X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=57822e02d4b8c3a57f7d0ddf26947c470bf9400b;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=bda6926c20ea79800e9f9cc8a06b87ce6f44c68c;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/treemap.h b/treemap.h
index bda6926..57822e0 100644
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,6 @@
  */
 
 #include "mothur.h"
-#include "groupmap.h"
 #include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
@@ -20,15 +19,14 @@ struct GroupIndex {
 	int		vectorIndex;
 };
 
-class GroupMap;
-class ListVector;
-
 class TreeMap {
 public:
 	TreeMap() { m = MothurOut::getInstance(); }
 	TreeMap(string);
 	~TreeMap();
-	void readMap();
+    
+	int readMap();
+    int readMap(string);
 	int getNumGroups();
 	int getNumSeqs();
 	void setIndex(string, int);  //sequencename, index
@@ -36,15 +34,27 @@ public:
 	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;
+	void addSeq(string, string);
+	void addGroup(string s) { setNamesOfGroups(s); }
+	vector<string> getNamesOfGroups() {
+		sort(namesOfGroups.begin(), namesOfGroups.end());
+		return namesOfGroups;
+	}
+    
+    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.	
+    vector<string> getNamesSeqs();
+	vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
+    int getCopy(TreeMap&);
+    
+    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.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;