X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.h;h=067228f88ae5c55406021880ea21f4dde2018ce0;hb=cc19310422f125d6628980bd1148e1e816792382;hp=bbe87abcbd1eeccb677a4e59c58ce64cb961944c;hpb=5553e33be3a45eee6bed2ac9a5c4ca0aa0e8d5e4;p=mothur.git

diff --git a/corraxescommand.h b/corraxescommand.h
index bbe87ab..067228f 100644
--- 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;