added template=self capability to chimers.slayer, worked on corr.axes and added accno...

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index a07178e720ba59716c22d8d685624db2e3d83c0b..a9ed223b112cdb50876024c893257549e159481f 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,17 +20,21 @@
 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();
        
                
 private:
-
        struct linePair {
-               int start;
-               int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long int start;
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
@@ -39,15 +43,16 @@ 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 int>&);
        #endif
 
-       bool abort, filter, MPIWroteAccnos;
+       bool abort, filter;
        string fastafile, templatefile, outputDir, maskfile;
        int processors, window, numwanted, numSeqs, templateSeqsLength;
        Chimera* chimera;
        vector<string> fastaFileNames;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        
 };