X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=595483d2b3e84aef55478a78bd84906771949e5d;hb=173a1a82a4e4aa6bef8e4ba77bce342fb9c6563e;hp=2cb653f790aeb970f2a8f9ba7e1122d2f8ef4c57;hpb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 2cb653f..595483d 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,40 +12,59 @@
 
 #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() {};
+	DistanceCommand(string);
+	DistanceCommand();
+	~DistanceCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
+	void help();
 	
 private:
-	GlobalData* globaldata;
-	ValidCalculators* validCalculator;
+	struct distlinePair {
+		int start;
+		int end;
+		
+	};
+	
 	Dist* distCalculator;
-	SequenceDB* seqDB;
-	ofstream out, outFile;
-	ifstream in;
-	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;
 	
-	void appendFiles(string, string);
+	bool abort;
+	vector<string>  Estimators, outputNames; //holds estimators to be used
+	map<string, vector<string> > outputTypes;
+	
+	//void m->appendFiles(string, string);
 	void createProcesses(string);
-	int driver(Dist*, SequenceDB*, int, int, string, float);
+	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
+	
+	//int convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };