changes to filter.seqs

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 2279689d4671d5a7fae99204d0ab5421b5070ed6..232b0acb9966c19d0dafe9a3875dbc702e925754 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,37 +11,39 @@
  */
 
 #include "command.hpp"
-#include "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
+#include "filters.h"
+#include "mpi.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-       FilterSeqsCommand();
+       FilterSeqsCommand(string);
        ~FilterSeqsCommand() {};
        int execute();  
+       void help();
        
 private:
-       void doTrump();
-       void doSoft();
-       void doHard();
-       void doVertical();
-       
-       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;
        
-       GlobalData* globaldata; 
-       ReadSeqs* readSeqs;
-       SequenceDB* db;
-       
-       string filter;
-
+       string createFilter();
+       int createProcessesCreateFilter(Filters&, string);
+       int driverCreateFilter(Filters&, string, linePair*);
 };
 
-#endif
\ No newline at end of file
+#endif