some bug fixes

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 56c9d82f1625a2a9481a203b7b217a9bc3b66bc4..071724f79cb45c69bb4c4237c072ddc462188439 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,25 +11,40 @@
  */
 #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 ScreenSeqsCommand : public Command {
        
 public:
-       ScreenSeqsCommand();
+       ScreenSeqsCommand(string);
        ~ScreenSeqsCommand();
        int execute();
+       void help();
+       
 private:
-       void screenNameGroupFile(set<string>);
-       void screenGroupFile(set<string>);
 
-       GlobalData* globaldata; 
+       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, alignreport, outputDir;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+       vector<string> outputNames;
 };
 
 #endif