finished mpi for filter.seqs

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 5eb49d3802177bf998e8fe9d0ba1dd80c2828709..1d2526fdca83114dcca76217917324d134bcc391 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -26,16 +26,17 @@ public:
 private:
        struct linePair {
                int start;
-               int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
+               int num;
+               linePair(long int i, long int j) : start(i), num(j) {}
        };
        vector<linePair*> lines;
-
+       vector<int> processIDS;
 
        string vertical, filter, fasta, hard, outputDir, filterFileName;
        vector<string> fastafileNames;  
        int alignmentLength, processors;
        vector<int> bufferSizes;
+       vector<string> outputNames;
 
        char trump;
        bool abort;
@@ -43,9 +44,13 @@ private:
        int numSeqs;
        
        string createFilter();
+       int filterSequences();
        int createProcessesCreateFilter(Filters&, string);
+       int createProcessesRunFilter(string, string);
        int driverCreateFilter(Filters&, string, linePair*);
-       int MPICreateFilter(Filters&, vector<string>&); 
+       int driverRunFilter(string, string, string, linePair*); 
+       int driverMPIRun(istringstream&, MPI_File&);
+       int MPICreateFilter(Filters&, string);  
        int setLines(string);
        int parseBuffer(string, vector<string>&);