added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index fb8f74dcb4f309387ccf3caa923354a466c9fccb..6716deb464eb0198b00159490d1f33572c6c6d23 100644 (file)
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -29,7 +29,7 @@ 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<int, oligosPair>, map<int, oligosPair>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, linker, spacer
+        TrimOligos(int,int, int, int, map<int, oligosPair>, map<int, oligosPair>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes
                ~TrimOligos();
        
                int stripBarcode(Sequence&, int&);      
@@ -58,8 +58,14 @@ class TrimOligos {
                vector<string> revPrimer;
         vector<string> linker;
         vector<string> spacer;
-        map<int, oligosPair> ibarcodes;
-        map<int, oligosPair> iprimers;
+        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;