X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=d4b506e6fb1d26675937f89f2cc1591e21a98c07;hb=dd173a49e37f6bae73a63c32dd7c98d317bb4a79;hp=60f75b388571aff503ac95b96df5946e6fcfa89f;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/treemap.h b/treemap.h
index 60f75b3..d4b506e 100644
--- a/treemap.h
+++ b/treemap.h
@@ -9,11 +9,9 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -22,11 +20,12 @@ struct GroupIndex {
 	int		vectorIndex;
 };
 
-
+class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
-	TreeMap() {};
+	TreeMap() { m = MothurOut::getInstance(); }
 	TreeMap(string);
 	~TreeMap();
 	void readMap();
@@ -34,12 +33,17 @@ public:
 	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);
+	void addSeq(string, 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
+	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.shared command.
+	void makeSim(ListVector*);  //takes listvector info and fills treemap for use by tree.shared command.	
 	
 private:
 	ifstream fileHandle;
@@ -48,6 +52,8 @@ private:
 	map<string, GroupIndex>::iterator it;
 	map<string, int>::iterator it2;
 	void setNamesOfGroups(string); 
+	MothurOut* m;
+	
 	
 };