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
  15 #define MAX_LINE                513
  16 #define SKIPLINE(f,c)   {while((c=f.get())!=EOF && ((c) != '\n')){}}
  17
  18 class Tree;
  19
  20 /****************************************************************************/
  21
  22 class ReadTree {
  23         public:
  24                 ReadTree();
  25                 virtual ~ReadTree() {};
  26
  27                 virtual int read(TreeMap*) = 0;
  28                 int readSpecialChar(istream&, char, string);
  29                 int readNodeChar(istream& f);
  30                 float readBranchLength(istream& f);
  31
  32                 vector<Tree*> getTrees() { return Trees; }
  33                 int AssembleTrees(map<string, string>);
  34
  35         protected:
  36                 vector<Tree*> Trees;
  37                 TreeMap* treeMap;
  38                 int numNodes, numLeaves;
  39                 MothurOut* m;
  40
  41
  42 };
  43
  44 /****************************************************************************/
  45
  46 class ReadNewickTree : public ReadTree {
  47
  48 public:
  49         ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; }
  50         ~ReadNewickTree() {};
  51         int read(TreeMap*);
  52
  53 private:
  54         Tree* T;
  55         int readNewickInt(istream&, int&, Tree*, TreeMap*);
  56         int readTreeString(TreeMap*);
  57         string nexusTranslation(TreeMap*);
  58         ifstream filehandle;
  59         string treeFile;
  60         string holder;
  61         int readOk;  // readOk = 0 means success, readOk = 1 means errors.
  62
  63 };
  64
  65 /****************************************************************************/
  66
  67 #endif