X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=305c6e34dd0fcf1a66e434b797ea3a5af991dfd0;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=9b2be27ef8337e694484927e33298d8ec9841359;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 9b2be27..305c6e3 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,22 +12,42 @@
 
 #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();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
-	GlobalData* globaldata;	
+	bool abort;
+	string fastafile, outputDir;
+	int processors;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
+	
+	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
+
 
 };