paralellized summary.seqs and added mpi code to it.

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 01dd450194c2f454ddd1b6c44de3fda99cde0798..58fbc0a8b4e9dddec4745f65882ac9b6b6dd8002 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,18 +12,35 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-
-
 
 class SeqSummaryCommand : public Command {
 public:
-       SeqSummaryCommand();
+       SeqSummaryCommand(string);
        ~SeqSummaryCommand();
        int execute();
+       void help();
        
 private:
-       GlobalData* globaldata; 
+       bool abort;
+       string fastafile, outputDir;
+       int processors;
+       
+       struct linePair {
+               int start;
+               int num;
+               linePair(long int i, long int j) : start(i), num(j) {}
+       };
+       vector<linePair*> lines;
+       vector<int> processIDS;
+       
+       int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
+       int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);       
+       int setLines(string);
+
+       #ifdef USE_MPI
+       int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<long>&);      
+       #endif
+
 
 };