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[mothur.git] / treereader.h

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+#ifndef Mothur_treereader_h
+#define Mothur_treereader_h
+
+//
+//  treereader.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 4/11/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "mothurout.h"
+#include "tree.h"
+
+class TreeReader {
+    
+public:
+    
+    TreeReader(string tf);
+       TreeReader(string tf, string gf);
+    TreeReader(string tf, string gf, string nf);
+       ~TreeReader() {}        
+    
+    vector<Tree*> getTrees()            { return trees;     }
+    map<string, string> getNames()      { return nameMap;   } //dups -> unique
+    map<string, string> getNameMap()    { return names;     } //unique -> dups list
+    
+    
+private:
+    MothurOut* m;
+       vector<Tree*> trees;
+    TreeMap* tmap;
+    map<string, string> nameMap; //dupName -> uniqueName
+    map<string, string> names;
+    
+    string treefile, groupfile, namefile;
+    
+    bool readTrees();
+    int readNamesFile();
+};
+
+
+
+#endif