added citation function to commands

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 02103e77e023fff8e60b1bc71cdd52e47bf09470..4bf6759dcda1d4eccda99658780a1e9d819bcece 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,25 +12,45 @@
 
 #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(string);
        SeqSummaryCommand();
-       ~SeqSummaryCommand();
-       int execute();
+       ~SeqSummaryCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
        
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
-       int numSeqs;    
-       GlobalData* globaldata; 
-       ReadSeqs* readSeqs;
-       SequenceDB* db;
+       bool abort;
+       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
+
+
 };
 
 #endif