X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.h;h=8547b0fa1978a6d5477b9d393d0846455a3ad00a;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=01c8d2bacd223d7c742a28a78fcfa65f91827192;hpb=1f7448f6ec056b30ed146a5f779dfd6029788316;p=mothur.git

diff --git a/corraxescommand.h b/corraxescommand.h
index 01c8d2b..8547b0f 100644
--- a/corraxescommand.h
+++ b/corraxescommand.h
@@ -11,10 +11,18 @@
  */
 
 #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);
@@ -28,6 +36,8 @@ public:
 	void help();
 	
 private:
+	
+	
 	GlobalData* globaldata;
 	string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
 	bool abort, pickedGroups;
@@ -36,16 +46,16 @@ private:
 	
 	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&);
 	int calcSpearman(map<string, vector<float> >&, ofstream&);
+	int calcKendall(map<string, vector<float> >&, ofstream&);
 	
 };