bugs fixes while testing for 1.5 release

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 12299731f89e10741926cd797fad2a02ed267c2d..0824ebf7f7e6cd109db4d3adb344c46d09738b21 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -11,6 +11,7 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -20,6 +21,7 @@ struct GroupIndex {
 };
 
 class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
@@ -32,14 +34,15 @@ public:
        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;
        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.groups command.
-       
+       void makeSim(GroupMap*);  //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:
        ifstream fileHandle;