X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=284c9a5ac1a0bd5c90dca6b4854b725d6b428023;hb=af9291809910b6ddf617490ed5c16254b77b449f;hp=291d8e6d1acd4605f4827159f10aa74269e1a771;hpb=57b3c96832667c1b70d4d526331f52e3d49e8237;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 291d8e6..284c9a5 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,7 +23,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "screen.seqs";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	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"; }
 
@@ -43,6 +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>);
@@ -55,12 +58,11 @@ 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;
 	map<string, int> nameMap;
-	int readNames();
 	
 	int getSummary(vector<unsigned long long>&);
 	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);