X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=81b915efcbf97e4b91bfca3bf27353da8f9ea8e9;hb=6a0001cc8c2f8de157f4979fd0d97a6e911b58e8;hp=071724f79cb45c69bb4c4237c072ddc462188439;hpb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 071724f..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();
 	
@@ -24,9 +29,10 @@ private:
 
 	struct linePair {
 		unsigned long int start;
-		int numSeqs;
-		linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
+
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 
@@ -34,17 +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