X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=284c9a5ac1a0bd5c90dca6b4854b725d6b428023;hb=3504e4e2feeb05aabb0c79aa42cb696522030924;hp=771113da1bda0ee34859faaa39b2fe7be1bc2672;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 771113d..284c9a5 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,8 +23,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "screen.seqs";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
 	string getDescription()		{ return "enables you to keep sequences that fulfill certain user defined criteria"; }
 
@@ -44,6 +45,7 @@ private:
 
 	int screenNameGroupFile(set<string>);
 	int screenGroupFile(set<string>);
+    int screenCountFile(set<string>);
 	int screenAlignReport(set<string>);
 	int screenQual(set<string>);
 	int screenTaxonomy(set<string>);
@@ -56,7 +58,7 @@ private:
 	#endif
 
 	bool abort;
-	string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+	string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile;
 	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
 	vector<string> outputNames;
 	vector<string> optimize;