removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 03ec3e0c101cb2a83f3d38bfd21ce75d044f3fc4..623c3c1e8f400f4262414a5cf546143d698840e7 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,24 +12,42 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-
-
 
 class SeqSummaryCommand : public Command {
 public:
        SeqSummaryCommand(string);
-       ~SeqSummaryCommand();
-       int execute();
-       void help();
+       SeqSummaryCommand();
+       ~SeqSummaryCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
        
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
-       GlobalData* globaldata; 
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
        bool abort;
-       string fastafile;
+       string fastafile, outputDir, namefile;
+       int processors;
+       vector<string> outputNames;
+       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*);       
+
+       #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
 
 
 };