added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index acb078173501a7d7cf48cc88f5c305e12eccc225..ddbb648593c349bc52ca13bf990a5bc7f31bf50a 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
-
+#include "referencedb.h"
 
 /***********************************************************/
 
@@ -35,11 +35,12 @@ public:
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          
 private:
-
+       ReferenceDB* rdb;
+       
        struct linePair {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
 
        vector<int> processIDS;   //processid
@@ -49,10 +50,10 @@ private:
        int createProcesses(string, string, string);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
-       bool abort, filter;
+       bool abort, filter, save;
        string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;