made make.table alias to count.seqs command. added large parameter to count.seqs...

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index 8830dff57af8985c4f0e0bd4464f0860a46e8b81..a32b3d8e4f2d388b15b3aa68ed66fa61f33c1681 100644 (file)
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -19,25 +19,39 @@
 class TrimOligos {
        
        public:
-               TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
+        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>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
+        TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
                ~TrimOligos();
        
                int stripBarcode(Sequence&, int&);      
                int stripBarcode(Sequence&, QualityScores&, int&);
+    
+        int stripRBarcode(Sequence&, int&);    
+        int stripRBarcode(Sequence&, QualityScores&, int&);
        
                int stripForward(Sequence&, int&);
-               int stripForward(Sequence&, QualityScores&, 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;
+               int pdiffs, bdiffs, ldiffs, sdiffs;
        
                map<string, int> barcodes;
+        map<string, int> rbarcodes;
                map<string, int> primers;
                vector<string> revPrimer;
+        vector<string> linker;
+        vector<string> spacer;
        
                MothurOut* m;