X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffmultiplecommand.h;h=1a492a82155fe0a7314b8c2ec54a9a4b37017909;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=4ab2c972557500c059b48ef38f712483f5731231;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d;p=mothur.git

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index 4ab2c97..1a492a8 100644
--- 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;