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;
}
void Ladder :: OutputTo (RGTextOutput& xmlFile, LadderInputFile& inputFile) {
RGString link ("http://www.w3.org/2001/XMLSchema-instance");
xmlFile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
xmlFile << "<KitData xmlns:xsi=\"" << link.GetData () << "\" xsi:noNamespaceSchemaLocation=\"MarkerSet.xsd\">\n";
xmlFile << "\t<Version>2.0</Version>\n";
xmlFile << "\t<Kits>\n";
xmlFile << "\t\t<Set>\n";
xmlFile << "\t\t\t<Name>" << mMarkerSetName.GetData () << "</Name>\n";
xmlFile << "\t\t\t<NChannels>" << mNumberOfChannels << "</NChannels>\n";
xmlFile << "\t\t\t<LS>\n";
OutputILSListTo (xmlFile);
xmlFile << "\t\t\t\t<ChannelNo>" << mChannelForILS << "</ChannelNo>\n";
xmlFile << "\t\t\t</LS>\n";
xmlFile << "\t\t\t<FileNameSuffix>" << mSuffix << "</FileNameSuffix>\n";
xmlFile << "\t\t\t<GenotypeSuffix>" << mSuffix << "</GenotypeSuffix>\n";
xmlFile << "\t\t\t<DirectorySearchString>" << mSuffix << "</DirectorySearchString>\n";
OutputChannelMapTo (xmlFile, inputFile);
list <Locus*>::const_iterator locusIterator;
Locus* nextLocus;
for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {
nextLocus = *locusIterator;
nextLocus->OutputTo (xmlFile);
}
xmlFile << "\t\t</Set>\n";
xmlFile << "\t</Kits>\n";
xmlFile << "</KitData>";
}
void Ladder :: OutputILSListTo (RGTextOutput& xmlFile) {
RGDListIterator it (mILSList);
RGString* nextName;
while (nextName = (RGString*) it ())
xmlFile << "\t\t\t\t<LSName>" << nextName->GetData () << "</LSName>\n";
}
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;
}
}
void IndividualGenotype :: WriteXML (RGTextOutput& text, const RGString& indent, const RGString& tag) {
Endl endLine;
RGString indent2 = indent + "\t";
RGString indent3 = indent2 + "\t";
text << indent.GetData () << "<" << tag << ">" << endLine;
text << indent2 << "<Name>" << mName << "</Name>" << endLine;
text << indent2 << "<Loci>" << endLine;
mLoci->WriteXML (text, indent3);
text << indent2 << "</Loci>" << endLine;
text << indent.GetData () << "</" << tag << ">" << endLine;
}
bool STRBaseLocus :: GetLadderSearchRegion (size_t& startIndex, RGString& input, const RGString& familyName) {
RGBracketStringSearch searchRegionsSearch ("<SearchRegions>", "</SearchRegions>", input);
RGString searchRegion;
RGString searchDetails;
RGBracketStringSearch individualRegionsSearch ("<Region>", "</Region>", searchRegion);
RGBracketStringSearch familyNameSearch ("<ILSName>", "</ILSName>", searchDetails);
RGBracketStringSearch minILSGridSearch ("<MinGrid>", "</MinGrid>", searchDetails);
RGBracketStringSearch maxILSGridSearch ("<MaxGrid>", "</MaxGrid>", searchDetails);
size_t start = startIndex;
size_t end;
size_t individualEnd;
bool foundData = false;
RGString searchName;
RGString number;
if (!searchRegionsSearch.FindNextBracketedString (start, end, searchRegion))
return false;
startIndex = end;
individualRegionsSearch.ResetSearch ();
start = 0;
while (individualRegionsSearch.FindNextBracketedString (start, end, searchDetails)) {
familyNameSearch.ResetSearch ();
if (!familyNameSearch.FindNextBracketedString (0, individualEnd, searchName))
return false;
if (searchName == familyName) {
minILSGridSearch.ResetSearch ();
maxILSGridSearch.ResetSearch ();
if (!minILSGridSearch.FindNextBracketedString (0, individualEnd, number))
return false;
LowerBoundGridLSBasePair = number.ConvertToDouble ();
if (!maxILSGridSearch.FindNextBracketedString (0, individualEnd, number))
return false;
UpperBoundGridLSBasePair = number.ConvertToDouble ();
return true;
}
start = end;
}
return false;
}
RGString PackedTime :: GetStringTime () const {
RGString temp;
RGString Ans;
temp.Convert (hour, 10);
Ans = temp + ":";
temp.Convert (minute, 10);
Ans += temp + ":";
