X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=065e6b4532e071383c39c54e38047b01a2b45344;hb=4e3080b15a3d0c02f7ef2fd779ead433ffdece31;hp=27bafd530cad4a66ef22e41696eef7e2328bde97;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 27bafd5..065e6b4 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,7 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "trim.flows";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
 	string getDescription()		{ return "trim.flows"; }
 
@@ -59,9 +61,7 @@ private:
 	bool allFiles;
 	int processors;
 	int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
 	int numFlows;
 	float signal, noise;
 	bool fasta;