added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 040d2dde543b9311762640680d1a8ba874e3fcf5..afbc2592a389f2faa971452d2fa12e3be4fa9680 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,8 +12,6 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "chimera.h"
-
 
 /***********************************************************/
 
@@ -27,26 +25,6 @@ public:
                
 private:
 
-       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, string);
-       int createProcesses(string, string, string);
-       void appendOutputFiles(string, string); 
-
-       bool abort;
-       string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir, search;
-       bool filter, correction, svg, printAll, realign;
-       int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
-       float divR;
-       Chimera* chimera;
-       
-       
 };
 
 /***********************************************************/