added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index d9617f5455e03f0f5fc702fffaf3516335351b15..73d02fcc4b0c58f29de00c130e3fa8a197dd3d53 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -9,11 +9,8 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "groupmap.h"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -22,10 +19,11 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-
+class GroupMap;
 
 class TreeMap {
 public:
+       TreeMap() {};
        TreeMap(string);
        ~TreeMap();
        void readMap();
@@ -33,18 +31,25 @@ public:
        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
        string getGroup(string);
        vector<string> 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(GroupMap*);  //takes groupmap info and fills treemap for use by tree.shared command.
+       
        
 private:
        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
+       
+       
 };
 
 #endif