fixed some bugs and added mgcluster command

[mothur.git] / cluster.hpp

diff --git a/cluster.hpp b/cluster.hpp
index 99d8b7d557a41cef684ad2f9aae7d636d621bbc7..a6024e79d45a52274040a53cca4f8b32d9d2e998 100644 (file)
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -14,8 +14,10 @@ class Cluster {
        
 public:
        Cluster(RAbundVector*, ListVector*, SparseMatrix*);
-    virtual void update();
+    virtual void update();                             
        virtual string getTag() = 0;
+       virtual void setMapWanted(bool m);  
+       virtual map<string, int> getSeqtoBin()  {  return seq2Bin;      }
 
 protected:     
        void getRowColCells();
@@ -25,6 +27,7 @@ protected:
 
        virtual void clusterBins();
        virtual void clusterNames();
+       virtual void updateMap();
        
        RAbundVector* rabund;
        ListVector* list;
@@ -33,8 +36,10 @@ protected:
        int smallRow;
        int smallCol;
        float smallDist;
+       bool mapWanted;
+       map<string, int> seq2Bin;
        
-       vector<MatVec> seqVec;          // contains vectors of cells related to a certain sequence\r
+       vector<MatVec> seqVec;          // contains vectors of cells related to a certain sequence
        MatVec rowCells;
        MatVec colCells;
        ull nRowCells;