X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.h;h=bd31173a48647e1bf2ed7b2f7ec95d25e0bfe388;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=9ebdf81ac4fbd06490f05d7be7c15b6f6a5d1179;hpb=cd9dbd8b53bbe32af3e9c6bead4aa6d796a278a5;p=mothur.git

diff --git a/phylosummary.h b/phylosummary.h
index 9ebdf81..bd31173 100644
--- a/phylosummary.h
+++ b/phylosummary.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "mothurout.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -32,21 +33,29 @@ struct rawTaxNode {
 class PhyloSummary {
 
 public:
-	PhyloSummary(string, string);
-	~PhyloSummary() { if (groupmap != NULL)  {  delete groupmap;  }  }
+	PhyloSummary(GroupMap*);
+	PhyloSummary(string, GroupMap*);
+    PhyloSummary(CountTable*);
+	PhyloSummary(string, CountTable*);
+	~PhyloSummary() {}
 	
-	void summarize(string);  //pass it a taxonomy file and a group file and it makes the tree
+	int summarize(string);  //pass it a taxonomy file and a group file and it makes the tree
 	int addSeqToTree(string, 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;
 	int numSeqs;