pat's differences before v.1.8

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index cfa56b39df6a4001014e1bc42048bed50bede8fa..0946396e3a0fe6623f3501feed5fc6e7b4ba239a 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,6 +11,7 @@
  */
 
 #include "command.hpp"
+#include "filters.h"
 
 class Sequence;
 class FilterSeqsCommand : public Command {
@@ -22,12 +23,7 @@ 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;
@@ -35,6 +31,8 @@ private:
        float soft;
        int numSeqs;
        
+       Filters F;
+               
        vector<int> a, t, g, c, gap;
 
 };