added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index d72b8146d36bc659ec13ddffc28463ef4a7b8204..5f4f9f06ba48032777e332c3267ae048937d9b48 100644 (file)
--- 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 {
        
@@ -55,10 +47,11 @@ class TrimOligos {
         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;
@@ -77,7 +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