temp.Convert (second, 10);
Ans += temp + ":";
temp.Convert (hsecond, 10);
Ans += temp;
return Ans;
}
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;
}
STRBaseAllele :: STRBaseAllele (const RGString& xmlInput) : BaseAllele (xmlInput) {
RGString Input (xmlInput);
RGBracketStringSearch BPToken ("<BP>", "</BP>", Input);
RGString bpString;
size_t EndPosition;
if (!BPToken.FindNextBracketedString (0, EndPosition, bpString)) {
BP = -1;
Valid = FALSE;
Msg << "Allele invalid...could not find BP string for allele named " << AlleleName << "\n";
// cout << "Allele invalid...could not find BP string...name: " << AlleleName << endl;
}
else
BP = bpString.ConvertToInteger ();
}
Boolean RGDirectory :: FileIsDirectory (const RGString& Name) {
unsigned long Attributes = GetFileAttributes (Name.GetData ());
if (Attributes & FILE_ATTRIBUTE_DIRECTORY)
return TRUE;
return FALSE;
}
Boolean RGDirectory :: FileIsDirectory (const RGString& Name) {
struct stat statbuf;
lstat(Name.GetData (), &statbuf);
if (S_ISDIR (statbuf.st_mode) == 0)
return FALSE;
return TRUE;
}
bool SynonymList :: DoesTargetStringEqualASynonymCaseIndep (const RGString& target) {
RGString lcTarget (target);
lcTarget.ToLower ();
mIt.Reset ();
RGString test;
RGString* nextString;
while (nextString = (RGString*) mIt ()) {
test = *nextString;
test.ToLower ();
if (lcTarget.IsEqualTo (&test))
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;
}
Boolean RGDirectory :: MoveDirectory (const RGString& oldName, const RGString& suffix, int MaxLevels) {
int i = 0;
RGString newName = oldName + suffix;
while (i < MaxLevels) {
if (!FileOrDirectoryExists (newName)) {
// FinalName = newName;
cout << "Attempting to move " << oldName.GetData () << " to " << newName.GetData () << endl;
return MoveFile (oldName.GetData (), newName.GetData ());
}
i++;
newName += suffix;
}
return FALSE;
}
RGString STRBaseLocus :: ReconstructAlleleName (int id, Allele* nearAllele) {
int difference = id - nearAllele->GetBioID ();
RGString nearName = nearAllele->GetAlleleName ();
if (difference == 0)
return nearName;
int KK = CoreRepeatNumber;
double nearDouble;
int nearInt;
int temp;
RGString intString;
RGString fractString;
RGString returnValue;
nearDouble = nearName.ConvertToDouble ();
nearInt = nearName.ConvertToInteger ();
temp = (int) floor (10 * (nearDouble - nearInt) + 0.5);
// temp is fractional part...should be integer mod 4
if (difference > 0) {
nearInt += (difference / KK);
temp += difference%KK;
nearInt += (temp / KK);
temp = temp%KK;
}
else {
difference = - difference;
nearInt -= (difference / KK);
temp -= difference%KK;
if (temp < 0) {
temp += KK;
nearInt--;
}
}
if (nearInt < 1) {
returnValue = "$";
return returnValue;
}
intString.Convert (nearInt, 10);
if (temp == 0)
return intString;
fractString.Convert (temp, 10);
returnValue = intString + "." + fractString;
return returnValue;
}
LocusWithAlleles :: LocusWithAlleles (const RGString& inputLine) : RGPersistent (), mLineNumber (0), mMaxRFU (0) {
RGStringArray tokens;
RGStringArray delimiters;
RGString locusString (inputLine);
locusString.FindAndReplaceAllSubstrings ("\t\t", "\t");
RGStringTokenizer tokenizer (locusString);
tokenizer.AddDelimiter ("\t");
tokenizer.Split (tokens, delimiters);
int size = tokens.Length ();
int rfu;
double fit;
double residual;
LocusAllele* newAllele;
int i;
if (size >= 8) {
for (i=0; i<8; i++) {
if ((tokens [i].Length () == 0) || (tokens [i] == "\t"))
return;
}
mLineNumber = tokens [0].ConvertToInteger ();
mLocusName = tokens [1];
rfu = tokens [2].ConvertToInteger ();
residual = tokens [3].ConvertToDouble ();
fit = tokens [4].ConvertToDouble ();
newAllele = new LocusAllele (rfu, residual, fit);
InsertAllele (newAllele);
rfu = tokens [5].ConvertToInteger ();
