fixed bug with trim.seqs allfiles=t

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index ff1933735b2862935b3283b61ca96f180f6df546..90f6b62f83fea0bc4abc980baacccb362e216554 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,22 +14,24 @@
 #include "command.hpp"
 #include "chimera.h"
 
-
 /***********************************************************/
 
 class ChimeraSlayerCommand : public Command {
 public:
        ChimeraSlayerCommand(string);
        ChimeraSlayerCommand();
-       ~ChimeraSlayerCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ChimeraSlayerCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.slayer";              }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
        
-               
 private:
 
        struct linePair {
@@ -43,19 +45,20 @@ private:
        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);
+       int divideInHalf(Sequence, string&, string&);
+       map<string, int> sortFastaFile(string, string);
                
        #ifdef USE_MPI
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
        bool abort, realign, trim, trimera;
-       string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
+       string fastafile, templatefile, outputDir, search, namefile;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
        vector<string> nameFileNames;