v 19.3

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 95541b2b6aac8a636242dba385c1114267416bb4..90f6b62f83fea0bc4abc980baacccb362e216554 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,42 +14,53 @@
 #include "command.hpp"
 #include "chimera.h"
 
-
 /***********************************************************/
 
 class ChimeraSlayerCommand : public Command {
 public:
        ChimeraSlayerCommand(string);
-       ~ChimeraSlayerCommand();
-       int execute();
-       void help();
+       ChimeraSlayerCommand();
+       ~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 {
                unsigned long int start;
-               int numSeqs;
-               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+
        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&);
+       map<string, int> sortFastaFile(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;
+       bool abort, realign, trim, trimera;
+       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;
        vector<string> fastaFileNames;
+       vector<string> nameFileNames;
        
 };