X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotree.h;h=e0002209e4d83aaaf9468573173858d9b0602b61;hp=f8365d53e7664f9a4ca02cb09dea59cabca11f0b;hb=615301e57c25e241356a9c2380648d117709458d;hpb=7a2154809d332281cf4006943a9bd94b8208c837

diff --git a/phylotree.h b/phylotree.h
index f8365d5..e000220 100644
--- a/phylotree.h
+++ b/phylotree.h
@@ -11,6 +11,7 @@
  */
 
 #include "mothur.h"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -31,24 +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&);
-	vector<int> getGenusNodes();	
-	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;	}
+	void printTreeNodes(string); //used by bayesian to save time
+	vector<int> getGenusNodes();
+	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);				
+	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;
 };
 
 /**************************************************************************************************/