added sharedRabundFloatVector class to represent the relabund file. modified read...

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 5b44091dbd07d044f0de288490ff0d4633495008..2c31ba2245b523b7f18c0a3559ee9cd6f85890df 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -21,13 +21,31 @@ public:
        void help();
        
 private:
-       void screenNameGroupFile(set<string>);
-       void screenGroupFile(set<string>);
-       void screenAlignReport(set<string>);
+
+       struct linePair {
+               unsigned long int start;
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(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, set<string>&);
+       int createProcesses(string, string, string, set<string>&);
+       
+       #ifdef USE_MPI
+       int driverMPI(int, int, 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;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+       vector<string> outputNames;
 };
 
 #endif