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#ifndef READTREE_H
#define READTREE_H
/*
* readtree.h
* Mothur
*
* Created by Sarah Westcott on 1/22/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "mothur.h"
#include "tree.h"
#include "counttable.h"
#include "utils.hpp"
#define MAX_LINE 513
#define SKIPLINE(f,c) {while((c=f.get())!=EOF && ((c) != '\n')){}}
class Tree;
/****************************************************************************/
class ReadTree {
public:
ReadTree();
virtual ~ReadTree() = default;;
virtual int read(CountTable*) = 0;
int readSpecialChar(istream&, char, string);
int readNodeChar(istream& f);
float readBranchLength(istream& f);
vector<Tree*> getTrees() { return Trees; }
int AssembleTrees();
protected:
vector<Tree*> Trees;
CountTable* ct;
int numNodes, numLeaves;
MothurOut* m;
Utils util;
};
/****************************************************************************/
class ReadNewickTree : public ReadTree {
public:
ReadNewickTree(string file, vector<string> T) : treeFile(file), Treenames(T) { Utils util; util.openInputFile(file, filehandle); readOk = 0; if (Treenames.size() == 0) { Treenames = util.parseTreeFile(treeFile); } }
~ReadNewickTree() = default;;
int read(CountTable*);
private:
Tree* T;
int readNewickInt(istream&, int&, Tree*, CountTable*);
int readTreeString(CountTable*);
string nexusTranslation(CountTable*);
ifstream filehandle;
string treeFile;
string holder;
int readOk; // readOk = 0 means success, readOk = 1 means errors.
vector<string> Treenames;
};
/****************************************************************************/
#endif
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