changing command name classify.shared to classifyrf.shared

[mothur.git] / phylotree.h

diff --git a/phylotree.h b/phylotree.h
index 6e5b58d85c2430807af15e0345a36fece9f0f90e..e0002209e4d83aaaf9468573173858d9b0602b61 100644 (file)
--- a/phylotree.h
+++ b/phylotree.h
@@ -11,6 +11,7 @@
  */
 
 #include "mothur.h"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -31,27 +32,46 @@ class PhyloTree {
 public:
        PhyloTree();
        PhyloTree(string);  //pass it a taxonomy file and it makes the tree
+       PhyloTree(ifstream&, string);  //pass it a taxonomy file and it makes the train.tree
        ~PhyloTree() {};
-       void addSeqToTree(string, string);
+       int addSeqToTree(string, string);
        void assignHeirarchyIDs(int);
-       void print(ofstream&);
+       void printTreeNodes(string); //used by bayesian to save time
        vector<int> getGenusNodes();
-       void binUnclassified();
+       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 getGenusIndex(string seqName);      
+       string getFullTaxonomy(string);  //pass a sequence name return taxonomy
+       
+       int getMaxLevel()               {       return maxLevel;        }
+       int getNumSeqs()                {       return numSeqs;         }
+       int getNumNodes()               {       return tree.size();     }
+       
+       bool ErrorCheck(vector<string>);
+       
 private:
-       string getNextTaxon(string&);
+       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;
        vector<int> genusIndex; //holds the indexes in tree where the genus level taxonomies are stored
+       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
-       void print(int, ofstream&);
+    map<string, int> name2GenusNodeIndex;
+       set<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;
        int maxLevel;
+       bool calcTotals;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/