moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 542f4283744024e58b297282f83212ad4b5b1292..4a257612a85c7d1b23ebf37fcc2a8435b996ab60 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -20,7 +20,7 @@
 class DistanceCommand : public Command {
 
 public:
-       DistanceCommand(string);        
+       DistanceCommand(string);
        ~DistanceCommand();
        int execute();  
        void help();
@@ -34,8 +34,8 @@ private:
        Dist* distCalculator;
        SequenceDB alignDB;
 
-       string countends, phylip, fastafile, calc;
-       int processors;
+       string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+       int processors, numNewFasta;
        float cutoff;
        map<int, int> processIDS;   //end line, processid
        vector<linePair*> lines;
@@ -43,9 +43,18 @@ private:
        bool abort;
        vector<string>  Estimators; //holds estimators to be used
        
-       //void appendFiles(string, string);
+       //void m->appendFiles(string, string);
        void createProcesses(string);
        int driver(/*Dist*, SequenceDB, */int, int, string, float);
+       
+       #ifdef USE_MPI 
+       int driverMPI(int, int, MPI_File&, float);
+       int driverMPI(int, int, string, long&);
+       #endif
+       
+       int convertMatrix(string);
+       bool sanityCheck();
+       int convertToLowerTriangle(string);
 
 };