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 "tree.h"
  18
  19 #define MAX_LINE                513
  20 #define SKIPLINE(f,c)   {while((c=f.get())!=EOF && ((c) != '\n')){}}
  21
  22 class Tree;
  23
  24 /****************************************************************************/
  25
  26 class ReadTree {
  27         public:
  28                 ReadTree();
  29                 ~ReadTree() {};
  30
  31                 virtual void read() {};
  32                 int readSpecialChar(istream&, char, string);
  33                 int readNodeChar(istream& f);
  34                 float readBranchLength(istream& f);
  35
  36         protected:
  37                 GlobalData* globaldata;
  38                 int numNodes, numLeaves;
  39
  40 };
  41
  42 /****************************************************************************/
  43
  44 class ReadNewickTree : public ReadTree {
  45
  46 public:
  47         ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle);  }
  48         ~ReadNewickTree() {};
  49         void read();
  50
  51 private:
  52         Tree* T;
  53         int readNewickInt(istream&, int&, Tree*);
  54         void readTreeString();
  55         void nexusTranslation();
  56         ifstream filehandle;
  57         string treeFile;
  58         string holder;
  59 };
  60
  61 /****************************************************************************/
  62
  63 #endif