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[mothur.git] / treemap.h

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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