added countgaps parameter to chop.seqs command

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 02103e77e023fff8e60b1bc71cdd52e47bf09470..a62572673c3d7497007ab959157fd41dfb6b124b 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,25 +12,36 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
 
 class SeqSummaryCommand : public Command {
 public:
-       SeqSummaryCommand();
+       SeqSummaryCommand(string);
        ~SeqSummaryCommand();
        int execute();
+       void help();
        
 private:
-       int numSeqs;    
-       GlobalData* globaldata; 
-       ReadSeqs* readSeqs;
-       SequenceDB* db;
+       bool abort;
+       string fastafile, outputDir;
+       int processors;
+       
+       struct linePair {
+               unsigned long int start;
+               int num;
+               linePair(unsigned 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<unsigned long int>&); 
+       #endif
+
+
 };
 
 #endif