X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=7ed8d04f0886367f5a17a5baeec4848e75687358;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=941ca9a8f79e4de463f99719d6ffd37fe7733961;hpb=06da1833191d5dee7e206f436d9631680f1e7c42;p=mothur.git

diff --git a/treemap.h b/treemap.h
index 941ca9a..7ed8d04 100644
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,8 @@
  */
 
 #include "mothur.h"
-#include "utilities.hpp"
+#include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -19,34 +20,44 @@ struct GroupIndex {
 	int		vectorIndex;
 };
 
-
+class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
-	TreeMap() {};
+	TreeMap() { m = MothurOut::getInstance(); }
 	TreeMap(string);
 	~TreeMap();
-	void readMap();
+	int readMap();
 	int getNumGroups();
 	int getNumSeqs();
 	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;
+	void addSeq(string, string);
+	void addGroup(string s) { setNamesOfGroups(s); }
+	vector<string> getNamesOfGroups() {
+		sort(namesOfGroups.begin(), namesOfGroups.end());
+		return 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(vector<string>);  //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:
+	vector<string> namesOfGroups;
 	ifstream fileHandle;
 	string groupFileName;
 	int numGroups;
 	map<string, GroupIndex>::iterator it;
 	map<string, int>::iterator it2;
 	void setNamesOfGroups(string); 
+	MothurOut* m;
 	
 	
 };