modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / phylotree.h

diff --git a/phylotree.h b/phylotree.h
index f8365d53e7664f9a4ca02cb09dea59cabca11f0b..345e2e72228d711942e2f0d036eed0bda8c8fa67 100644 (file)
--- a/phylotree.h
+++ b/phylotree.h
@@ -11,6 +11,7 @@
  */
 
 #include "mothur.h"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -35,11 +36,16 @@ public:
        void addSeqToTree(string, string);
        void assignHeirarchyIDs(int);
        void print(ofstream&);
-       vector<int> getGenusNodes();    
-       TaxNode get(int i)                              {       return tree[i]; }
+       vector<int> getGenusNodes();
+       void binUnclassified();
+               
+       TaxNode get(int i)                              {       return tree[i];                                                 }
        TaxNode get(string seqName)             {       return tree[name2Taxonomy[seqName]];    }
-       int getIndex(string seqName)    {       return name2Taxonomy[seqName];  }
-       string getName(int i)                   {       return tree[i].name;    }
+       int getIndex(string seqName)    {       return name2Taxonomy[seqName];                  }
+       string getName(int i)                   {       return tree[i].name;                                    }
+       string getFullTaxonomy(string);  //pass a sequence name return taxonomy
+       int getMaxLevel()                               {       return maxLevel;                                                }
+       
 private:
        string getNextTaxon(string&);
        vector<TaxNode> tree;
@@ -49,6 +55,8 @@ private:
        void print(int, ofstream&);
        int numNodes;
        int numSeqs;
+       int maxLevel;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/