X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=49d992ac193c7aa42ad4492c9190bda40671fc0b;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=b165bba2f2f343a8a20a4b07cb2290a43fd13c32;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index b165bba..49d992a 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -24,7 +24,8 @@ public:
 	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()); }	
 	
@@ -32,9 +33,9 @@ public:
 private:
 
 	struct linePair {
-		unsigned long int start;
-		unsigned long int end;
-		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+		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
@@ -44,23 +45,24 @@ private:
 	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 int>&, set<string>&);
+	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;
+	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 int>&);
+	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*);	
 };