working on pam

[mothur.git] / sffmultiplecommand.h

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index 4ab2c972557500c059b48ef38f712483f5731231..1a492a82155fe0a7314b8c2ec54a9a4b37017909 100644 (file)
--- a/sffmultiplecommand.h
+++ b/sffmultiplecommand.h
@@ -26,8 +26,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "sff.multiple";                        }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
        string getDescription()         { return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
     
@@ -41,7 +42,8 @@ private:
                int end;
                linePair(int i, int j) : start(i), end(j) {}
        };
-
+    
+    string inputDir;
        string filename, outputDir, flowOrder, lookupFileName, minDelta;
        vector<string> outputNames;
        bool abort, trim, large, flip, allFiles, keepforward, append, makeGroup;