X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=c1dac1443a4d2a213ab715d79908e6dd76027a62;hb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;hp=8bdf845e372a9dfc25c8700b14afaa9f6802c8b8;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 8bdf845..c1dac14 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,37 +12,47 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
 
 
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand();	
-	~DistanceCommand() {};
+	DistanceCommand(string);
+	~DistanceCommand();
 	int execute();	
+	void help();
 	
 private:
-	GlobalData* globaldata;
-	ValidCalculators* validCalculator;
+	struct linePair {
+		int start;
+		int end;
+	};
+	
 	Dist* distCalculator;
-	SequenceDB* seqDB;
-	ReadSeqs* readSeqs;
-	ofstream out;
-	string outputFileName;
-	string countends;
+	SequenceDB alignDB;
+
+	string countends, output, fastafile, calc, outputDir;
 	int processors;
 	float cutoff;
+	map<int, int> processIDS;   //end line, processid
+	vector<linePair*> lines;
+	
+	bool abort;
+	vector<string>  Estimators; //holds estimators to be used
+	
+	//void appendFiles(string, string);
+	void createProcesses(string);
+	int driver(/*Dist*, SequenceDB, */int, int, string, float);
+	
+	#ifdef USE_MPI 
+	int driverMPI(int, int, MPI_File&, float);
+	#endif
 	
-	void appendFiles(string, string);
-	int driver(Dist*, SequenceDB*, int, int, string, float);
+	int convertMatrix(string);
+	int convertToLowerTriangle(string);
 
 };