added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / corraxescommand.h

diff --git a/corraxescommand.h b/corraxescommand.h
index bbe87abcbd1eeccb677a4e59c58ce64cb961944c..067228f88ae5c55406021880ea21f4dde2018ce0 100644 (file)
--- a/corraxescommand.h
+++ b/corraxescommand.h
@@ -19,25 +19,26 @@ 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 getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; }
+       string getDescription()         { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
        
-       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;