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

   1 #ifndef __UPGMAALGORITHM_H
   2 #define __UPGMAALGORITHM_H
   3
   4 #include "Node.h"
   5 #include <limits>
   6 #include "../../general/clustalw.h"
   7 #include "../AlignmentSteps.h"
   8 #include "RootedGuideTree.h"
   9 #include <list>
  10 #include <memory>
  11
  12 namespace clustalw
  13 {
  14
  15 using namespace std;
  16
  17 class UPGMAAlgorithm
  18 {
  19     public:
  20         bool overwriteMatrix;
  21
  22         UPGMAAlgorithm();
  23         auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
  24                                     DistMatrix* distMat, SeqInfo* seqInfo,
  25                                     bool overwrite, ofstream* tree = 0);
  26         void setVerbose(bool _verbose){verbose = _verbose;}
  27
  28     private:
  29         Node **initialiseNodes(double *distanceMatrix, int firstSeq);
  30
  31         Node *doUPGMA(Node **nodes, ofstream* tree);
  32         void printAllNodes(Node** nodes);
  33         void addAlignmentStep(vector<int>* group1, vector<int>* group2);
  34         Node** getNodeWithMinDist(Node** clusters);
  35         void recomputeNodeToJoin1DistMatRow(Node* nodeToJoin1, double** nodeToJoin2DistIter);
  36         void computeAllOtherDistsToNewNode(Node* nodeToJoin1, Node* nodeToJoin2,
  37                                                    double** nodeToJoin2DistIter);
  38         void computeDistsUpToNodeToJoin2(Node* nToJoin1, Node* nToJoin2,
  39                                          double** nodeToJoin2DistIter);
  40         void computeDistsForNodesAfterNode2(Node* nToJoin2);
  41         void movePtrPastUnusedDistances(double** ptrToDist)
  42         {
  43             while(**ptrToDist < 0)
  44             {
  45                 (*ptrToDist)++;
  46             }
  47         }
  48         double calcNewDist(double dist1, double dist2);
  49         //vector<Node*>::iterator getIterToNodeWithMinDist(vector<Node*>* nodesLeft);
  50
  51         auto_ptr<AlignmentSteps> progSteps;
  52         int numSeqs;
  53         bool verbose;
  54         int orderNode1, orderNode2, orderNewNode;
  55 };
  56
  57 }
  58
  59 #endif