residual = tokens [6].ConvertToDouble ();
fit = tokens [7].ConvertToDouble ();
newAllele = new LocusAllele (rfu, residual, fit);
InsertAllele (newAllele);
}
}
bool SynonymList :: DoesTargetStringEqualASynonym (const RGString& target) {
RGString* nextString;
mIt.Reset ();
while (nextString = (RGString*) mIt()) {
if (target.IsEqualTo (nextString))
return true;
}
return false;
}
RGString LocusData :: FormXMLString () {
RGString Result;
if (AlleleStringIsEmpty ())
return Result;
RGTPtrDList<RGString> temp;
RGString sixTabs = "\t\t\t\t\t\t";
RGString sevenTabs = "\t\t\t\t\t\t\t";
RGString eightTabs = "\t\t\t\t\t\t\t\t";
Result << sixTabs << "<Locus>\n";
Result << sevenTabs << "<Name>" << (char*)mLocusName.GetData () << "</Name>\n";
RGString* nextAllele;
while (mAlleleList.entries () > 0) {
nextAllele = mAlleleList.RemoveFirst ();
nextAllele->FindAndReplaceAllSubstrings ("\"", "");
temp.append (nextAllele);
Result << sevenTabs << "<Allele>\n";
Result << eightTabs << "<Name>" << (char*)nextAllele->GetData () << "</Name>\n";
Result << eightTabs << "<BioID>0</BioID>\n";
Result << sevenTabs << "</Allele>\n";
}
Result << sixTabs << "</Locus>\n";
//cout << (char*) Result.GetData ();
while (temp.entries () > 0) {
nextAllele = temp.RemoveFirst ();
mAlleleList.append (nextAllele);
}
return Result;
}
int SmartNoticeWarehouse :: AddType (SmartNotice* NewType) {
RGPersistent* test = ClassTypes->Append (NewType);
int val;
if (SmartNoticeWarehouse::DebugFlag) {
RGString name (NewType->GetName ());
cout << "Adding class to notice list, Name = " << name.GetData () << endl;
}
if (test != NULL) {
val = ClassTypes->Entries ();
}
else {
val = 0;
}
return val;
}
bool SynonymList :: DoesTargetStringContainASynonymCaseIndep (const RGString& target) {
mIt.Reset ();
RGString* nextString;
size_t pos = 0;
while (nextString = (RGString*) mIt ()) {
if (target.FindSubstringCaseIndependent (*nextString, pos))
return true;
}
return false;
}
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);
}
}
}
}
int CopyVolumeFile (const RGString& inputFileName, const RGString& outputFileName) {
RGFile inputFile (inputFileName, "rt");
if (!inputFile.isValid ()) {
cout << "Could not read " << inputFileName.GetData () << " for default volume...exiting" << endl;
return -1;
}
RGString inputFileString;
inputFileString.ReadTextFile (inputFile);
RGTextOutput outputFile (outputFileName, FALSE);
if (!outputFile.FileIsValid ()) {
cout << "Could not create " << outputFileName.GetData () << "...exiting" << endl;
return -1;
}
outputFile << inputFileString;
return 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);
}
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;
}*/
}
}
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 ();
}
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;
}
}
int CoreBioComponent :: InitializeSM (SampleData& fileData, PopulationCollection* collection, const RGString& markerSetName, Boolean isGrid) {
//
// This is ladder and sample stage 1
//
mTime = fileData.GetCollectionStartTime ();
mDate = fileData.GetCollectionStartDate ();
mName = fileData.GetName ();
mRunStart = mDate.GetOARString () + mTime.GetOARString ();
mMarkerSet = collection->GetNamedPopulationMarkerSet (markerSetName);
Progress = 0;
smMarkerSetNameUnknown noNamedMarkerSet;
smNamedILSUnknown noNamedILS;
smChannelIsILS channelIsILS;
if (mMarkerSet == NULL) {
ErrorString = "*******COULD NOT FIND MARKER SET NAMED ";
ErrorString << markerSetName << " IN POPULATION COLLECTION********\n";
SetMessageValue (noNamedMarkerSet, true);
AppendDataForSmartMessage (noNamedMarkerSet, markerSetName);
return -1;
}
mLaneStandard = mMarkerSet->GetLaneStandard ();
mNumberOfChannels = mMarkerSet->GetNumberOfChannels ();
