X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.h;h=fb8f74dcb4f309387ccf3caa923354a466c9fccb;hb=cc19310422f125d6628980bd1148e1e816792382;hp=e3ea7d55537e323f3869a6157ff3aed4bbd99eea;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;p=mothur.git

diff --git a/trimoligos.h b/trimoligos.h
index e3ea7d5..fb8f74d 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -15,19 +15,30 @@
 #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 {
 	
 	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,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,int, int, int, map<int, oligosPair>, map<int, oligosPair>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, linker, spacer
 		~TrimOligos();
 	
 		int stripBarcode(Sequence&, int&);	
 		int stripBarcode(Sequence&, QualityScores&, int&);
-	
+        int stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
+    	
 		int stripForward(Sequence&, int&);
 		int stripForward(Sequence&, QualityScores&, int&, bool);
+        int stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
 	
 		bool stripReverse(Sequence&);
 		bool stripReverse(Sequence&, QualityScores&);
@@ -47,6 +58,8 @@ class TrimOligos {
 		vector<string> revPrimer;
         vector<string> linker;
         vector<string> spacer;
+        map<int, oligosPair> ibarcodes;
+        map<int, oligosPair> iprimers;
 	
 		MothurOut* m;