website/archive/binaries/mac/src/clustalw/src/tree/NJTree.h

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 #ifndef NJTREE_H
   7 #define NJTREE_H
   8
   9 #include <vector>
  10 #include <iomanip>
  11 #include "ClusterTreeAlgorithm.h"
  12 #include "../general/userparams.h"
  13
  14 namespace clustalw
  15 {
  16
  17 class NJTree : public ClusterTreeAlgorithm
  18 {
  19     public:
  20         NJTree(): verbose(false){};
  21         virtual ~NJTree(){};
  22
  23         /** calculate an NJ tree
  24          *
  25          * @param phyTree the tree structure
  26          * @param distMat distance matrix
  27          * @param seqInfo holding sequence number info
  28          * @param log ofstream to log info to (used by -outputtree)
  29          *
  30          */
  31         virtual void generateTree(clustalw::PhyloTree* phyTree,
  32                                   clustalw::DistMatrix* distMat,
  33                                   clustalw::SeqInfo* seqInfo,
  34                                   ofstream* log = 0);
  35         /** be verbose during tree generation
  36          *
  37          *  if set to true, generateTree will need a log ofstream
  38          */
  39         virtual void setVerbose(bool choice){verbose = choice;};
  40     private:
  41         vector<double> av;
  42         vector<int> tkill;
  43         bool verbose;
  44 };
  45
  46 }
  47 #endif