Example #1
0
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;
}
Example #2
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;
}