X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimoligos.h;h=5f4f9f06ba48032777e332c3267ae048937d9b48;hp=8830dff57af8985c4f0e0bd4464f0860a46e8b81;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063

diff --git a/trimoligos.h b/trimoligos.h
index 8830dff..5f4f9f0 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -19,30 +19,64 @@
 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>, 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>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes
 		~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&);
+		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&);
-				
+    
+        bool stripLinker(Sequence&);
+        bool stripLinker(Sequence&, QualityScores&);
+    
+        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;
+		int pdiffs, bdiffs, ldiffs, sdiffs;
+        bool paired;
 	
 		map<string, int> barcodes;
 		map<string, int> primers;
 		vector<string> revPrimer;
+        vector<string> linker;
+        vector<string> spacer;
+        map<string, vector<int> > ifbarcodes;
+        map<string, vector<int> > ifprimers;
+        map<string, vector<int> > irbarcodes;
+        map<string, vector<int> > irprimers;
+        map<int, oligosPair> ipbarcodes;
+        map<int, oligosPair> ipprimers;
+    
+        int maxFBarcodeLength, maxRBarcodeLength, maxFPrimerLength, maxRPrimerLength, maxLinkerLength, maxSpacerLength;
 	
 		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