working on topdown in pre.cluster

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index 6716deb464eb0198b00159490d1f33572c6c6d23..d72b8146d36bc659ec13ddffc28463ef4a7b8204 100644 (file)
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -35,10 +35,12 @@ class TrimOligos {
                int stripBarcode(Sequence&, int&);      
                int stripBarcode(Sequence&, QualityScores&, int&);
         int stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
+        int stripBarcode(Sequence&, Sequence&, int&);
        
                int stripForward(Sequence&, int&);
                int stripForward(Sequence&, QualityScores&, int&, bool);
         int stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
+        int stripForward(Sequence&, Sequence&, int&);
        
                bool stripReverse(Sequence&);
                bool stripReverse(Sequence&, QualityScores&);
@@ -48,6 +50,11 @@ class TrimOligos {
     
         bool stripSpacer(Sequence&);
         bool stripSpacer(Sequence&, QualityScores&);
+    
+        //seq, primerStart, primerEnd
+        bool findForward(Sequence&, int&, int&);
+        bool findReverse(Sequence&, int&, int&);
+    
                                
        
        private: