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[mothur.git] / trimoligos.h

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+#ifndef TRIMOLIGOS_H
+#define TRIMOLIGOS_H
+
+/*
+ *  trimoligos.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/1/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "sequence.hpp"
+#include "qualityscores.h"
+
+
+class TrimOligos {
+       
+       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 stripBarcode(Sequence&, int&);      
+               int stripBarcode(Sequence&, QualityScores&, int&);
+       
+               int stripForward(Sequence&, int&);
+               int stripForward(Sequence&, QualityScores&, int&, bool);
+       
+               bool stripReverse(Sequence&);
+               bool stripReverse(Sequence&, QualityScores&);
+    
+        bool stripLinker(Sequence&);
+        bool stripLinker(Sequence&, QualityScores&);
+    
+        bool stripSpacer(Sequence&);
+        bool stripSpacer(Sequence&, QualityScores&);
+                               
+       
+       private:
+               int pdiffs, bdiffs, ldiffs, sdiffs;
+       
+               map<string, int> barcodes;
+               map<string, int> primers;
+               vector<string> revPrimer;
+        vector<string> linker;
+        vector<string> spacer;
+       
+               MothurOut* m;
+       
+               bool compareDNASeq(string, string);                             
+               int countDiffs(string, string);                 
+};
+
+#endif
+