const RGString& fileName) {
int length = (int)fileName.Length ();
RGString Extension;
Boolean FoundControl;
// size_t position;
// RGString localFileName (fileName);
// localFileName.ToLower ();
if (length > 4)
Extension = fileName.ExtractSubstring (length-4, length-1);
// FoundControl = localFileName.FindSubstring ("ladder", position);
FoundControl = mPServer->LadderDoesTargetStringContainASynonymCaseIndep (fileName);
if ((length > 4) && (Extension == DirectoryManager::DataFileTypeWithDot) && !FoundControl) //old = if ((length > 4) && (Extension == ".fsa") && !FoundControl)
return TRUE;
return FALSE;
}
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 ();
}
void DataSignal :: WriteSmartArtifactInfoToXML (RGTextOutput& text, const RGString& indent, const RGString& bracketTag, const RGString& locationTag) {
int peak;
Endl endLine;
RGString suffix;
RGString label;
SmartMessageReporter* notice;
int i;
RGString virtualAllele;
int reportedMessageLevel;
reportedMessageLevel = GetHighestMessageLevelWithRestrictionSM ();
bool thisIsFirstNotice = true;
if ((!DontLook ()) && (NumberOfSmartNoticeObjects () != 0)) {
peak = (int) floor (Peak () + 0.5);
if (mOffGrid)
suffix = " OL";
virtualAllele = GetVirtualAlleleName ();
RGDListIterator it (*mSmartMessageReporters);
i = 0;
while (notice = (SmartMessageReporter*) it ()) {
if (!notice->GetDisplayOsirisInfo ())
continue;
if (thisIsFirstNotice) {
text << indent << "<" << bracketTag << ">" << endLine;
text << indent << "\t<level>" << reportedMessageLevel << "</level>" << endLine;
text << indent << "\t<mean>" << GetMean () << "</mean>" << endLine;
text << indent << "\t<height>" << peak << "</height>" << endLine;
// text << indent << "\t<" << locationTag << ">" << (int) floor (GetApproximateBioID () + 0.5) << "</" << locationTag << ">" << endLine;
text << indent << "\t<" << locationTag << ">" << GetApproximateBioID () << "</" << locationTag << ">" << endLine;
text << indent << "\t<PeakArea>" << TheoreticalArea () << "</PeakArea>" << endLine;
if (virtualAllele.Length () > 0)
text << indent << "\t<equivAllele>" << virtualAllele << suffix << "</equivAllele>" << endLine;
text << indent << "\t<width>" << 4.0 * GetStandardDeviation () << "</width>" << endLine;
text << indent << "\t<fit>" << GetCurveFit () << "</fit>" << endLine;
label = indent + "\t<label>";
thisIsFirstNotice = false;
}
if (i > 0)
label << " ";
label += notice->GetMessage ();
label += notice->GetMessageData ();
i++;
}
RGString temp = GetVirtualAlleleName () + suffix;
if (temp.Length () > 0) {
if (i > 0)
label << " ";
label += "Allele " + temp;
}
if (i > 0) {
label << "</label>";
text << label << endLine;
text << indent << "</" + bracketTag << ">" << endLine;
}
/*if ((signalLink != NULL) && (!signalLink->xmlArtifactInfoWritten)) {
signalLink->xmlArtifactInfoWritten = true;
peak = signalLink->height;
text << indent << "<" << bracketTag << ">" << endLine;
text << indent << "\t<mean>" << signalLink->mean << "</mean>" << endLine;
text << indent << "\t<height>" << peak << "</height>" << endLine;
text << indent << "\t<" << locationTag << ">" << signalLink->bioID << "</" << locationTag << ">" << endLine;
text << indent << "\t<fit>" << GetCurveFit () << "</fit>" << endLine;
label = indent + "\t<label>";
mNoticeObjectIterator.Reset ();
i = 0;
while (notice = (Notice*) mNoticeObjectIterator ()) {
if (i > 0)
label << " ";
label += notice->GetLabel ();
i++;
}
if (temp.Length () > 0) {
if (i > 0)
label << " ";
label += "Allele " + temp;
}
label << "</label>";
text << label << endLine;
text << indent << "</" + bracketTag << ">" << endLine;
