test

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 3f1e4c46d349d9da15837466502bd06a2f243883..0946396e3a0fe6623f3501feed5fc6e7b4ba239a 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,9 +11,9 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "sequence.hpp"
+#include "filters.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
@@ -23,23 +23,16 @@ public:
        void help();
        
 private:
-       void doHard();
-       void doTrump(Sequence);
-       void doVertical();
-       void doSoft();
-       void getFreqs(Sequence);
-       string vertical, filter, fastafile, hard;       
+       string vertical, filter, fastafile, hard, outputDir;    
        int alignmentLength;
 
        char trump;
        bool abort;
        float soft;
        int numSeqs;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
        
-       GlobalData* globaldata; 
+       Filters F;
+               
        vector<int> a, t, g, c, gap;
 
 };