X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=bda6926c20ea79800e9f9cc8a06b87ce6f44c68c;hb=291eaab661778e1fd02c5c22bc388daa97bb1d54;hp=12299731f89e10741926cd797fad2a02ed267c2d;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/treemap.h b/treemap.h
index 1229973..bda6926 100644
--- a/treemap.h
+++ b/treemap.h
@@ -11,6 +11,7 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -20,10 +21,11 @@ struct GroupIndex {
 };
 
 class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
-	TreeMap() {};
+	TreeMap() { m = MothurOut::getInstance(); }
 	TreeMap(string);
 	~TreeMap();
 	void readMap();
@@ -32,14 +34,15 @@ public:
 	void setIndex(string, int);  //sequencename, index
 	int getIndex(string);		//returns vector index of sequence
 	bool isValidGroup(string);  //return true if string is a valid group
+	void removeSeq(string);  //removes a sequence, this is to accomadate trees that do not contain all the seqs in your groupfile
 	string getGroup(string);
 	vector<string> namesOfGroups;
 	vector<string> namesOfSeqs;
     map<string,int> seqsPerGroup;	//groupname, number of seqs in that group.
 	map<string, GroupIndex> treemap; //sequence name and <groupname, vector index>
 	void print(ostream&);
-	void makeSim(GroupMap*);  //takes groupmap info and fills treemap for use by tree.groups command.
-	
+	void makeSim(GroupMap*);  //takes groupmap info and fills treemap for use by tree.shared command.
+	void makeSim(ListVector*);  //takes listvector info and fills treemap for use by tree.shared command.	
 	
 private:
 	ifstream fileHandle;
@@ -48,6 +51,7 @@ private:
 	map<string, GroupIndex>::iterator it;
 	map<string, int>::iterator it2;
 	void setNamesOfGroups(string); 
+	MothurOut* m;
 	
 	
 };