working on pam

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index 9a0efb951348b7f0a0f1bc511eb76facb21c6d9f..52bf07d01f6a411b870e119f82ef97f7b6f45cbd 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,17 +20,27 @@
 class ChimeraCcodeCommand : public Command {
 public:
        ChimeraCcodeCommand(string);
-       ~ChimeraCcodeCommand();
-       int execute();
-       void help();
+       ChimeraCcodeCommand();
+       ~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 {
-               int start;
-               int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(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;
@@ -39,15 +49,15 @@ private:
        int createProcesses(string, string, string);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
-       bool abort, filter, MPIWroteAccnos;
+       bool abort, filter, save;
        string fastafile, templatefile, outputDir, maskfile;
        int processors, window, numwanted, numSeqs, templateSeqsLength;
        Chimera* chimera;
-       
-       
+       vector<string> fastaFileNames;
+       vector<string> outputNames;
 };
 
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