moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
deleted file mode 100644 (file)
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