X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.h;h=bd31173a48647e1bf2ed7b2f7ec95d25e0bfe388;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=cdec0d0a4ac7ca83cb0845988adb90152bcae07b;hpb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;p=mothur.git

diff --git a/phylosummary.h b/phylosummary.h
index cdec0d0..bd31173 100644
--- a/phylosummary.h
+++ b/phylosummary.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "mothurout.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -32,23 +33,28 @@ struct rawTaxNode {
 class PhyloSummary {
 
 public:
-	PhyloSummary(string);
-	PhyloSummary(string, string);
-	~PhyloSummary() { if (groupmap != NULL)  {  delete groupmap;  }  }
+	PhyloSummary(GroupMap*);
+	PhyloSummary(string, GroupMap*);
+    PhyloSummary(CountTable*);
+	PhyloSummary(string, CountTable*);
+	~PhyloSummary() {}
 	
 	int summarize(string);  //pass it a taxonomy file and a group file and it makes the tree
 	int addSeqToTree(string, string);
-	int addSeqToTree(string, vector<string>);
+	int addSeqToTree(string, map<string, bool>);
 	void print(ofstream&);
+    void print(ofstream&, bool);
 	int getMaxLevel() { return maxLevel; }
 	
 private:
 	string getNextTaxon(string&);
 	vector<rawTaxNode> tree;
 	void print(int, ofstream&);
+    void print(int, ofstream&, bool);
 	void assignRank(int);
 	void readTreeStruct(ifstream&);
 	GroupMap* groupmap;
+    CountTable* ct;
 	bool ignore;
 	
 	int numNodes;