readtree.h

   1 #ifndef READTREE_H
   2 #define READTREE_H
   3 /*
   4  *  readtree.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 1/22/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 using namespace std;
  13
  14 #include <string>
  15 #include <iostream>
  16 #include "globaldata.hpp"
  17 #include "utilities.hpp"
  18 #include "tree.h"
  19
  20 #define MAX_LINE                513
  21 #define SKIPLINE(f,c)   {while((c=f.get())!=EOF && ((c) != '\n')){}}
  22
  23 class Tree;
  24
  25 /****************************************************************************/
  26
  27 class ReadTree {
  28         public:
  29                 ReadTree();
  30                 ~ReadTree() {};
  31
  32                 virtual void read() {};
  33                 int readSpecialChar(istream&, char, string);
  34                 int readNodeChar(istream& f);
  35                 float readBranchLength(istream& f);
  36
  37         protected:
  38                 GlobalData* globaldata;
  39                 int numNodes, numLeaves;
  40
  41 };
  42
  43 /****************************************************************************/
  44
  45 class ReadNewickTree : public ReadTree {
  46
  47 public:
  48         ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle);  }
  49         ~ReadNewickTree() {};
  50         void read();
  51
  52 private:
  53         Tree* T;
  54         int readNewickInt(istream&, int&, Tree*);
  55         void readTreeString();
  56         void nexusTranslation();
  57         ifstream filehandle;
  58         string treeFile;
  59         string holder;
  60 };
  61
  62 /****************************************************************************/
  63
  64 #endif