made make.table alias to count.seqs command. added large parameter to count.seqs...

[mothur.git] / phylotree.h

diff --git a/phylotree.h b/phylotree.h
index a57cf256ecf0e0eded1182681f7ab91601e0a1a5..7aae8f1adedcf5f1db6b94d1bbe76a968a8e3100 100644 (file)
--- a/phylotree.h
+++ b/phylotree.h
@@ -41,17 +41,22 @@ public:
        vector<int> getGenusTotals();   
        void setUp(string);  //used to create file needed for summary file if you use () constructor and add seqs manually instead of passing taxonomyfile
                
-       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;                                    }
+       TaxNode get(int i);                             
+       TaxNode get(string seqName);
+       string getName(int i);                  
+       int getIndex(string seqName);   
        string getFullTaxonomy(string);  //pass a sequence name return taxonomy
-       int getMaxLevel()                               {       return maxLevel;                                                }
-       int getNumSeqs()  {  return numSeqs;  }
+       
+       int getMaxLevel()               {       return maxLevel;        }
+       int getNumSeqs()                {       return numSeqs;         }
+       int getNumNodes()               {       return tree.size();     }
+       
+       bool ErrorCheck(vector<string>);
        
 private:
-       string getNextTaxon(string&);
-       void print(ofstream&, vector<TaxNode>&);
+       string getNextTaxon(string&, string);
+       void print(ofstream&, vector<TaxNode>&); //used to create static reference taxonomy file
+       void fillOutTree(int, vector<TaxNode>&); //used to create static reference taxonomy file
        void binUnclassified(string);
        
        vector<TaxNode> tree;
@@ -59,6 +64,7 @@ private:
        vector<int> totals; //holds the numSeqs at each genus level taxonomy
        map<string, int> name2Taxonomy;  //maps name to index in tree
        map<int, int> uniqueTaxonomies;  //map of unique taxonomies
+       map<int, int> leafNodes; //used to create static reference taxonomy file
        //void print(int, ofstream&);
        int numNodes;
        int numSeqs;