public:
TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
- TrimOligos(int,int, int, int, map<int, oligosPair>, map<int, oligosPair>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, linker, spacer
+ TrimOligos(int,int, int, int, map<int, oligosPair>, map<int, oligosPair>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes
~TrimOligos();
int stripBarcode(Sequence&, int&);
vector<string> revPrimer;
vector<string> linker;
vector<string> spacer;
- map<int, oligosPair> ibarcodes;
- map<int, oligosPair> iprimers;
+ map<string, vector<int> > ifbarcodes;
+ map<string, vector<int> > ifprimers;
+ map<string, vector<int> > irbarcodes;
+ map<string, vector<int> > irprimers;
+ map<int, oligosPair> ipbarcodes;
+ map<int, oligosPair> ipprimers;
+
+ int maxFBarcodeLength, maxRBarcodeLength, maxFPrimerLength, maxRPrimerLength, maxLinkerLength, maxSpacerLength;
MothurOut* m;