removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 34dd65e66ee0984d298e68ba0cc587343d191d5b..23cc6a580a16756d5b30420cb825b5d43d21ae83 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,39 +12,61 @@
 
 #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"
 
 
-using namespace std;
-
 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;
-       ReadSeqs* readSeqs;
-       ofstream out;
-       string outputFileName;
-       string ends;
-       int processors;
+       SequenceDB alignDB;
+
+       string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
+       int processors, numNewFasta;
        float cutoff;
+       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);
-       int driver(Dist*, SequenceDB*, int, int, string, float);
+       //int convertMatrix(string);
+       bool sanityCheck();
+       //int convertToLowerTriangle(string);
 
 };