working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
new file mode 100644 (file)
index 0000000..8830dff
--- /dev/null
+++ b/trimoligos.h
@@ -0,0 +1,49 @@
+#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 stripBarcode(Sequence&, int&);      
+               int stripBarcode(Sequence&, QualityScores&, int&);
+       
+               int stripForward(Sequence&, int&);
+               int stripForward(Sequence&, QualityScores&, int&);
+       
+               bool stripReverse(Sequence&);
+               bool stripReverse(Sequence&, QualityScores&);
+                               
+       
+       private:
+               int pdiffs, bdiffs;
+       
+               map<string, int> barcodes;
+               map<string, int> primers;
+               vector<string> revPrimer;
+       
+               MothurOut* m;
+       
+               bool compareDNASeq(string, string);                             
+               int countDiffs(string, string);                 
+};
+
+#endif
+