added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 5b55120e0d0981b432f71332dc1db57e8fae5ce7..56477a11c5249b88ded4acd2c87ac547e8bc9754 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,13 +12,8 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "filterseqscommand.h"
-#include "sequence.hpp"
-#include "sparsematrix.hpp"
-#include "dist.h"
+#include "chimera.h"
 
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
 
 /***********************************************************/
 
@@ -29,31 +24,29 @@ public:
        int execute();
        void help();
        
+               
 private:
-       //Dist* distCalculator;
-       
-       struct Preference {
-               string leftParent;
-               string rightParent;
-               float score;
 
+       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);
+       void createProcesses(string, string, string);
+       void appendOutputFiles(string, string); 
 
-       Dist* distCalculator;
        bool abort;
-       string method, fastafile;
-       bool filter, correction;
-       int processors, midpoint;
-       FilterSeqsCommand* filterSeqs;
-       vector<Sequence> seqs;
-       vector<Preference> pref;
+       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;
        
-       int findAverageMidPoint();
-       void readSeqs();
-       void generatePreferences(SparseMatrix*, SparseMatrix*);
-       int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
        
-
 };
 
 /***********************************************************/