added MPI to dist.seqs command

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 6a7ac93fa1d7b28d9fe03e1e27f1e4a1ec3ef491..3fa69d553ef857cb854e4ecfe9853ad36ecd2e0c 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;
+       string countends, output, fastafile, calc, outputDir;
        int processors;
        float cutoff;
        map<int, int> processIDS;   //end line, processid
@@ -43,9 +43,12 @@ private:
        bool abort;
        vector<string>  Estimators; //holds estimators to be used
        
-       void appendFiles(string, string);
+       //void appendFiles(string, string);
        void createProcesses(string);
        int driver(/*Dist*, SequenceDB, */int, int, string, float);
+       int driverMPI(int, int, string&, float);
+       
+       int convertMatrix(string);
 
 };