created mothurOut class to handle logfiles

[mothur.git] / hcluster.h

diff --git a/hcluster.h b/hcluster.h
index 679abbc2cc19e54f5a3028155de3d6d18372d937..5005ec6c55c9edc608a1ecbf73e65affea0a88a2 100644 (file)
--- a/hcluster.h
+++ b/hcluster.h
@@ -17,16 +17,6 @@
 class RAbundVector;
 class ListVector;
 
-/***********************************************************************/
-struct linkNode {
-       int     links;
-       float dist;
-       
-       linkNode() {};
-       linkNode(int l, float a) : links(l), dist(a) {};
-       ~linkNode() {};
-};
-
 /***********************************************************************/
 class HCluster {
        
@@ -50,7 +40,7 @@ protected:
        vector<seqDist> getSeqsAN();
        void combineFile();
        void processFile();
-       seqDist getNextDist(char*, int&, int);
+       //seqDist getNextDist(char*, int&, int);
                
        RAbundVector* rabund;
        ListVector* list;
@@ -71,13 +61,14 @@ protected:
        int smallCol;
        float smallDist, cutoff;
        map<string, int> seq2Bin;
-       bool mapWanted, exitedBreak, firstRead;
+       bool mapWanted, exitedBreak;
        seqDist next;
        string method, distfile;
        ifstream filehandle;
        
        vector<seqDist> mergedMin;
        string partialDist;
+       MothurOut* m;
        
        
 };