precluster command finished

[mothur.git] / hcluster.h

diff --git a/hcluster.h b/hcluster.h
index dd4c679123f12d90fbc2ca1daaae5045be9a1dc1..065d559d1223865313b95a32f20dd6fb14fc5fc0 100644 (file)
--- a/hcluster.h
+++ b/hcluster.h
@@ -12,6 +12,7 @@
 
 
 #include "mothur.h"
+#include "nameassignment.hpp"
 
 class RAbundVector;
 class ListVector;
@@ -20,11 +21,12 @@ class ListVector;
 class HCluster {
        
 public:
-       HCluster(RAbundVector*, ListVector*);
+       HCluster(RAbundVector*, ListVector*, string);
        ~HCluster(){};
     void update(int, int, float);
        void setMapWanted(bool m); 
        map<string, int> getSeqtoBin()  {  return seq2Bin;      }
+       vector<seqDist> getSeqs(ifstream&, NameAssignment*, float);
 
 protected:     
        void clusterBins();
@@ -49,7 +51,9 @@ protected:
        int smallCol;
        float smallDist;
        map<string, int> seq2Bin;
-       bool mapWanted;
+       bool mapWanted, exitedBreak;
+       seqDist next;
+       string method;
        
 };