moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
deleted file mode 100644 (file)
index e3ea7d5..0000000
--- a/trimoligos.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#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
-