working on current change

[mothur.git] / shhhercommand.h

diff --git a/shhhercommand.h b/shhhercommand.h
index 8d29d86e0ec606379e471a363dbe33af34336d8e..a95815fd154be1027d79cb33861c733be207ef1d 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "shhh.seqs";   }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString(); 
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          
@@ -32,7 +33,7 @@ private:
        
        int abort;
        
-       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
 
        int processors, maxIters;
        float cutoff, sigma, minDelta;
@@ -65,7 +66,9 @@ private:
        vector<int> mapSeqToUnique;
        vector<int> mapUniqueToSeq;
        vector<int> uniqueLengths;
-       
+
+       vector<string> outputNames;
+
        int numSeqs, numUniques, numOTUs, numFlowCells;
        
        void getSingleLookUp();