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 "tree.h"
  14 #include "counttable.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(CountTable*) = 0;
  29                 int readSpecialChar(istream&, char, string);
  30                 int readNodeChar(istream& f);
  31                 float readBranchLength(istream& f);
  32
  33                 vector<Tree*> getTrees() { return Trees; }
  34                 int AssembleTrees();
  35
  36         protected:
  37                 vector<Tree*> Trees;
  38                 CountTable* ct;
  39                 int numNodes, numLeaves;
  40                 MothurOut* m;
  41
  42
  43 };
  44
  45 /****************************************************************************/
  46
  47 class ReadNewickTree : public ReadTree {
  48
  49 public:
  50         ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; }
  51         ~ReadNewickTree() {};
  52         int read(CountTable*);
  53
  54 private:
  55         Tree* T;
  56         int readNewickInt(istream&, int&, Tree*, CountTable*);
  57         int readTreeString(CountTable*);
  58         string nexusTranslation(CountTable*);
  59         ifstream filehandle;
  60         string treeFile;
  61         string holder;
  62         int readOk;  // readOk = 0 means success, readOk = 1 means errors.
  63
  64 };
  65
  66 /****************************************************************************/
  67
  68 #endif