}*/
}
}
STRBaseLaneStandard :: STRBaseLaneStandard (const RGString& xmlString) : BaseLaneStandard (xmlString),
mCharacteristicArray (NULL), mDifferenceArray (NULL), mUnnormalizedDifferenceArray(0),
mNormsLeft (NULL), mNormsRight (NULL), mRelativeSizes (NULL),
mSize (0), mDifferenceSize (0), mOmissionSize (0), mOmissionArray (NULL), mNumberOfLargePeaks (0),
mLargeCharacteristicArray (NULL), mLargeDifferenceArray (NULL), mNumberOfLargeDifferences (0),
mFirstIntervalFraction (-1.0), mSmallestIntervalFraction (-1.0), mMaxRelativeHeight (-1),
mCorrelationAcceptanceThreshold (0.993), mCorrelationAutoAcceptanceThreshold (0.9975)
//
//, mLastHalfSize (0), mLastHalfCharacteristicArray (NULL), mLastHalfUnnormalizedDifferenceArray (NULL),
//mLastHalfRelativeSizes (NULL), mLastHalfDifferenceSize (0), mLastHalfNormsLeft (NULL), mLastHalfNormsRight (NULL)
{
RGString TextInput (xmlString);
RGBracketStringSearch CharacteristicsToken ("<Characteristics>", "</Characteristics>", TextInput);
RGString CharacteristicsString;
RGString HeightString;
RGBracketStringSearch HeightToken ("<RelativeHeights>", "</RelativeHeights>", TextInput);
RGBracketStringSearch OmissionSearch ("<Omissions>", "</Omissions>", TextInput);
RGBracketStringSearch AcceptanceThresholdSearch ("<CorrelationAcceptanceThreshold>", "</CorrelationAcceptanceThreshold>", TextInput);
RGBracketStringSearch AutoAcceptanceThresholdSearch ("<CorrelationAutoAcceptanceThreshold>", "</CorrelationAutoAcceptanceThreshold>", TextInput);
RGString OmissionString;
size_t endPosition;
RGString token;
RGString delim;
RGString numberString;
double minChar;
double maxChar;
RGDList tokens;
double value;
RGPDouble* valuePtr;
double previous;
double next;
double cumulative;
int i = 0;
double temp;
int k;
int j;
if (!CharacteristicsToken.FindNextBracketedString (0, endPosition, CharacteristicsString)) {
Msg << "Internal Lane Standard named " << Name << " could not find Characteristics token from string\n";
Msg << TextInput << "\n";
Valid = FALSE;
}
else {
RGStringTokenizer data (CharacteristicsString);
data.AddDelimiter (' ');
data.AddDelimiter (" ");
data.AddDelimiter (" ");
data.AddDelimiter (" ");
data.AddDelimiter (" ");
data.AddRemoveItem (',');
data.AddDelimiter ('\t');
data.AddDelimiter ('\n');
while (data.NextToken (token, delim)) {
if (token.Length () > 0) {
value = token.ConvertToDouble ();
valuePtr = new RGPDouble (value);
if (tokens.Entries () == 0) {
minChar = maxChar = value;
tokens.Append (valuePtr);
}
else if (value < minChar) {
minChar = value;
tokens.Prepend (valuePtr);
}
else if (value > maxChar) {
maxChar = value;
tokens.Append (valuePtr);
}
else
tokens.Insert (valuePtr);
}
}
mSize = (int)tokens.Entries ();
NCharacteristics = mSize;
mCharacteristicArray = new double [mSize];
mDifferenceSize = mSize - 1;
mDifferenceArray = new double [mDifferenceSize];
mUnnormalizedDifferenceArray = new double [mDifferenceSize];
mNormsLeft = new double [mDifferenceSize];
mNormsRight = new double [mDifferenceSize];
//mLastHalfSize = mSize / 2;
//if (2 * mLastHalfSize < mSize)
// mLastHalfSize += 1;
//mLastHalfDifferenceSize = mLastHalfSize - 1;
//mLastHalfCharacteristicArray = new double [mLastHalfSize];
//mLastHalfUnnormalizedDifferenceArray = new double [mLastHalfDifferenceSize];
//mLastHalfNormsLeft = new double [mLastHalfDifferenceSize];
//mLastHalfNormsRight = new double [mLastHalfDifferenceSize];
while (valuePtr = (RGPDouble*)tokens.GetFirst ()) {
mCharacteristicArray [i] = valuePtr->GetDouble ();
delete valuePtr;
i++;
}
//int displacement = mSize - mLastHalfSize; // +0, +1, -1?????
