added blastlocation to chimera.slayer and fixed issue with clearcut getting current...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index ff1933735b2862935b3283b61ca96f180f6df546..1b173911c3d79218413e76533da53b7a3ffa3649 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"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       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;
+       bool abort, realign, trim, trimera, save;
+       string fastafile, templatefile, outputDir, search, namefile, blastlocation;
        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;