working on pam

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index a9ed223b112cdb50876024c893257549e159481f..52bf07d01f6a411b870e119f82ef97f7b6f45cbd 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -21,20 +21,26 @@ class ChimeraCcodeCommand : public Command {
 public:
        ChimeraCcodeCommand(string);
        ChimeraCcodeCommand();
-       ~ChimeraCcodeCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ChimeraCcodeCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.ccode";               }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
                
 private:
        struct linePair {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
@@ -43,18 +49,15 @@ private:
        int createProcesses(string, 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&, vector<unsigned long long>&);
        #endif
 
-       bool abort, filter;
+       bool abort, filter, save;
        string fastafile, templatefile, outputDir, maskfile;
        int processors, window, numwanted, numSeqs, templateSeqsLength;
        Chimera* chimera;
        vector<string> fastaFileNames;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-       
-       
 };
 
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