//for (i=0; i<mLastHalfSize; i++)
// mLastHalfCharacteristicArray [i] = mCharacteristicArray [i + displacement];
previous = mCharacteristicArray [0];
for (i=0; i<mDifferenceSize; i++) {
next = mCharacteristicArray [i+1];
mUnnormalizedDifferenceArray [i] = mDifferenceArray [i] = next - previous;
previous = next;
}
//for (i=0; i<mLastHalfSize; i++)
// mLastHalfUnnormalizedDifferenceArray [i] = mUnnormalizedDifferenceArray [i + displacement];
double norm = 0.0;
for (i=0; i<mDifferenceSize; i++)
norm += mDifferenceArray [i] * mDifferenceArray [i];
norm = sqrt (norm);
if (norm > 0.0) {
for (i=0; i<mDifferenceSize; i++)
mDifferenceArray [i] /= norm;
}
cumulative = 0.0;
for (i=0; i<mDifferenceSize; i++) {
temp = mUnnormalizedDifferenceArray [i];
cumulative += temp * temp;
mNormsLeft [i] = cumulative;
}
cumulative = 0.0;
for (i=mDifferenceSize-1; i>=0; i--) {
temp = mUnnormalizedDifferenceArray [i];
cumulative += temp * temp;
mNormsRight [i] = cumulative;
}
//cumulative = 0.0;
//for (i=0; i<mLastHalfDifferenceSize; i++) {
// temp = mLastHalfUnnormalizedDifferenceArray [i];
// cumulative += temp * temp;
// mLastHalfNormsLeft [i] = cumulative;
//}
//cumulative = 0.0;
//for (i=mLastHalfDifferenceSize-1; i>=0; i--) {
// temp = mLastHalfUnnormalizedDifferenceArray [i];
// cumulative += temp * temp;
// mLastHalfNormsRight [i] = cumulative;
//}
MaxCharacteristic = maxChar;
MinCharacteristic = minChar;
double width = mCharacteristicArray [mSize - 1] - mCharacteristicArray [0];
if (width > 0.0)
mFirstIntervalFraction = mUnnormalizedDifferenceArray [0] / width;
else
mFirstIntervalFraction = 1.0;
double temp = mUnnormalizedDifferenceArray [0];
double value;
for (i=0; i<mDifferenceSize; i++) {
value = mUnnormalizedDifferenceArray [i];
if (value < temp)
temp = value;
}
if (width > 0.0)
mSmallestIntervalFraction = temp / width;
else
mSmallestIntervalFraction = 1.0;
if (!HeightToken.FindNextBracketedString (0, endPosition, HeightString)) {
mRelativeSizes = NULL;
// mLastHalfRelativeSizes = NULL;
}
else {
RGStringTokenizer data2 (HeightString);
data2.AddDelimiter (' ');
data2.AddDelimiter (" ");
data2.AddDelimiter (" ");
data2.AddDelimiter (" ");
data2.AddDelimiter (" ");
data2.AddRemoveItem (',');
data2.AddDelimiter ('\t');
data2.AddDelimiter ('\n');
mRelativeSizes = new int [mSize];
for (k=0; k<mSize; k++)
mRelativeSizes [k] = -1;
k = 0;
while (data2.NextToken (token, delim)) {
if (token.Length () > 0) {
token.ToUpper ();
char first = token.GetFirstCharacter ();
switch (first) {
case 'H':
mRelativeSizes [k] = 5;
break;
case 'L':
mRelativeSizes [k] = 1;
break;
case 'M':
if (token.Length () == 1)
mRelativeSizes [k] = 3;
else if (token.GetLastCharacter () == 'H')
mRelativeSizes [k] = 4;
else
mRelativeSizes [k] = 2;
break;
default:
mRelativeSizes [k] = -1;
