X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;fp=treemap.h;h=57822e02d4b8c3a57f7d0ddf26947c470bf9400b;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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+#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