#include "mothur.h"
#include "tree.h"
+#include "counttable.h"
#define MAX_LINE 513
#define SKIPLINE(f,c) {while((c=f.get())!=EOF && ((c) != '\n')){}}
ReadTree();
virtual ~ReadTree() {};
- virtual int read(TreeMap*) = 0;
+ 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(map<string, string>);
+ int AssembleTrees();
protected:
vector<Tree*> Trees;
- TreeMap* treeMap;
+ CountTable* ct;
int numNodes, numLeaves;
MothurOut* m;
public:
ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; }
~ReadNewickTree() {};
- int read(TreeMap*);
+ int read(CountTable*);
private:
Tree* T;
- int readNewickInt(istream&, int&, Tree*, TreeMap*);
- int readTreeString(TreeMap*);
- string nexusTranslation(TreeMap*);
+ int readNewickInt(istream&, int&, Tree*, CountTable*);
+ int readTreeString(CountTable*);
+ string nexusTranslation(CountTable*);
ifstream filehandle;
string treeFile;
string holder;