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;
}
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;
}
