X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.h;h=4d3464f70472cdd2d2f8575934fcb96f6efbb3e5;hb=f6a58db15cdc7b90a601f8bf9c9d3b69d642f85d;hp=3adcc3f5fb0ed1f31bf0f2c223dff553f487a61a;hpb=763d07b1c215b1bdc9d5d63431f78cfecc60acf5;p=mothur.git

diff --git a/phylosummary.h b/phylosummary.h
index 3adcc3f..4d3464f 100644
--- a/phylosummary.h
+++ b/phylosummary.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "mothurout.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -32,31 +33,34 @@ struct rawTaxNode {
 class PhyloSummary {
 
 public:
-	PhyloSummary(string);
-	PhyloSummary(string, string);
-	~PhyloSummary() { if (groupmap != NULL)  {  delete groupmap;  }  }
+	PhyloSummary(GroupMap*, bool);
+	PhyloSummary(string, GroupMap*, bool);
+    PhyloSummary(CountTable*, bool);
+	PhyloSummary(string, CountTable*, bool);
+	~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;
-	bool ignore;
+    CountTable* ct;
+	bool ignore, relabund;
 	
 	int numNodes;
 	int numSeqs;
 	int maxLevel;
 	MothurOut* m;
-	
-	void removeConfidences(string&);
 };
 
 /**************************************************************************************************/