X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=81b915efcbf97e4b91bfca3bf27353da8f9ea8e9;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=2c31ba2245b523b7f18c0a3559ee9cd6f85890df;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 2c31ba2..81b915e 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -16,7 +16,12 @@ class ScreenSeqsCommand : public Command {
 	
 public:
 	ScreenSeqsCommand(string);
+	ScreenSeqsCommand();
 	~ScreenSeqsCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
@@ -44,8 +49,14 @@ private:
 
 	bool abort;
 	string fastafile, namefile, groupfile, alignreport, outputDir;
-	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
 	vector<string> outputNames;
+	vector<string> optimize;
+	map<string, vector<string> > outputTypes;
+	
+	int getSummary(vector<unsigned long int>&);
+	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);	
 };
 
 #endif