X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimoligos.h;h=5f4f9f06ba48032777e332c3267ae048937d9b48;hp=8aa44bdd365356f195069e4f11528300844fbc7a;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=10f24e97c62351b0611159a13e116f359deade96

diff --git a/trimoligos.h b/trimoligos.h
index 8aa44bd..5f4f9f0 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -15,14 +15,6 @@
 #include "sequence.hpp"
 #include "qualityscores.h"
 
-struct oligosPair {
-	string forward;
-	string reverse;
-	
-	oligosPair() { forward = ""; reverse = "";  }
-	oligosPair(string f, string r) : forward(f), reverse(r) {}
-	~oligosPair() {}
-};
 
 class TrimOligos {
 	
@@ -50,10 +42,16 @@ class TrimOligos {
     
         bool stripSpacer(Sequence&);
         bool stripSpacer(Sequence&, QualityScores&);
-				
+    
+        //seq, primerStart, primerEnd
+        bool findForward(Sequence&, int&, int&);
+        bool findReverse(Sequence&, int&, int&);
+    
+        string reverseOligo(string);
 	
 	private:
 		int pdiffs, bdiffs, ldiffs, sdiffs;
+        bool paired;
 	
 		map<string, int> barcodes;
 		map<string, int> primers;
@@ -72,7 +70,13 @@ class TrimOligos {
 		MothurOut* m;
 	
 		bool compareDNASeq(string, string);				
-		int countDiffs(string, string);			
+		int countDiffs(string, string);
+        
+        int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
+        int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
+        int stripPairedBarcode(Sequence& seq,  int& group);
+        int stripPairedPrimers(Sequence& seq,  int& group);
+
 };
 
 #endif