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 bac02852744952477c97c0ea7dc284f56ff589bc..7e51748b3b7c8b16bf983e44f0771275f7cd532f 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,41 +12,26 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "chimera.h"
-
 
 /***********************************************************/
 
 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:
+       vector<string> outputNames;
+       map< string, vector<string> > outputTypes;
 
-       struct linePair {
-               int start;
-               int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
-       };
-       vector<int> processIDS;   //processid
-       vector<linePair*> lines;
-       
-       int driver(linePair*, string, string);
-       void createProcesses(string, string);
-       void appendOutputFiles(string, string); 
-
-       bool abort;
-       string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir;
-       bool filter, correction, svg, printAll;
-       int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs;
-       float divR;
-       Chimera* chimera;
-       
-       
 };
 
 /***********************************************************/