changes to filter.seqs

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 06eaa6db7e2deb8b74344d7f408f09734cbf43cf..232b0acb9966c19d0dafe9a3875dbc702e925754 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,35 +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 doFilter();
-       
-       GlobalData* globaldata;
-       string filename, trump, filter;
-       
-       ReadSeqs* readSeqs;
+       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;
        
-       vector<bool> columnsToRemove;
-       SequenceDB* db;
-       double soft;
+       string createFilter();
+       int createProcessesCreateFilter(Filters&, string);
+       int driverCreateFilter(Filters&, string, linePair*);
 };
 
-#endif
\ No newline at end of file
+#endif