void GenotypesForAMarkerSet :: WriteXML (RGTextOutput& text, const RGString& indent, const RGString& offLadderTag, const RGString& triallelesTag, const RGString& posTriTag) {
RGDListIterator it (mGenotypes);
IndividualGenotype* nextGenotype;
Endl endLine;
RGString indent2 = indent + "\t";
text << indent << "<MarkerSetName>" << mMarkerSetName << "</MarkerSetName>" << endLine;
text << indent << "<PositiveControls>" << endLine;
while (nextGenotype = (IndividualGenotype*) it ())
nextGenotype->WriteXML (text, indent2, "PositiveControl");
text << indent << "</PositiveControls>" << endLine;
text << indent << "<" << offLadderTag << ">" << endLine;
mOffLadderAlleles->WriteXML (text, indent2);
text << indent << "</" << offLadderTag << ">" << endLine;
text << indent << "<" << triallelesTag << ">" << endLine;
mSampleTriAlleles->WriteXML (text, indent2);
text << indent << "</" << triallelesTag << ">" << endLine;
text << indent << "<" << posTriTag << ">" << endLine;
mControlTriAlleles->WriteXML (text, indent2);
text << indent << "</" << posTriTag << ">" << endLine;
}
int CoreBioComponent :: TestPositiveControlSM (GenotypesForAMarkerSet* genotypes) {
//
// This is sample stage 5
//
IndividualGenotype* genotype;
smNamedPosCtrlNotFound posCtrlNotFound;
int returnValue = 0;
if (!mIsPositiveControl)
return 0;
genotype = genotypes->FindGenotypeForFileName (mControlIdName);
if (genotype == NULL) {
ParameterServer* pServer = new ParameterServer;
mPositiveControlName = pServer->GetStandardPositiveControlName ();
genotype = genotypes->FindGenotypeForFileName (mPositiveControlName);
delete pServer;
if (genotype == NULL) {
SetMessageValue (posCtrlNotFound, true);
if (mPositiveControlName.Length () > 0)
AppendDataForSmartMessage (posCtrlNotFound, mPositiveControlName);
return -1;
}
}
else
mPositiveControlName = genotype->GetName ();
for (int i=1; i<=mNumberOfChannels; i++) {
if (i != mLaneStandardChannel) {
if (mDataChannels [i]->TestPositiveControlSM (genotype) < 0)
returnValue = -1;
}
}
return returnValue;
}
IndividualGenotype* GenotypesForAMarkerSet :: FindGenotypeThatMatchesFileName (const RGString& fileName) {
RGDListIterator it (mGenotypes);
IndividualGenotype* genotype;
RGString name;
size_t position = 0;
while (genotype = (IndividualGenotype*) it ()) {
name = genotype->GetName ();
if (fileName == name)
return genotype;
}
return NULL;
}
IndividualGenotype* GenotypesForAMarkerSet :: FindGenotypeForFileName (const RGString& fileName) {
RGDListIterator it (mGenotypes);
IndividualGenotype* genotype;
RGString name;
size_t position = 0;
while (genotype = (IndividualGenotype*) it ()) {
// name = genotype->GetName ();
name = genotype->GetFileNameSearchCriterion ();
if (fileName.FindSubstringCaseIndependent (name, position))
return genotype;
}
return NULL;
}
bool GenotypesForAMarkerSet :: AddCollectionToTables (const RGString& xmlString, const RGString& offLadderTag, const RGString& triallelesTag, const RGString& posTriTag) {
RGString XMLString (xmlString);
RGString positiveControlString;
RGString pControlsString;
RGString fullPathControlFileName = GenotypesForAMarkerSet::PathToStandardControlFile + "/LadderSpecifications/StandardPositiveControls.xml";
RGFile* allPositiveControls = new RGFile (fullPathControlFileName, "rt");
if (!allPositiveControls->isValid ()) {
cout << "Could not find positive controls file: " << (char*)fullPathControlFileName.GetData () << endl;
return false;
}
RGString posXMLString;
posXMLString.ReadTextFile (*allPositiveControls);
delete allPositiveControls;
RGXMLTagSearch nameSearch ("MarkerSetName", XMLString);
RGXMLTagSearch positiveControlsSearch ("PositiveControls", posXMLString);
RGXMLTagSearch oldPositiveControlsSearch ("PositiveControls", XMLString);
RGXMLTagSearch posCtrlSearch ("PositiveControl", pControlsString);
RGXMLTagSearch offLadderSearch (offLadderTag, XMLString);
RGXMLTagSearch trialleleSearch (triallelesTag, XMLString);
RGXMLTagSearch posTriSearch (posTriTag, XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
RGString collectionString;
RGString offLadderString;
RGString triString;
RGString posTriString;
size_t startPControls = 0;
size_t endPControls = 0;
bool returnValue = true;
RGString markerSetName;
IndividualGenotype* nextGenotype;
if (!nameSearch.FindNextTag (startOffset, endOffset, markerSetName))
return false;
if (mMarkerSetName.Length () == 0)
mMarkerSetName = markerSetName;
else if (mMarkerSetName != markerSetName)
return false;
startOffset = endOffset;
size_t startOffsetPos = 0;
size_t endOffsetPos = 0;
RGString temp;
if (oldPositiveControlsSearch.FindNextTag (startOffset, endOffset, temp))
startOffset = endOffset;
