added sort parameter to get.otulist

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index c7aaf46137a97715baee381d56824482a0e08e80..f825cfbf343455b9ba5ef4bfb89836df8775cebe 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();
@@ -34,7 +34,7 @@ private:
        Dist* distCalculator;
        SequenceDB alignDB;
 
-       string countends, phylip, fastafile, calc, outputDir;
+       string countends, output, fastafile, calc, outputDir;
        int processors;
        float cutoff;
        map<int, int> processIDS;   //end line, processid
@@ -46,6 +46,14 @@ private:
        //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);
+       int driverMPI(int, int, string, long&);
+       #endif
+       
+       int convertMatrix(string);
+       int convertToLowerTriangle(string);
 
 };