added namefile to summary.seqs

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 01dd450194c2f454ddd1b6c44de3fda99cde0798..fb24141f08a1314a386bc58899ec57ecf6c56e56 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,18 +12,44 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-
-
 
 class SeqSummaryCommand : public Command {
 public:
+       SeqSummaryCommand(string);
        SeqSummaryCommand();
        ~SeqSummaryCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
-       GlobalData* globaldata; 
+       bool abort;
+       string fastafile, outputDir, namefile;
+       int processors;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       map<string, int> nameMap;
+       
+       struct linePair {
+               unsigned long int start;
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(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 readNames();
+
+       #ifdef USE_MPI
+       int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&); 
+       #endif
+
 
 };