changed sequence class so that when constructor is called aligned and unaligned value...

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 5b55120e0d0981b432f71332dc1db57e8fae5ce7..7721ef8e9428a9e12b1ad0e930f419389d813fca 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,13 +12,8 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "filterseqscommand.h"
-#include "sequence.hpp"
-#include "sparsematrix.hpp"
-#include "dist.h"
+#include "chimera.h"
 
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
 
 /***********************************************************/
 
@@ -29,31 +24,16 @@ public:
        int execute();
        void help();
        
+               
 private:
-       //Dist* distCalculator;
        
-       struct Preference {
-               string leftParent;
-               string rightParent;
-               float score;
-
-       };
-
-       Dist* distCalculator;
        bool abort;
-       string method, fastafile;
+       string method, fastafile, templatefile, consfile, quanfile;
        bool filter, correction;
-       int processors, midpoint;
-       FilterSeqsCommand* filterSeqs;
-       vector<Sequence> seqs;
-       vector<Preference> pref;
+       int processors, midpoint, averageLeft, averageRight, window, iters, increment;
+       Chimera* chimera;
        
-       int findAverageMidPoint();
-       void readSeqs();
-       void generatePreferences(SparseMatrix*, SparseMatrix*);
-       int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
        
-
 };
 
 /***********************************************************/