added getCommandInfoCommand for gui

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 84c75ac8b8ff49e85cec777ffb8d2beeec544990..221d35fe504bea29e6757b35aadd9449703543ab 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -21,18 +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;
        
@@ -50,7 +58,6 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
-               
 };
 
 /***********************************************************/