Merge remote-tracking branch 'origin/master'

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index f4faacb899a8fd547a14d2bd2224b07882356cdf..b7fbf4342b821d1f6eb6dbb7094d94c3e85d19a3 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,6 +26,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
        string getDescription()         { return "trim.flows"; }
@@ -49,7 +50,8 @@ private:
        vector<unsigned long long> getFlowFileBreaks();
        int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
        int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+    string reverseOligo(string);
+    
        vector<string> outputNames;
        set<string> filesToRemove;
        
@@ -66,7 +68,6 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;