if ((mLaneStandard == NULL) || !mLaneStandard->IsValid ()) {
ErrorString = "Could not find named internal lane standard associated with marker set named ";
ErrorString << markerSetName << "\n";
cout << "Could not find named internal lane standard associated with marker set named " << (char*)markerSetName.GetData () << endl;
SetMessageValue (noNamedILS, true);
AppendDataForSmartMessage (noNamedILS, markerSetName);
return -1;
}
mDataChannels = new ChannelData* [mNumberOfChannels + 1];
int i;
const int* fsaChannelMap = mMarkerSet->GetChannelMap ();
for (i=0; i<=mNumberOfChannels; i++)
mDataChannels [i] = NULL;
mLaneStandardChannel = mMarkerSet->GetLaneStandardChannel ();
for (i=1; i<=mNumberOfChannels; i++) {
if (i == mLaneStandardChannel)
mDataChannels [i] = GetNewLaneStandardChannel (i, mLaneStandard);
else {
if (isGrid)
mDataChannels [i] = GetNewGridDataChannel (i, mLaneStandard);
else
mDataChannels [i] = GetNewDataChannel (i, mLaneStandard);
}
mDataChannels [i]->SetFsaChannel (fsaChannelMap [i]);
}
mLSData = mDataChannels [mLaneStandardChannel];
mLSData->SetMessageValue (channelIsILS, true);
mMarkerSet->ResetLocusList ();
Locus* nextLocus;
while (nextLocus = mMarkerSet->GetNextLocus ())
mDataChannels [nextLocus->GetLocusChannel ()]->AddLocus (nextLocus);
Progress = 1;
return 0;
}
STRBaseLocus :: STRBaseLocus (const RGString& xmlInput) : BaseLocus (xmlInput), LowerBoundGridLSIndex (-1.0),
UpperBoundGridLSIndex (-1.0), MinimumGridTime (-1.0), MaximumGridTime (-1.0), LowerBoundGridLSBasePair (-1.0),
UpperBoundGridLSBasePair (-1.0), mNoExtension (false) {
mSampleLocusSpecificStutterThreshold = Locus::GetSampleStutterThreshold ();
mSampleLocusSpecificPlusStutterThreshold = Locus::GetSamplePlusStutterThreshold ();
mSampleLocusSpecificAdenylationThreshold = Locus::GetSampleAdenylationThreshold ();
mSampleLocusSpecificFractionalFilter = Locus::GetSampleFractionalFilter ();
mSampleLocusSpecificPullupFractionalFilter = Locus::GetSamplePullupFractionalFilter ();
mSampleLocusSpecificHeterozygousImbalanceThreshold = Locus::GetHeterozygousImbalanceLimit ();
mSampleLocusSpecificMinBoundForHomozygote = Locus::GetMinBoundForHomozygote ();
mLadderLocusSpecificStutterThreshold = Locus::GetGridStutterThreshold ();
mLadderLocusSpecificAdenylationThreshold = Locus::GetGridAdenylationThreshold ();
mLadderLocusSpecificFractionalFilter = Locus::GetGridFractionalFilter ();
mLadderLocusSpecificPullupFractionalFilter = Locus::GetGridPullupFractionalFilter ();
RGString Input (xmlInput);
RGBracketStringSearch MinToken ("<MinBP>", "</MinBP>", Input);
RGBracketStringSearch MaxToken ("<MaxBP>", "</MaxBP>", Input);
RGBracketStringSearch LowerGridIndex ("<MinGridLSIndex>", "</MinGridLSIndex>", Input);
RGBracketStringSearch UpperGridIndex ("<MaxGridLSIndex>", "</MaxGridLSIndex>", Input);
RGBracketStringSearch CoreRepeatSearch ("<CoreRepeatNumber>", "</CoreRepeatNumber>", Input);
RGBracketStringSearch LowerGridBasePair ("<MinGridLSBasePair>", "</MinGridLSBasePair>", Input);
RGBracketStringSearch UpperGridBasePair ("<MaxGridLSBasePair>", "</MaxGridLSBasePair>", Input);
RGBracketStringSearch NoExtensionSearch ("<NoExtension>", "</NoExtension>", Input);
RGXMLTagSearch yLinkedSearch ("YLinked", Input);
RGXMLTagSearch maxExpectedAllelesSearch ("MaxExpectedAlleles", Input);
RGXMLTagSearch minExpectedAllelesSearch ("MinExpectedAlleles", Input);
size_t EndPosition;
RGString BPString;
RGString extString;
bool lowerBoundFound = false;
bool upperBoundFound = false;
RGString trueString ("true");
RGString familyName = BaseLocus::GetILSFamilyName ();
// cout << "Current Family Name = " << familyName.GetData () << endl; // This was a test to make sure the family name is known at this point. Test succeeded 12/31/2015.
