added cutoff change to mgcluster

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index d980288ac3585916321edec15114d0c47303e120..2bf7a70fd159a93fcc813c3236aed97a8c18c916 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,9 +20,18 @@
 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 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:
@@ -47,8 +56,6 @@ private:
        Chimera* chimera;
        vector<string> fastaFileNames;
        vector<string> outputNames;
-       
-       
 };
 
 /***********************************************************/