removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 6e81812e469772b18a737930354f1bdf943a9ef9..221d35fe504bea29e6757b35aadd9449703543ab 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -22,15 +22,17 @@ 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();
+       ~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 {
@@ -56,8 +58,6 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-               
 };
 
 /***********************************************************/