X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hcluster.h;h=d8598867a7bf247509a7736203a5ef505ce70f9e;hp=6b2862b7919b8d74e7a28a0442ef10bceb863db0;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=f5023c911c377e5320c5110c78af98dd8841ef58

diff --git a/hcluster.h b/hcluster.h
index 6b2862b..d859886 100644
--- a/hcluster.h
+++ b/hcluster.h
@@ -12,6 +12,7 @@
 
 
 #include "mothur.h"
+#include "nameassignment.hpp"
 
 class RAbundVector;
 class ListVector;
@@ -20,10 +21,12 @@ class ListVector;
 class HCluster {
 	
 public:
-	HCluster(RAbundVector*, ListVector*);
+	HCluster(RAbundVector*, ListVector*, string, string, NameAssignment*, float);
 	~HCluster(){};
-    bool update(int, int, float);
-	//string getTag();
+    double update(int, int, float);
+	void setMapWanted(bool m); 
+	map<string, int> getSeqtoBin()  {  return seq2Bin;	}
+	vector<seqDist> getSeqs();
 
 protected:	
 	void clusterBins();
@@ -32,21 +35,41 @@ protected:
 	int makeActive();
 	void printInfo();
 	void updateArrayandLinkTable();
+	void updateMap();
+	vector<seqDist> getSeqsFNNN();
+	vector<seqDist> getSeqsAN();
+	int combineFile();
+	int processFile();
+	//seqDist getNextDist(char*, int&, int);
 		
 	RAbundVector* rabund;
 	ListVector* list;
+	NameAssignment* nameMap;
 	
 	vector<clusterNode> clusterArray;
+	
+	//note: the nearest and average neighbor method do not use the link table or active links
 	vector< map<int, int> > linkTable;  // vector of maps - linkTable[1][6] = 2  would mean sequence in spot 1 has 2 links with sequence in 6
 	map<int, int> activeLinks;  //maps sequence to index in linkTable
 	map<int, int>::iterator it;
+	map<int, int>::iterator itActive;
+	map<int, int>::iterator it2Active;
 	map<int, int>::iterator it2;
 	
 	int numSeqs;
-	
 	int smallRow;
 	int smallCol;
-	float smallDist;
+	float smallDist, cutoff;
+	map<string, int> seq2Bin;
+	bool mapWanted, exitedBreak;
+	seqDist next;
+	string method, distfile;
+	ifstream filehandle;
+	
+	vector<seqDist> mergedMin;
+	string partialDist;
+	MothurOut* m;
+	
 	
 };