Ladder* Bins :: AssembleAllLoci (RGDList& doNotExtend) {
int nLoci;
Ladder* newLadder = new Ladder ();
Locus* nextLocus;
nLoci = SplitFileIntoLocusStrings ();
int i;
int status;
RGString name;
if (nLoci <= 0) {
cout << "Could not complete ladder setup" << endl;
delete newLadder;
return NULL;
}
for (i=1; i<=nLoci; i++) {
SplitLocusStringIntoLines (i);
nextLocus = AssembleLocusFromLineStrings ();
status = newLadder->AddLocus (nextLocus);
if (status < 0) {
cout << "Locus name repeated in bins file: " << nextLocus->GetName ().GetData () << endl;
delete newLadder;
return NULL;
}
name = nextLocus->GetName ();
if (doNotExtend.Contains (&name))
nextLocus->SetDoNotExtend ();
}
return newLadder;
}
Locus* Ladder :: FindLocusByName (const RGString& locusName) {
Locus* nextLocus;
list <Locus*>::const_iterator locusIterator;
for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {
nextLocus = *locusIterator;
if (nextLocus->GetName () == locusName)
return nextLocus;
}
return NULL;
}