X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=4bf6759dcda1d4eccda99658780a1e9d819bcece;hb=ec1b5bc7460ac8ad40f54f0729900d9ed98e7292;hp=e6b3b879b8f25e72d2151ae69fae8a75f211909d;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index e6b3b87..4bf6759 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -16,13 +16,40 @@
 class SeqSummaryCommand : public Command {
 public:
 	SeqSummaryCommand(string);
-	~SeqSummaryCommand();
-	int execute();
-	void help();
+	SeqSummaryCommand();
+	~SeqSummaryCommand(){}
 	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 private:
 	bool abort;
-	string fastafile, outputDir;
+	string fastafile, outputDir, namefile;
+	int processors;
+	vector<string> outputNames;
+	map<string, int> nameMap;
+	
+	struct linePair {
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+	};
+
+	vector<linePair*> lines;
+	vector<int> processIDS;
+	
+	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);	
+
+	#ifdef USE_MPI
+	int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);	
+	#endif
+
 
 };