X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.h;h=afbc2592a389f2faa971452d2fa12e3be4fa9680;hb=cf9a187f89caf821e454d1547d9b3893e17a1e76;hp=5b55120e0d0981b432f71332dc1db57e8fae5ce7;hpb=6e63c5ff52bd2830b689417df8ba3db831e63a96;p=mothur.git

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 5b55120..afbc259 100644
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,13 +12,6 @@
 
 #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
 
 /***********************************************************/
 
@@ -29,30 +22,8 @@ public:
 	int execute();
 	void help();
 	
+		
 private:
-	//Dist* distCalculator;
-	
-	struct Preference {
-		string leftParent;
-		string rightParent;
-		float score;
-
-	};
-
-	Dist* distCalculator;
-	bool abort;
-	string method, fastafile;
-	bool filter, correction;
-	int processors, midpoint;
-	FilterSeqsCommand* filterSeqs;
-	vector<Sequence> seqs;
-	vector<Preference> pref;
-	
-	int findAverageMidPoint();
-	void readSeqs();
-	void generatePreferences(SparseMatrix*, SparseMatrix*);
-	int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
-	
 
 };