int Ladder :: MergeLocusIntoLadder (const Locus* locus) {
// This combines info and then computes the rest
Locus* matchingLocus = FindLocusByName (locus->GetName ());
if (matchingLocus == NULL) {
cout << "Could not find locus matching name: " << locus->GetName ().GetData () << endl;
return -1;
}
matchingLocus->SetFirstCoreLocusBP (locus->GetFirstCoreLocusBP ());
matchingLocus->SetFirstExtendedAllele (locus->GetFirstExtendedAllele ());
matchingLocus->SetLastExtendedAllele (locus->GetLastExtendedAllele ());
matchingLocus->ComputeAllBPs ();
matchingLocus->SetMinMaxSearchILSBP (locus->GetMinSearchILSBP (), locus->GetMaxSearchILSBP ());
matchingLocus->AdjustSearchRegion ();
matchingLocus->SetMerged ();
return 0;
}
Locus* Bins :: AssembleLocusFromLineStrings () {
// uses current values in mLocusLineStrings
Locus* newLocus = new Locus ();
int nLines = mLocusLineStrings.Length ();
SplitLocusLine (mLocusLineStrings [0]); // This should give us the name field
RGString name = mLocusLineFieldString [1];
cout << "Locus name = " << name.GetData () << endl;
//cout << "Bins locus line 1: ";
int i;
int len = mLocusLineFieldString.Length ();
//for (i=0; i<len; i++) {
// cout << mLocusLineFieldString [i].GetData ();
// if (i < len - 1)
// cout << ", ";
//}
//cout << endl;
RGString firstAlleleName;
int firstLocusBP;
double firstILSBP;
double lastILSBP;
RGString firstExtendedAlleleName;
RGString lastExtendedAlleleName;
int lineForFirstAllele = 0;
for (i=1; i<nLines; i++) {
SplitLocusLine (mLocusLineStrings [i]);
if (mLocusLineFieldString.Length () < 4) {
cout << "Could not find first allele for locus " << name.GetData () << endl;
delete newLocus;
return NULL;
}
if (mLocusLineFieldString.Length () >= 5) {
if (mLocusLineFieldString [4] == "virtual") {
if (i == 1) {
firstExtendedAlleleName = mLocusLineFieldString [0];
}
continue;
}
}
firstAlleleName = mLocusLineFieldString [0];
firstILSBP = mLocusLineFieldString [1].ConvertToDouble ();
firstLocusBP = (int) floor (firstILSBP + 0.5);
lineForFirstAllele = i;
break;
}
if (firstExtendedAlleleName.Length () == 0)
firstExtendedAlleleName = firstAlleleName;
bool foundLastExtendedAllele = false;
for (i=nLines-1; i>lineForFirstAllele; i--) {
SplitLocusLine (mLocusLineStrings [i]);
if (mLocusLineFieldString.Length () < 4)
continue;
if (!foundLastExtendedAllele) {
lastExtendedAlleleName = mLocusLineFieldString [0];
foundLastExtendedAllele = true;
}
if ((mLocusLineFieldString.Length () >= 5) && (mLocusLineFieldString [4] == "virtual"))
continue;
lastILSBP = mLocusLineFieldString [1].ConvertToDouble ();
break;
}
if (lastExtendedAlleleName.Length () == 0) {
cout << "Could not locate last extended allele name for locus: " << name.GetData () << endl;
delete newLocus;
return NULL;
}
newLocus->SetFirstCoreAllele (firstAlleleName);
newLocus->SetFirstExtendedAllele (firstExtendedAlleleName);
newLocus->SetLastExtendedAllele (lastExtendedAlleleName);
newLocus->SetMinMaxSearchILSBP (firstILSBP, lastILSBP); // These will have to be adjusted later when core repeat number is known
newLocus->SetFirstCoreLocusBP (firstLocusBP);
newLocus->SetName (name);
// Need to add to Locus ability to compute first and last extended bp
return newLocus;
}