X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=4bf6759dcda1d4eccda99658780a1e9d819bcece;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=02103e77e023fff8e60b1bc71cdd52e47bf09470;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 02103e7..4bf6759 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,25 +12,45 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
 
 class SeqSummaryCommand : public Command {
 public:
+	SeqSummaryCommand(string);
 	SeqSummaryCommand();
-	~SeqSummaryCommand();
-	int execute();
+	~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:
-	int numSeqs;	
-	GlobalData* globaldata;	
-	ReadSeqs* readSeqs;
-	SequenceDB* db;
+	bool abort;
+	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
+
+
 };
 
 #endif