moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / hcluster.h

diff --git a/hcluster.h b/hcluster.h
deleted file mode 100644 (file)
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
-
-