X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.h;h=a32b3d8e4f2d388b15b3aa68ed66fa61f33c1681;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=8830dff57af8985c4f0e0bd4464f0860a46e8b81;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/trimoligos.h b/trimoligos.h
index 8830dff..a32b3d8 100644
--- 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;