removed unused copy constructors and comments within comments that where causing...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 137cb735719fba42f0d103af842de80c9930cc3e..b6050f2ee58a3db6f56714e7f313fa9ed93b77b5 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -52,8 +52,8 @@ private:
        bool abort, createGroup;
        string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
        
-       bool flip, allFiles, qtrim;
-       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+       bool flip, allFiles, qtrim, keepforward;
+       int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
        int qWindowSize, qWindowStep, keepFirst, removeLast;
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
        vector<string> revPrimer, outputNames;
@@ -61,6 +61,8 @@ private:
        map<string, int> barcodes;
        vector<string> groupVector;
        map<string, int> primers;
+    vector<string>  linker;
+    vector<string>  spacer;
        map<string, int> combos;
        map<string, int> groupToIndex;
        vector<string> primerNameVector;        //needed here?