changes while testing

[mothur.git] / hcluster.h

diff --git a/hcluster.h b/hcluster.h
index 6b2862b7919b8d74e7a28a0442ef10bceb863db0..d8598867a7bf247509a7736203a5ef505ce70f9e 100644 (file)
--- 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;
+       
        
 };