added set.current and get.current commands and modified existing commands to update...

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 7c4934470f448e8fee497fbbdafe5f5cda57115e..6e81812e469772b18a737930354f1bdf943a9ef9 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
+#include "chimeracheckrdp.h"
 
 
 /***********************************************************/
@@ -20,7 +21,12 @@
 class ChimeraCheckCommand : public Command {
 public:
        ChimeraCheckCommand(string);
+       ChimeraCheckCommand();
        ~ChimeraCheckCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -29,9 +35,10 @@ 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;
        
@@ -39,7 +46,7 @@ private:
        int createProcesses(string, string);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
        bool abort, svg;
@@ -49,6 +56,7 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
                
 };