averagelinkage.cpp

   1 #ifndef AVERAGE_H
   2 #define AVERAGE_H
   3
   4 #include "cluster.hpp"
   5 #include "rabundvector.hpp"
   6 #include "sparsematrix.hpp"
   7 #include <exception>
   8
   9 /* This class implements the average UPGMA, average neighbor clustering algorithm */
  10
  11 /***********************************************************************/
  12
  13 AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm) :
  14 Cluster(rav, lv, dm)
  15 {}
  16
  17 /***********************************************************************/
  18 //THis function clusters based on the average method
  19 void AverageLinkage::update(){
  20         try{
  21                 getRowColCells();
  22
  23                 vector<int> found(nColCells, 0);
  24
  25                 int rowBin = rabund->get(smallRow);
  26                 int colBin = rabund->get(smallCol);
  27                 int totalBin = rowBin + colBin;
  28
  29                 for(int i=1;i<nRowCells;i++){
  30
  31                         int search;
  32
  33                         if(rowCells[i]->row == smallRow){
  34                                 search = rowCells[i]->column;
  35                         }
  36                         else{
  37                                 search = rowCells[i]->row;
  38                         }
  39
  40                         for(int j=1;j<nColCells;j++){
  41
  42                                 if(colCells[j]->row == search || colCells[j]->column == search){
  43                                         colCells[j]->dist = (colBin * colCells[j]->dist + rowBin * rowCells[i]->dist) / totalBin;
  44
  45                                         found[j] = 1;
  46
  47                                         if(colCells[j]->vectorMap != NULL){
  48                                                 *(colCells[j]->vectorMap) = NULL;
  49                                                 colCells[j]->vectorMap = NULL;
  50                                         }
  51
  52                                         break;
  53                                 }
  54
  55                         }
  56                         dMatrix->rmCell(rowCells[i]);
  57                 }
  58
  59                 clusterBins();
  60                 clusterNames();
  61
  62                 for(int i=0;i<nColCells;i++){
  63                         if(found[i] == 0){
  64                                 dMatrix->rmCell(colCells[i]);
  65                         }
  66                 }
  67         }
  68         catch(exception& e) {
  69                 cout << "Standard Error: " << e.what() << " has occurred in the AverageLinkage class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72         catch(...) {
  73                 cout << "An unknown error has occurred in the AverageLinkage class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  74                 exit(1);
  75         }
  76
  77
  78 }
  79
  80 /***********************************************************************/
  81
  82 #endif
  83
  84