averagelinkage.cpp

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