X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=treemap.h;h=7ffd1e7003154d672d544aa8a993f371a7f9a28a;hp=0dc74eec2fad5ebc157b4fd12e63a7b8b37c967a;hb=615301e57c25e241356a9c2380648d117709458d;hpb=bfbc55964f1977da72c2cea984288a427d370a59

diff --git a/treemap.h b/treemap.h
index 0dc74ee..7ffd1e7 100644
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,7 @@
  */
 
 #include "mothur.h"
-#include "utilities.hpp"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -19,33 +19,50 @@ struct GroupIndex {
 	int		vectorIndex;
 };
 
-
-
 class TreeMap {
 public:
-	TreeMap() {};
+	TreeMap() { m = MothurOut::getInstance(); }
 	TreeMap(string);
 	~TreeMap();
-	void readMap();
+    
+	int readMap();
+    int readMap(string);
 	int getNumGroups();
 	int getNumSeqs();
-	void setIndex(string, int);  //sequencename, index
-	int getIndex(string);		//returns vector index of sequence
+	//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;
+	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&);
-	
+
+    
 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;
+	
 	
 };