X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=6abf06a6fcf11bba1a714c6b3efdfd2be37b7285;hb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;hp=2334628d08b87e00a4823ebcbe4859cf872358b2;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 2334628..6abf06a 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,21 +12,35 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
 
 class SeqSummaryCommand : public Command {
 public:
-	SeqSummaryCommand();
+	SeqSummaryCommand(string);
 	~SeqSummaryCommand();
 	int execute();
+	void help();
 	
 private:
-	GlobalData* globaldata;	
+	bool abort;
+	string fastafile, outputDir;
+	int processors;
+	
+	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
+
 
 };