bool useILSFamilies = PopulationCollection::UseILSFamiliesInLadderFile (); // if true, use families; otherwise, use the old way.
bool isValid = true;
size_t StartPosition = 0;
if (NoExtensionSearch.FindNextBracketedString (0, EndPosition, extString)) {
if (extString.FindNextSubstringCaseIndependent (0, trueString, EndPosition))
mNoExtension = true;
else
mNoExtension = false;
}
if (!MinToken.FindNextBracketedString (0, EndPosition, BPString)) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Minimum Base Pair token\n";
MinimumBP = -1;
}
else
MinimumBP = BPString.ConvertToInteger ();
if (!MaxToken.FindNextBracketedString (0, EndPosition, BPString)) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Maximum Base Pair token\n";
MaximumBP = -1;
}
else
MaximumBP = BPString.ConvertToInteger ();
if (LowerGridIndex.FindNextBracketedString (0, EndPosition, BPString)) {
LowerBoundGridLSIndex = BPString.ConvertToDouble ();
lowerBoundFound = true;
}
if (UpperGridIndex.FindNextBracketedString (0, EndPosition, BPString)) {
UpperBoundGridLSIndex = BPString.ConvertToDouble ();
upperBoundFound = true;
}
// test for ladder with ILS Family names here and, if found, use family name instead of the following four if's *******
if (useILSFamilies) {
isValid = GetLadderSearchRegion (StartPosition, Input, familyName);
if (!isValid) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find family-based search region\n";
}
}
else {
if (LowerGridBasePair.FindNextBracketedString (0, EndPosition, BPString)) {
LowerBoundGridLSBasePair = BPString.ConvertToDouble ();
lowerBoundFound = true;
}
if (UpperGridBasePair.FindNextBracketedString (0, EndPosition, BPString)) {
UpperBoundGridLSBasePair = BPString.ConvertToDouble ();
upperBoundFound = true;
}
if (!lowerBoundFound) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Minimum Grid Internal Lane Standard token, either index or base pair\n";
}
if (!upperBoundFound) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Maximum Grid Internal Lane Standard token, either index or base pair\n";
}
}
if (!CoreRepeatSearch.FindNextBracketedString (0, EndPosition, BPString))
CoreRepeatNumber = 4;
else
CoreRepeatNumber = BPString.ConvertToInteger ();
if (!yLinkedSearch.FindNextTag (0, EndPosition, BPString))
mIsYLinked = false;
else {
if (BPString == "false")
mIsYLinked = false;
else
mIsYLinked = true;
}
if (!maxExpectedAllelesSearch.FindNextTag (0, EndPosition, BPString))
mMaxExpectedAlleles = 2;
else
mMaxExpectedAlleles = BPString.ConvertToInteger ();
if (!minExpectedAllelesSearch.FindNextTag (0, EndPosition, BPString))
mMinExpectedAlleles = 1;
else
mMinExpectedAlleles = BPString.ConvertToInteger ();
if (!Valid) {
Msg << "XML Input:\n" << Input << "\n";
}
}
