added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / anosimcommand.h

diff --git a/anosimcommand.h b/anosimcommand.h
index ab724007237d508e1b2dabf1bba521c5c38f7497..593033d2fb086d9a3157ea4a27f1eae4e278e72e 100644 (file)
--- a/anosimcommand.h
+++ b/anosimcommand.h
@@ -20,18 +20,20 @@ class AnosimCommand : public Command {
 public:
        AnosimCommand(string);
        AnosimCommand();
-       ~AnosimCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~AnosimCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "anosim";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+       
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
        bool abort;
        GroupMap* designMap;
-       map<string, vector<string> > outputTypes;
        string outputDir, inputDir, designFileName, phylipFileName;
        
        vector<vector<double> > convertToRanks(vector<vector<double> >);