added getCommandInfoCommand for gui

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 7c4934470f448e8fee497fbbdafe5f5cda57115e..221d35fe504bea29e6757b35aadd9449703543ab 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
+#include "chimeracheckrdp.h"
 
 
 /***********************************************************/
@@ -20,18 +21,26 @@
 class ChimeraCheckCommand : public Command {
 public:
        ChimeraCheckCommand(string);
-       ~ChimeraCheckCommand();
-       int execute();
-       void help();
+       ChimeraCheckCommand();
+       ~ChimeraCheckCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.check";               }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
-               
 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 +48,7 @@ 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;
@@ -49,7 +58,6 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
-               
 };
 
 /***********************************************************/