binaries/src/clustalw/src/tree/UPGMA/RootedGuideTree.h

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 /**
   7  * Changes:
   8  * mark May 8th 2007: removed makeEmpty(Node* t function), changed makeEmpty(). I also
   9  * made changes to any functions that accessed Node's data members
  10  */
  11 #ifndef ROOTEDGUIDETREE_H
  12 #define ROOTEDGUIDETREE_H
  13
  14 #include "Node.h"
  15 #include <fstream>
  16
  17 #include "../../alignment/Alignment.h"
  18
  19 namespace clustalw
  20 {
  21
  22 using namespace std;
  23
  24 class RootedGuideTree
  25 {
  26     public:
  27         RootedGuideTree();
  28         RootedGuideTree(Node* root);
  29         ~RootedGuideTree();
  30         void setRoot(Node* r);
  31         void makeEmpty();
  32         void calcSeqWeights(int firstSeq, int lastSeq, vector<int>* seqWeights);
  33         Node* getRoot(){return root;}
  34     private:
  35         void orderNodes();
  36         int calcOrderNode(Node* node);
  37         void calcWeights(vector<int>* seqWeights);
  38         void doWeightCalc(float weightSoFar, vector<float>* seqWeights, Node* t);
  39         Node* root;
  40 };
  41
  42 }
  43 #endif