modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index c7aaf46137a97715baee381d56824482a0e08e80..b0a3c049025066a566365db37b0229c92920e6bf 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 +46,10 @@ private:
        //void appendFiles(string, string);
        void createProcesses(string);
        int driver(/*Dist*, SequenceDB, */int, int, string, float);
+       int driverMPI(int, int, MPI_File&, float);
+       
+       int convertMatrix(string);
+       int convertToLowerTriangle(string);
 
 };