indicator command

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 9567fcab31c20f22987d04eb0a2a409dd1dfc50b..35ff7627552d2e2d15fe4e03adcd9c634e8b8b3c 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 {
@@ -41,21 +43,22 @@ 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&);
+       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, namefile, includeAbunds;
+       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;
-       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
        vector<string> nameFileNames;