X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=81b915efcbf97e4b91bfca3bf27353da8f9ea8e9;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=8f62ae48af466148c56b2b7b53aef7240cb95761;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 8f62ae4..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();
 	
@@ -35,17 +40,23 @@ private:
 	int screenGroupFile(set<string>);
 	int screenAlignReport(set<string>);
 	
-	int driver(linePair*, string, string, string, string, set<string>&);
-	int createProcesses(string, string, string, string, set<string>&);
+	int driver(linePair*, string, string, string, set<string>&);
+	int createProcesses(string, string, string, set<string>&);
 	
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
 	#endif
 
 	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