pca command

[mothur.git] / corraxescommand.h

diff --git a/corraxescommand.h b/corraxescommand.h
index 01c8d2bacd223d7c742a28a78fcfa65f91827192..8547b0fa1978a6d5477b9d393d0846455a3ad00a 100644 (file)
--- 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&);
        
 };