added versioning info to all shortcut files mothur makes.

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 97b36155af670c3d038c882e742356a1c6ee9a03..071724f79cb45c69bb4c4237c072ddc462188439 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,7 +11,6 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 
 class ScreenSeqsCommand : public Command {
        
@@ -22,16 +21,30 @@ public:
        void help();
        
 private:
-       void screenNameGroupFile(set<string>);
-       void screenGroupFile(set<string>);
 
-       GlobalData* globaldata; 
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
+       struct linePair {
+               unsigned long int start;
+               int numSeqs;
+               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+       };
+       vector<int> processIDS;   //processid
+       vector<linePair*> lines;
+
+       int screenNameGroupFile(set<string>);
+       int screenGroupFile(set<string>);
+       int screenAlignReport(set<string>);
+       
+       int driver(linePair*, string, string, string, string, set<string>&);
+       int createProcesses(string, string, string, string, set<string>&);
+       
+       #ifdef USE_MPI
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
+       #endif
+
        bool abort;
-       string fastafile, namefile, groupfile;
-       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+       string fastafile, namefile, groupfile, alignreport, outputDir;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+       vector<string> outputNames;
 };
 
 #endif