added command descriptions

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 71e1f0cdad86dc4610a65711c57c355eb9ee2aaf..d29744ba39ba1791e27c306c7fd09f950ac15c0f 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -21,11 +21,20 @@
 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(); 
+       string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
-               
 private:
 
        struct linePair {
@@ -51,7 +60,6 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
-               
 };
 
 /***********************************************************/