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

[mothur.git] / corraxescommand.h

diff --git a/corraxescommand.h b/corraxescommand.h
index bbe87abcbd1eeccb677a4e59c58ce64cb961944c..5f04c6a754393bda843abdf057e0f47763fd21cf 100644 (file)
--- a/corraxescommand.h
+++ b/corraxescommand.h
@@ -19,25 +19,23 @@ class CorrAxesCommand : public Command {
 public:
        CorrAxesCommand(string);
        CorrAxesCommand();
-       ~CorrAxesCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
-       
-private:
+       ~CorrAxesCommand(){}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "corr.axes";                           }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
        
-       GlobalData* globaldata;
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
+private:
+
        string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
        bool abort, pickedGroups;
        int numaxes;
        set<string> names;
        
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
        vector<SharedRAbundFloatVector*> lookupFloat;
        vector<string> metadataLabels;