binaries/src/clustalw/src/tree/ClusterTreeOutput.h

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 #ifndef CLUSTERTREEOUTPUT_H
   7 #define CLUSTERTREEOUTPUT_H
   8
   9 #include <memory>
  10 #include <fstream>
  11 #include "../alignment/Alignment.h"
  12 #include "../general/clustalw.h"
  13
  14 namespace clustalw
  15 {
  16
  17 class ClusterTreeOutput
  18 {
  19     public:
  20         ClusterTreeOutput(clustalw::SeqInfo* seqInfo, int boot);
  21         void printNexusTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
  22                    clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
  23         void printTree(clustalw::PhyloTree* phyloTree, ofstream* tree, vector<int>* totals);
  24         void printPhylipTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
  25                    clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
  26         void printTreeDesc(clustalw::PhyloTree* phyloTree);
  27
  28     private:
  29         ClusterTreeOutput(); // Dont allow contruction with default!!!!
  30         int twoWaySplit(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow,
  31                     int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
  32         int twoWaySplitNexus(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow,
  33                     int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
  34         /* Attributes! */
  35         int firstSeq;
  36         int lastSeq;
  37         int numSeqs;
  38         int bootstrap;
  39 };
  40
  41 }
  42
  43 #endif