continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 455ac926a494d162839444a5e192f9a030556d07..b2bce8107590e3d4906ea68b7e758cd5bf15b951 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,9 +12,7 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "filterseqscommand.h"
-#include "sequence.hpp"
-
+#include "chimera.h"
 
 
 /***********************************************************/
@@ -26,29 +24,16 @@ public:
        int execute();
        void help();
        
+               
 private:
-       //Dist* distCalculator;
        
-       struct Preference {
-               string leftParent;
-               string rightParent;
-               float score;
-
-       };
-
-
        bool abort;
-       string method, fastafile;
+       string method, fastafile, templatefile, consfile, quanfile, maskfile;
        bool filter, correction;
-       int processors, midpoint;
-       FilterSeqsCommand* filterSeqs;
-       vector<Sequence> seqs;
-       vector<Preference> pref;
+       int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize;
+       Chimera* chimera;
        
-       int findAverageMidPoint();
-       void readSeqs();
        
-
 };
 
 /***********************************************************/