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 "globaldata.hpp"
  15 #include "utilities.hpp"
  16 #include "tree.h"
  17
  18 #define MAX_LINE                513
  19 #define SKIPLINE(f,c)   {while((c=f.get())!=EOF && ((c) != '\n')){}}
  20
  21 class Tree;
  22
  23 /****************************************************************************/
  24
  25 class ReadTree {
  26         public:
  27                 ReadTree();
  28                 ~ReadTree() {};
  29
  30                 virtual void read() {};
  31                 int readSpecialChar(istream&, char, string);
  32                 int readNodeChar(istream& f);
  33                 float readBranchLength(istream& f);
  34
  35         protected:
  36                 GlobalData* globaldata;
  37                 int numNodes, numLeaves;
  38
  39 };
  40
  41 /****************************************************************************/
  42
  43 class ReadNewickTree : public ReadTree {
  44
  45 public:
  46         ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); }
  47         ~ReadNewickTree() {};
  48         void read();
  49
  50 private:
  51         Tree* T;
  52         int readNewickInt(istream&, int&, Tree*);
  53         void readTreeString();
  54         void nexusTranslation();
  55         ifstream filehandle;
  56         string treeFile;
  57         string holder;
  58 };
  59
  60 /****************************************************************************/
  61
  62 #endif