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 #include "mothur.h"
  13 #include "globaldata.hpp"
  14 #include "tree.h"
  15
  16 #define MAX_LINE                513
  17 #define SKIPLINE(f,c)   {while((c=f.get())!=EOF && ((c) != '\n')){}}
  18
  19 class Tree;
  20
  21 /****************************************************************************/
  22
  23 class ReadTree {
  24         public:
  25                 ReadTree();
  26                 virtual ~ReadTree() {};
  27
  28                 virtual int read() = 0;
  29                 int readSpecialChar(istream&, char, string);
  30                 int readNodeChar(istream& f);
  31                 float readBranchLength(istream& f);
  32
  33         protected:
  34                 GlobalData* globaldata;
  35                 int numNodes, numLeaves;
  36                 MothurOut* m;
  37
  38
  39 };
  40
  41 /****************************************************************************/
  42
  43 class ReadNewickTree : public ReadTree {
  44
  45 public:
  46         ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; }
  47         ~ReadNewickTree() {};
  48         int read();
  49
  50 private:
  51         Tree* T;
  52         int readNewickInt(istream&, int&, Tree*);
  53         int readTreeString();
  54         void nexusTranslation();
  55         ifstream filehandle;
  56         string treeFile;
  57         string holder;
  58         int readOk;  // readOk = 0 means success, readOk = 1 means errors.
  59
  60 };
  61
  62 /****************************************************************************/
  63
  64 #endif