}
}
k++;
if (k >= mSize)
break;
}
//mLastHalfRelativeSizes = new int [mLastHalfSize];
//for (i=0; i<mLastHalfSize; i++)
// mLastHalfRelativeSizes [i] = mRelativeSizes [i + displacement];
int maxRelativeSize = 0;
int relativeSize;
for (j=0; j<mSize; j++) {
relativeSize = mRelativeSizes [j];
if (relativeSize > maxRelativeSize)
maxRelativeSize = relativeSize;
}
int numberOfHighsInILS = 0;
mMaxRelativeHeight = maxRelativeSize;
for (j=0; j<mSize; j++) {
if (mRelativeSizes [j] == maxRelativeSize)
numberOfHighsInILS++;
}
mNumberOfLargePeaks = numberOfHighsInILS;
mNumberOfLargeDifferences = numberOfHighsInILS - 1;
mLargeCharacteristicArray = new double [numberOfHighsInILS];
if (mNumberOfLargeDifferences > 0)
mLargeDifferenceArray = new double [mNumberOfLargeDifferences];
k = 0;
for (j=0; j<mSize; j++) {
if (mRelativeSizes [j] == maxRelativeSize) {
mLargeCharacteristicArray [k] = mCharacteristicArray [j];
k++;
}
}
if (mLargeDifferenceArray != NULL) {
for (j=0; j<mNumberOfLargeDifferences; j++)
mLargeDifferenceArray [j] = mLargeCharacteristicArray [j + 1] - mLargeCharacteristicArray [j];
}
}
if (OmissionSearch.FindNextBracketedString (0, endPosition, OmissionString)) {
RGStringTokenizer omissionData (OmissionString);
omissionData.AddDelimiter (' ');
omissionData.AddDelimiter (" ");
omissionData.AddDelimiter (" ");
omissionData.AddDelimiter (" ");
omissionData.AddDelimiter (" ");
omissionData.AddRemoveItem (',');
omissionData.AddDelimiter ('\t');
omissionData.AddDelimiter ('\n');
while (omissionData.NextToken (token, delim)) {
if (token.Length () > 0) {
value = token.ConvertToDouble ();
valuePtr = new RGPDouble (value);
if (tokens.Entries () == 0) {
minChar = maxChar = value;
tokens.Append (valuePtr);
}
else if (value < minChar) {
minChar = value;
tokens.Prepend (valuePtr);
}
else if (value > maxChar) {
maxChar = value;
tokens.Append (valuePtr);
}
else
tokens.Insert (valuePtr);
}
}
mOmissionSize = (int)tokens.Entries ();
if (mOmissionSize == 0)
return;
mOmissionArray = new double [mOmissionSize];
i = 0;
while (valuePtr = (RGPDouble*)tokens.GetFirst ()) {
mOmissionArray [i] = valuePtr->GetDouble ();
delete valuePtr;
i++;
}
}
}
cout << "ILS Name = " << Name.GetData () << endl;
if (!AcceptanceThresholdSearch.FindNextBracketedString (0, endPosition, numberString))
cout << "\tCould not find ILS acceptance threshold...using " << mCorrelationAcceptanceThreshold << endl;
else {
mCorrelationAcceptanceThreshold = numberString.ConvertToDouble ();
cout << "\tFrom ILS settings...ILS acceptance threshold = " << mCorrelationAcceptanceThreshold << endl;
}
if (!AutoAcceptanceThresholdSearch.FindNextBracketedString (0, endPosition, numberString))
cout << "\tCould not find ILS auto acceptance threshold...using default value = " << mCorrelationAutoAcceptanceThreshold << endl << endl;
