added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 20bbcfee7090f0aad18e9eee8324358a2f69c5ba..7ed8d04f0886367f5a17a5baeec4848e75687358 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -9,12 +9,9 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -23,29 +20,46 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-
+class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
+       TreeMap() { m = MothurOut::getInstance(); }
        TreeMap(string);
        ~TreeMap();
-       void readMap();
+       int readMap();
        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);
-       vector<string> namesOfGroups;
+       void addSeq(string, string);
+       void addGroup(string s) { setNamesOfGroups(s); }
+       vector<string> getNamesOfGroups() {
+               sort(namesOfGroups.begin(), namesOfGroups.end());
+               return namesOfGroups;
+       }
        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&);
+       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.   
        
 private:
+       vector<string> namesOfGroups;
        ifstream fileHandle;
        string groupFileName;
        int numGroups;
        map<string, GroupIndex>::iterator it;
+       map<string, int>::iterator it2;
        void setNamesOfGroups(string); 
-       map<string, GroupIndex> treemap; //sequence name and groupname
+       MothurOut* m;
+       
+       
 };
 
-#endif
\ No newline at end of file
+#endif