bool GenotypesForAMarkerSet :: ContainsSampleTriallele (const RGString& locusName, RGDList& alleles) {
RGDList locusCollection;
if (mSampleTriAlleles == NULL)
return false;
if (!mSampleTriAlleles->FindAllCopiesOfNamedLocus (locusName, locusCollection))
return false;
RGDListIterator itCollection (locusCollection);
IndividualLocus* nextLocus;
while (nextLocus = (IndividualLocus*) itCollection ()) {
if (nextLocus->IsContainedIn (alleles)) {
locusCollection.Clear ();
return true;
}
}
locusCollection.Clear ();
return false;
}
bool GenotypesForAMarkerSet :: ContainsOffLadderAllele (const RGString& locusName, const RGString& alleleName) {
RGDList alleleList;
bool returnValue;
if (mOffLadderAlleles == NULL)
return false;
if (!mOffLadderAlleles->FindAllAllelesForNamedLocus (locusName, alleleList)) {
alleleList.Clear ();
return false;
}
IndividualAllele target;
target.SetName (alleleName);
if (alleleList.Contains (&target))
returnValue = true;
else
returnValue = false;
alleleList.Clear ();
return returnValue;
}
Boolean STRBaseLocus :: ExtractGridSignals (RGDList& channelSignalList, const LaneStandard* ls, RGDList& locusDataSignalList, ChannelData* lsData, Locus* locus) {
int lsSize = ls->GetNumberOfCharacteristics ();
int i1;
int i2;
double c1;
double c2;
Notice* newNotice;
if (lsSize < 0) {
Msg << "Number of characteristics not available for Locus named " << LocusName << "\n";
newNotice = new SetupErrorNumberPeaksUnavailableForLocus;
locus->AddNoticeToList (newNotice);
return FALSE;
}
if (LowerBoundGridLSBasePair < 0.0) {
i1 = (int) floor (LowerBoundGridLSIndex);
if (i1 < 0) {
Msg << "Internal Lane Standard lower bound index for Grid is out of bounds for Locus named " << LocusName << "\n";
return FALSE;
}
i2 = i1 + 1;
c2 = LowerBoundGridLSIndex - i1;
c1 = 1.0 - c2;
MinimumGridTime = c1 * ls->GetLaneStandardTimeForCharacteristicNumber (i1) +
c2 * ls->GetLaneStandardTimeForCharacteristicNumber (i2);
// cout << "Not using base pairs for minimum of locus " << LocusName << endl;
}
else
MinimumGridTime = lsData->GetTimeForSpecifiedID (LowerBoundGridLSBasePair);
if (UpperBoundGridLSBasePair < 0.0) {
i1 = (int) floor (UpperBoundGridLSIndex);
if (i1 < 0) {
Msg << "Internal Lane Standard upper bound index for Grid is out of bounds for Locus named " << LocusName << "\n";
return FALSE;
}
i2 = i1 + 1;
c2 = UpperBoundGridLSIndex - i1;
c1 = 1.0 - c2;
MaximumGridTime = c1 * ls->GetLaneStandardTimeForCharacteristicNumber (i1) +
c2 * ls->GetLaneStandardTimeForCharacteristicNumber (i2);
// cout << "Not using base pairs for maximum of locus " << LocusName << endl;
}
else
MaximumGridTime = lsData->GetTimeForSpecifiedID (UpperBoundGridLSBasePair);
RGDListIterator it (channelSignalList);
DataSignal* nextSignal;
double nextMean;
locusDataSignalList.Clear ();
// Assume channelSignalList is in increasing order by signal means
while (nextSignal = (DataSignal*) it ()) {
nextMean = nextSignal->GetMean ();
if (nextMean >= MinimumGridTime) {
if (nextMean <= MaximumGridTime) {
it.RemoveCurrentItem ();
locusDataSignalList.Append (nextSignal);
}
else
break;
}
}
if (locusDataSignalList.Entries () < mLocusSize) {
Msg << "Locus named " << LocusName << " could not find the required number of unanalyzed peaks in range\n";
newNotice = new LocusHasTooFewPeaks;
locus->AddNoticeToList (newNotice);
return FALSE;
}
return TRUE;
}
