X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.h;h=a91a24019c46b1b8d7346fd87e5a45ea957242a9;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=45a2b785401ead3f70bd87ea43777e8db05c5fbf;hpb=de67504f85e091a3049ef4c5df8e77f7dcb1d814;p=mothur.git

diff --git a/corraxescommand.h b/corraxescommand.h
index 45a2b78..a91a240 100644
--- a/corraxescommand.h
+++ b/corraxescommand.h
@@ -11,48 +11,40 @@
  */
 
 #include "command.hpp"
-#include "sharedrabundvector.h"
 #include "sharedrabundfloatvector.h"
 #include "inputdata.h"
 
-/***************************************************************/
-struct spearmanRank {
-	string name;
-	float score;
-	
-	spearmanRank(string n, float s) : name(n), score(s) {}
-};
-/***************************************************************/
 
 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();
+	~CorrAxesCommand(){}
 	
-private:
+	vector<string> setParameters();
+	string getCommandName()			{ return "corr.axes";				}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
 	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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<SharedRAbundVector*> lookup;
 	vector<SharedRAbundFloatVector*> lookupFloat;
+	vector<string> metadataLabels;
 	
-	int getShared();
-	int getSharedFloat();
-	int convertToRelabund();
+	int getSharedFloat(InputData*);
+	int getMetadata();
 	int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
 	map<string, vector<float> > readAxes();
 	int calcPearson(map<string, vector<float> >&, ofstream&);