Initial revision

[mothur.git] / averagelinkage.cpp

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
new file mode 100644 (file)
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--- /dev/null
+++ b/averagelinkage.cpp
@@ -0,0 +1,78 @@
+
+#include "cluster.hpp"
+#include "rabundvector.hpp"
+#include "sparsematrix.hpp"
+#include <exception>
+
+/* This class implements the average UPGMA, average neighbor clustering algorithm */
+
+/***********************************************************************/
+
+AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm) :
+Cluster(rav, lv, dm)
+{}
+
+/***********************************************************************/
+//THis function clusters based on the average method
+void AverageLinkage::update(){
+       try{
+               getRowColCells();               
+       
+               vector<int> found(nColCells, 0);
+       
+               int rowBin = rabund->get(smallRow);
+               int colBin = rabund->get(smallCol);
+               int totalBin = rowBin + colBin;
+       
+               for(int i=1;i<nRowCells;i++){
+               
+                       int search;
+               
+                       if(rowCells[i]->row == smallRow){
+                               search = rowCells[i]->column;
+                       }
+                       else{
+                               search = rowCells[i]->row;
+                       }
+               
+                       for(int j=1;j<nColCells;j++){
+                       
+                               if(colCells[j]->row == search || colCells[j]->column == search){
+                                       colCells[j]->dist = (colBin * colCells[j]->dist + rowBin * rowCells[i]->dist) / totalBin;               
+                               
+                                       found[j] = 1;
+                               
+                                       if(colCells[j]->vectorMap != NULL){
+                                               *(colCells[j]->vectorMap) = NULL;
+                                               colCells[j]->vectorMap = NULL;
+                                       }
+                               
+                                       break;
+                               }
+                       
+                       }                       
+                       dMatrix->rmCell(rowCells[i]);
+               }       
+       
+               clusterBins();
+               clusterNames();
+       
+               for(int i=0;i<nColCells;i++){
+                       if(found[i] == 0){
+                               dMatrix->rmCell(colCells[i]);
+                       }
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the AverageLinkage class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the AverageLinkage class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+       
+}
+
+/***********************************************************************/