X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimoligos.h;h=a86eb9ae1c815a8c71c4331934f88bf6b83f773f;hp=a32b3d8e4f2d388b15b3aa68ed66fa61f33c1681;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7

diff --git a/trimoligos.h b/trimoligos.h
index a32b3d8..a86eb9a 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -15,23 +15,32 @@
 #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>, 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,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 stripRBarcode(Sequence&, int&);	
-        int stripRBarcode(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&);
@@ -41,22 +50,38 @@ 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> rbarcodes;
 		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);
 };
 
 #endif