X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=23cc6a580a16756d5b30420cb825b5d43d21ae83;hb=1b49ed179327150ebf24d77b33d9b3e6872cc8c0;hp=8322eeedee6721ae333fdcbd6bc0447c9d654c53;hpb=e7fe6dd9db877b98c362f9524c3130bbbd037200;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 8322eee..23cc6a5 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,41 +12,61 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
 
-struct linePair {
-	int start;
-	int end;
-};
 
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand();	
-	~DistanceCommand() {};
-	int execute();	
+	DistanceCommand(string);
+	DistanceCommand();
+	~DistanceCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "dist.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	ValidCalculators* validCalculator;
+	struct distlinePair {
+		int start;
+		int end;
+		
+	};
+	
 	Dist* distCalculator;
-	SequenceDB* seqDB;
-	ofstream out, phylipOut;
-	ifstream in;
-	string outputFileName;
-	string countends, phylip;
-	int processors;
+	SequenceDB alignDB;
+
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
+	int processors, numNewFasta;
 	float cutoff;
-	map<int, int> processIDS;   //end line, processid
-	map<int, int>::iterator it;
-	vector<linePair*> lines;
+	vector<int> processIDS;   //end line, processid
+	vector<distlinePair> lines;
+	
+	bool abort;
+	vector<string>  Estimators, outputNames; //holds estimators to be used
+	
+	//void m->appendFiles(string, string);
+	void createProcesses(string);
+	int driver(/*Dist*, SequenceDB, */int, int, string, float);
+	int driver(int, int, string, string);
+	
+	#ifdef USE_MPI 
+	int driverMPI(int, int, MPI_File&, float);
+	int driverMPI(int, int, string, unsigned long int&);
+	int driverMPI(int, int, string, unsigned long int&, string);
+	#endif
 	
-	void appendFiles(string, string);
-	void createProcesses(string, string);
-	int driver(Dist*, SequenceDB*, int, int, string, string, float);
+	//int convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };