#include "mothur.h"
+#include "nameassignment.hpp"
class RAbundVector;
class ListVector;
-/************************************************************/
-struct clusterNode {
- int numSeq;
- int parent;
- int smallChild; //used to make linkTable work with list and rabund. represents bin number of this cluster node
- clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {};
-};
/***********************************************************************/
class HCluster {
public:
- HCluster(RAbundVector*, ListVector*);
- bool update(int, int, float);
- //string getTag();
+ 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();
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;
+
};