X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=3642295b54af9d46fd246ad642065952af7295ab;hb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;hp=071724f79cb45c69bb4c4237c072ddc462188439;hpb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 071724f..3642295 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -16,35 +16,54 @@ class ScreenSeqsCommand : public Command {
 	
 public:
 	ScreenSeqsCommand(string);
-	~ScreenSeqsCommand();
-	int execute();
-	void help();
+	ScreenSeqsCommand();
+	~ScreenSeqsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "screen.seqs";				}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
+	string getDescription()		{ return "enables you to keep sequences that fulfill certain user defined criteria"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 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;
 
 	int screenNameGroupFile(set<string>);
 	int screenGroupFile(set<string>);
 	int screenAlignReport(set<string>);
+	int screenQual(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;
+	string fastafile, namefile, groupfile, alignreport, outputDir, qualfile;
+	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 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