else {
mCorrelationAutoAcceptanceThreshold = numberString.ConvertToDouble ();
cout << "\tFrom ILS settings...ILS auto acceptance threshold = " << mCorrelationAutoAcceptanceThreshold << endl << endl;
}
}
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 ();
}
Locus* Bins :: AssembleLocusFromLineStrings () {
// uses current values in mLocusLineStrings
Locus* newLocus = new Locus ();
int nLines = mLocusLineStrings.Length ();
SplitLocusLine (mLocusLineStrings [0]); // This should give us the name field
RGString name = mLocusLineFieldString [1];
cout << "Locus name = " << name.GetData () << endl;
//cout << "Bins locus line 1: ";
int i;
int len = mLocusLineFieldString.Length ();
//for (i=0; i<len; i++) {
// cout << mLocusLineFieldString [i].GetData ();
// if (i < len - 1)
// cout << ", ";
//}
//cout << endl;
RGString firstAlleleName;
int firstLocusBP;
double firstILSBP;
double lastILSBP;
RGString firstExtendedAlleleName;
RGString lastExtendedAlleleName;
int lineForFirstAllele = 0;
for (i=1; i<nLines; i++) {
SplitLocusLine (mLocusLineStrings [i]);
if (mLocusLineFieldString.Length () < 4) {
cout << "Could not find first allele for locus " << name.GetData () << endl;
delete newLocus;
return NULL;
}
if (mLocusLineFieldString.Length () >= 5) {
if (mLocusLineFieldString [4] == "virtual") {
if (i == 1) {
firstExtendedAlleleName = mLocusLineFieldString [0];
}
continue;
}
}
firstAlleleName = mLocusLineFieldString [0];
firstILSBP = mLocusLineFieldString [1].ConvertToDouble ();
firstLocusBP = (int) floor (firstILSBP + 0.5);
lineForFirstAllele = i;
break;
}
if (firstExtendedAlleleName.Length () == 0)
firstExtendedAlleleName = firstAlleleName;
bool foundLastExtendedAllele = false;
for (i=nLines-1; i>lineForFirstAllele; i--) {
SplitLocusLine (mLocusLineStrings [i]);
if (mLocusLineFieldString.Length () < 4)
continue;
if (!foundLastExtendedAllele) {
lastExtendedAlleleName = mLocusLineFieldString [0];
foundLastExtendedAllele = true;
}
if ((mLocusLineFieldString.Length () >= 5) && (mLocusLineFieldString [4] == "virtual"))
continue;
lastILSBP = mLocusLineFieldString [1].ConvertToDouble ();
break;
}
if (lastExtendedAlleleName.Length () == 0) {
cout << "Could not locate last extended allele name for locus: " << name.GetData () << endl;
delete newLocus;
return NULL;
}
newLocus->SetFirstCoreAllele (firstAlleleName);
newLocus->SetFirstExtendedAllele (firstExtendedAlleleName);
newLocus->SetLastExtendedAllele (lastExtendedAlleleName);
newLocus->SetMinMaxSearchILSBP (firstILSBP, lastILSBP); // These will have to be adjusted later when core repeat number is known
newLocus->SetFirstCoreLocusBP (firstLocusBP);
newLocus->SetName (name);
// Need to add to Locus ability to compute first and last extended bp
return newLocus;
}
