X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hcluster.h;fp=hcluster.h;h=0000000000000000000000000000000000000000;hp=d8598867a7bf247509a7736203a5ef505ce70f9e;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76

diff --git a/hcluster.h b/hcluster.h
deleted file mode 100644
index d859886..0000000
--- a/hcluster.h
+++ /dev/null
@@ -1,86 +0,0 @@
-#ifndef HCLUSTER_H
-#define HCLUSTER_H
-
-/*
- *  hcluster.h
- *  Mothur
- *
- *  Created by westcott on 10/13/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "mothur.h"
-#include "nameassignment.hpp"
-
-class RAbundVector;
-class ListVector;
-
-/***********************************************************************/
-class HCluster {
-	
-public:
-	HCluster(RAbundVector*, ListVector*, string, string, NameAssignment*, float);
-	~HCluster(){};
-    double update(int, int, float);
-	void setMapWanted(bool m); 
-	map<string, int> getSeqtoBin()  {  return seq2Bin;	}
-	vector<seqDist> getSeqs();
-
-protected:	
-	void clusterBins();
-	void clusterNames();
-	int getUpmostParent(int);
-	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, cutoff;
-	map<string, int> seq2Bin;
-	bool mapWanted, exitedBreak;
-	seqDist next;
-	string method, distfile;
-	ifstream filehandle;
-	
-	vector<seqDist> mergedMin;
-	string partialDist;
-	MothurOut* m;
-	
-	
-};
-
-/***********************************************************************/
-
-
-
-
-
-
-
-#endif
-
-