changing command name classify.shared to classifyrf.shared

[mothur.git] / sharedchao1.h

diff --git a/sharedchao1.h b/sharedchao1.h
index 86f718fdaae07b85e8f9d796af51b3b0761b4524..ae07a8706c30fa76d1b2c975db417201a9470b5f 100644 (file)
--- a/sharedchao1.h
+++ b/sharedchao1.h
@@ -13,18 +13,37 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/
 
+
 class SharedChao1 : public Calculator  {
        
-public: 
-       SharedChao1() : Calculator("SharedChao", 3) {};
-       EstOutput getValues(SAbundVector*) {return data;};
-       EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+       public: 
+               SharedChao1() : Calculator("sharedchao", 1, true) {};
+               EstOutput getValues(SAbundVector*) {return data;};
+               EstOutput getValues(vector<SharedRAbundVector*>);
+               string getCitation() { return "http://www.mothur.org/wiki/Sharedchao"; }
+       private:
+               IntNode* f1root;
+               IntNode* f2root;
+               vector<IntNode*> f1leaves;
+               vector<IntNode*> f2leaves;
+               int numLeaves;
+               int numNodes;
+
+               void initialTree(int);  //builds trees structure with n leaf nodes initialized to 0.
+               void setCoef(IntNode*, int);
+               void updateTree(vector<int>); //take vector containing the abundance info. for a bin and updates trees.
+               void updateBranchf1(IntNode*, vector<int>, int);  //pointer, vector of abundance values, index into vector
+               void updateBranchf2(IntNode*, vector<int>, int);  //pointer, vector of abundance values, index into vector
+               
+               //for debugging
+               void printTree();
+               void printBranch(IntNode*);
 };
 
 /***********************************************************************/
-#endif
\ No newline at end of file
+
+#endif