testing

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 3cc007c059c63de5f28eee57ac0afcf78d00dc33..2f318c0abbb575b6087477344199275b61305706 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -30,12 +30,13 @@ private:
                linePair(long int i, int j) : start(i), numSeqs(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;
@@ -43,8 +44,12 @@ private:
        int numSeqs;
        
        string createFilter();
+       int filterSequences();
        int createProcessesCreateFilter(Filters&, string);
+       int createProcessesRunFilter(string, string);
        int driverCreateFilter(Filters&, string, linePair*);
+       int driverRunFilter(string, string, string, linePair*); 
+       int driverMPIRun(istringstream&, MPI_File&);
        int MPICreateFilter(Filters&, string);  
        int setLines(string);
        int parseBuffer(string, vector<string>&);