if (positiveControlsSearch.FindNextTag (startOffsetPos, endOffsetPos, pControlsString)) {
posCtrlSearch.ResetSearch ();
// cout << "Found positive controls in file" << endl;
while (posCtrlSearch.FindNextTag (startPControls, endPControls, positiveControlString)) {
// cout << "Found positive control..." << endl;
startPControls = endPControls;
nextGenotype = new IndividualGenotype (positiveControlString);
if (!nextGenotype->isValid ()) {
returnValue = false;
delete nextGenotype;
}
else {
if (!mGenotypes.Contains (nextGenotype)) {
mGenotypes.Insert (nextGenotype);
// cout << "Inserted genotype in list..." << endl;
}
else {
returnValue = false;
delete nextGenotype;
}
}
}
}
startOffset = endOffset;
if (offLadderSearch.FindNextTag (startOffset, endOffset, offLadderString)) {
if (mOffLadderAlleles == NULL) {
mOffLadderAlleles = new LocusCollection (offLadderString);
if (!mOffLadderAlleles->isValid ())
returnValue = false;
}
else {
if (!mOffLadderAlleles->AddLoci (offLadderString))
returnValue = false;
}
}
startOffset = endOffset;
if (trialleleSearch.FindNextTag (startOffset, endOffset, triString)) {
if (mSampleTriAlleles == NULL) {
mSampleTriAlleles = new LocusCollection (triString);
if (!mSampleTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mSampleTriAlleles->AddLoci (triString))
returnValue = false;
}
}
startOffset = endOffset;
if (posTriSearch.FindNextTag (startOffset, endOffset, posTriString)) {
if (mControlTriAlleles == NULL) {
mControlTriAlleles = new LocusCollection (posTriString);
if (!mControlTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mControlTriAlleles->AddLoci (posTriString))
returnValue = false;
}
}
return returnValue;
}
bool GenotypesForAMarkerSet :: AddCollectionToTablesFromLabSettings (const RGString& xmlString, const RGString& offLadderTag, const RGString& triallelesTag, const RGString& posTriTag) {
RGString XMLString (xmlString);
RGString positiveControlString;
RGString pControlsString;
RGXMLTagSearch nameSearch ("MarkerSetName", XMLString);
RGXMLTagSearch positiveControlsSearch ("PositiveControls", XMLString);
RGXMLTagSearch posCtrlSearch ("PositiveControl", pControlsString);
RGXMLTagSearch offLadderSearch (offLadderTag, XMLString);
RGXMLTagSearch trialleleSearch (triallelesTag, XMLString);
RGXMLTagSearch posTriSearch (posTriTag, XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
RGString collectionString;
RGString offLadderString;
RGString triString;
RGString posTriString;
size_t startPControls = 0;
size_t endPControls = 0;
bool returnValue = true;
RGString markerSetName;
IndividualGenotype* nextGenotype;
if (!nameSearch.FindNextTag (startOffset, endOffset, markerSetName))
return false;
if (mMarkerSetName.Length () == 0)
mMarkerSetName = markerSetName;
else if (mMarkerSetName != markerSetName)
return false;
startOffset = endOffset;
if (positiveControlsSearch.FindNextTag (startOffset, endOffset, pControlsString)) {
posCtrlSearch.ResetSearch ();
startOffset = endOffset;
cout << "Found positive controls in lab settings file" << endl;
while (posCtrlSearch.FindNextTag (startPControls, endPControls, positiveControlString)) {
cout << "Found positive control..." << endl;
startPControls = endPControls;
nextGenotype = new IndividualGenotype (positiveControlString);
if (!nextGenotype->isValid ()) {
returnValue = false;
delete nextGenotype;
}
else {
if (!mGenotypes.Contains (nextGenotype)) {
mGenotypes.Insert (nextGenotype);
cout << "Inserted genotype in list..." << endl;
}
else {
//returnValue = false;
cout << "\nWARNING***Found duplicate positive control named " << nextGenotype->GetName ().GetData () << ". Ignoring...\n" << endl;
delete nextGenotype;
}
}
}
}
startOffset = endOffset;
if (offLadderSearch.FindNextTag (startOffset, endOffset, offLadderString)) {
if (mOffLadderAlleles == NULL) {
mOffLadderAlleles = new LocusCollection (offLadderString);
if (!mOffLadderAlleles->isValid ())
returnValue = false;
}
else {
if (!mOffLadderAlleles->AddLoci (offLadderString))
returnValue = false;
}
}
startOffset = endOffset;
if (trialleleSearch.FindNextTag (startOffset, endOffset, triString)) {
if (mSampleTriAlleles == NULL) {
mSampleTriAlleles = new LocusCollection (triString);
if (!mSampleTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mSampleTriAlleles->AddLoci (triString))
returnValue = false;
}
}
startOffset = endOffset;
if (posTriSearch.FindNextTag (startOffset, endOffset, posTriString)) {
if (mControlTriAlleles == NULL) {
mControlTriAlleles = new LocusCollection (posTriString);
if (!mControlTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mControlTriAlleles->AddLoci (posTriString))
returnValue = false;
}
}
return returnValue;
}
