unifrac parallelization done, changed dist.seqs output=square to calc all distance...

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index b0a3c049025066a566365db37b0229c92920e6bf..64eac8d57affc1090bbc324bb76ccb6f7fa5648d 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -34,8 +34,8 @@ private:
        Dist* distCalculator;
        SequenceDB alignDB;
 
-       string countends, output, fastafile, calc, outputDir;
-       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;
@@ -43,13 +43,20 @@ 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);
+       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
        
-       int convertMatrix(string);
-       int convertToLowerTriangle(string);
+       //int convertMatrix(string);
+       bool sanityCheck();
+       //int convertToLowerTriangle(string);
 
 };