X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;fp=treemap.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=57822e02d4b8c3a57f7d0ddf26947c470bf9400b;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/treemap.h b/treemap.h
deleted file mode 100644
index 57822e0..0000000
--- a/treemap.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef TREEMAP_H
-#define TREEMAP_H
-/*
- *  treemap.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 1/26/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "listvector.hpp"
-
-/* This class is used by the read.tree command to build the tree container. */
-
-struct GroupIndex {
-	string	groupname;
-	int		vectorIndex;
-};
-
-class TreeMap {
-public:
-	TreeMap() { m = MothurOut::getInstance(); }
-	TreeMap(string);
-	~TreeMap();
-    
-	int readMap();
-    int readMap(string);
-	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);
-	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>
-
-    
-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;
-	
-	
-};
-
-#endif