fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it,...

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 2398ce63b257935d857e06bf6525b6b94e8efd05..7e51748b3b7c8b16bf983e44f0771275f7cd532f 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,53 +12,25 @@
 
 #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;
-
-};
-
-
 
 /***********************************************************/
 
 class ChimeraSeqsCommand : public Command {
 public:
        ChimeraSeqsCommand(string);
+       ChimeraSeqsCommand() {}
        ~ChimeraSeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map< string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
                
 private:
-       
-       Dist* distCalculator;
-       bool abort;
-       string method, fastafile;
-       bool filter, correction;
-       int processors, midpoint, averageLeft, averageRight, window, iters, increment;
-       FilterSeqsCommand* filterSeqs;
-       ListVector* list;
-       vector<Sequence> seqs;
-       vector<Preference> pref;
-       
-       void readSeqs();
-       void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
-       int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
-       
+       vector<string> outputNames;
+       map< string, vector<string> > outputTypes;
 
 };