X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hcluster.h;h=d8598867a7bf247509a7736203a5ef505ce70f9e;hp=679abbc2cc19e54f5a3028155de3d6d18372d937;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=92f998cc7debc4bf3e8594848586b8153d96db16

diff --git a/hcluster.h b/hcluster.h
index 679abbc..d859886 100644
--- a/hcluster.h
+++ b/hcluster.h
@@ -17,23 +17,13 @@
 class RAbundVector;
 class ListVector;
 
-/***********************************************************************/
-struct linkNode {
-	int	links;
-	float dist;
-	
-	linkNode() {};
-	linkNode(int l, float a) : links(l), dist(a) {};
-	~linkNode() {};
-};
-
 /***********************************************************************/
 class HCluster {
 	
 public:
 	HCluster(RAbundVector*, ListVector*, string, string, NameAssignment*, float);
 	~HCluster(){};
-    bool update(int, int, float);
+    double update(int, int, float);
 	void setMapWanted(bool m); 
 	map<string, int> getSeqtoBin()  {  return seq2Bin;	}
 	vector<seqDist> getSeqs();
@@ -48,9 +38,9 @@ protected:
 	void updateMap();
 	vector<seqDist> getSeqsFNNN();
 	vector<seqDist> getSeqsAN();
-	void combineFile();
-	void processFile();
-	seqDist getNextDist(char*, int&, int);
+	int combineFile();
+	int processFile();
+	//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;
 	
 	
 };