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;
}
void RGHashTable :: ResizeTable (int size) {
RGPersistent* next;
unsigned hash;
unsigned index;
int i;
if (NumberOfLists < size) {
RGDList** NewArray = new RGDList* [size];
for (i=0; i<size; i++) {
if (i < NumberOfLists)
NewArray [i] = ListArray [i];
else
NewArray [i] = new RGDList;
}
delete[] ListArray;
ListArray = NewArray;
for (i=0; i<NumberOfLists; i++) {
if (ListArray [i]->Entries() > 0) {
RGDListIterator* it = new RGDListIterator (*ListArray [i]);
while (next = (*it)()) {
hash = next->HashNumber (size);
index = hash%size;
if (index != i) {
it->RemoveCurrentItem ();
ListArray [index]->Insert (next);
}
}
delete it;
}
}
NumberOfLists = size;
}
else if ((NumberOfLists > size) && (size > 0)) {
RGDList** NewArray = new RGDList* [size];
for (int i=0; i<NumberOfLists; i++) {
if (i < size)
NewArray [i] = ListArray [i];
if (ListArray [i]->Entries() > 0) {
RGDListIterator* it = new RGDListIterator (*ListArray [i]);
while (next = (*it)()) {
hash = next->HashNumber (size);
index = hash%size;
if (index != i) {
it->RemoveCurrentItem ();
ListArray [index]->Insert (next);
}
}
delete it;
}
if (i >= size)
delete ListArray [i];
}
delete[] ListArray;
ListArray = NewArray;
NumberOfLists = size;
}
}
