changes to filter.seqs

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 611cbbc1b226c13d859273dc0cb356bb3b3d13d5..232b0acb9966c19d0dafe9a3875dbc702e925754 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -12,6 +12,7 @@
 
 #include "command.hpp"
 #include "filters.h"
+#include "mpi.h"
 
 class Sequence;
 class FilterSeqsCommand : public Command {
@@ -23,18 +24,26 @@ public:
        void help();
        
 private:
-       string vertical, filter, fastafile, hard;       
-       int alignmentLength;
+       struct linePair {
+               int start;
+               int numSeqs;
+               linePair(long int i, int j) : start(i), numSeqs(j) {}
+       };
+       vector<linePair*> lines;
+
+
+       string vertical, filter, fasta, hard, outputDir, filterFileName;
+       vector<string> fastafileNames;  
+       int alignmentLength, processors;
 
        char trump;
        bool abort;
        float soft;
        int numSeqs;
        
-       Filters F;
-               
-       vector<int> a, t, g, c, gap;
-
+       string createFilter();
+       int createProcessesCreateFilter(Filters&, string);
+       int driverCreateFilter(Filters&, string, linePair*);
 };
 
 #endif