added sorted option to get.rabund command

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 2398ce63b257935d857e06bf6525b6b94e8efd05..dc7df8fad969d33a2fa51f46718f5aa4812321f1 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,25 +12,7 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "filterseqscommand.h"
-#include "sequence.hpp"
-#include "sparsematrix.hpp"
-#include "dist.h"
-
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
-
-struct Preference {
-               string name;
-               vector<string> leftParent; //keep the name of closest left associated with the two scores
-               vector<string> rightParent; //keep the name of closest right associated with the two scores
-               vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
-               vector<float> closestLeft;  //keep the closest left associated with the two scores
-               vector<float> closestRight; //keep the closest right associated with the two scores
-               int midpoint;
-
-};
-
+#include "chimera.h"
 
 
 /***********************************************************/
@@ -45,21 +27,13 @@ public:
                
 private:
        
-       Dist* distCalculator;
        bool abort;
-       string method, fastafile;
+       string method, fastafile, templatefile;
        bool filter, correction;
        int processors, midpoint, averageLeft, averageRight, window, iters, increment;
-       FilterSeqsCommand* filterSeqs;
-       ListVector* list;
-       vector<Sequence> seqs;
-       vector<Preference> pref;
+       Chimera* chimera;
        
-       void readSeqs();
-       void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
-       int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
        
-
 };
 
 /***********************************************************/