X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=49d992ac193c7aa42ad4492c9190bda40671fc0b;hb=3094cb29c613d9687e861e1d0cf9104b7141d24e;hp=f88fe2c442cf1d8ea6b0457a45390383c0c45698;hpb=dc874a77f24b3808775e2ce7e39595c647a07f82;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index f88fe2c..49d992a 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,27 +11,60 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-#include <set>
-
-using namespace std;
 
 class ScreenSeqsCommand : public Command {
 	
 public:
+	ScreenSeqsCommand(string);
 	ScreenSeqsCommand();
-	~ScreenSeqsCommand();
-	int execute();
+	~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:
-	void screenNameGroupFile(set<string>);
-	int numSeqs;	
-	GlobalData* globaldata;	
-	ReadSeqs* readSeqs;
-	SequenceDB* db;
+
+	struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long 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 screenTaxonomy(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&, vector<unsigned long long>&, set<string>&);
+	#endif
+
+	bool abort;
+	string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+	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);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);	
 };
 
 #endif