added warning about average neighbor merges around cutoff. fixed little bugs.

[mothur.git] / cluster.hpp

diff --git a/cluster.hpp b/cluster.hpp
index a6024e79d45a52274040a53cca4f8b32d9d2e998..38897c9cf0a2a2c0c95933eb7cabc8732f95839e 100644 (file)
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -13,7 +13,7 @@ typedef vector<MatData> MatVec;
 class Cluster {
        
 public:
-       Cluster(RAbundVector*, ListVector*, SparseMatrix*);
+       Cluster(RAbundVector*, ListVector*, SparseMatrix*, float);
     virtual void update();                             
        virtual string getTag() = 0;
        virtual void setMapWanted(bool m);  
@@ -37,6 +37,7 @@ protected:
        int smallCol;
        float smallDist;
        bool mapWanted;
+       float cutoff;
        map<string, int> seq2Bin;
        
        vector<MatVec> seqVec;          // contains vectors of cells related to a certain sequence
@@ -50,7 +51,7 @@ protected:
 
 class CompleteLinkage : public Cluster {
 public:
-       CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+       CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float);
        bool updateDistance(MatData& colCell, MatData& rowCell);
        string getTag();
        
@@ -62,7 +63,7 @@ private:
 
 class SingleLinkage : public Cluster {
 public:
-       SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+       SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*, float);
     void update();
        bool updateDistance(MatData& colCell, MatData& rowCell);
        string getTag();
@@ -75,7 +76,7 @@ private:
 
 class AverageLinkage : public Cluster {
 public:
-       AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+       AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float);
        bool updateDistance(MatData& colCell, MatData& rowCell);
        string getTag();