added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 9ff0c8ffb0753f799133b3ee54424f0a7aff8345..d201ccb5f1baa2c628f217c7c763523e832d70eb 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -41,15 +41,16 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        
-       int driver(linePair*, string, string, string);
-       int createProcesses(string, string, string);
+       int driver(linePair*, string, string, string, string);
+       int createProcesses(string, string, string, string);
+       int divideInHalf(Sequence, string&, string&);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
-       bool abort, realign;
-       string fastafile, templatefile, outputDir, search, namefile;
+       bool abort, realign, trim, trimera;
+       string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;