cluster.cpp

   1 /*
   2  *  cluster.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 8/14/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "cluster.hpp"
  11 #include "rabundvector.hpp"
  12 #include "listvector.hpp"
  13 #include <exception>
  14
  15 /***********************************************************************/
  16
  17 Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm) :
  18 rabund(rav), list(lv), dMatrix(dm)
  19 {
  20 }
  21
  22 /***********************************************************************/
  23
  24 void Cluster::getRowColCells(){
  25         try {
  26                 PCell* smallCell = dMatrix->getSmallestCell();  //find the smallest cell - this routine should probably not be in the SpMat class
  27
  28                 smallRow = smallCell->row;              //get its row
  29                 smallCol = smallCell->column;   //get its column
  30                 smallDist = smallCell->dist;    //get the smallest distance
  31
  32                 rowCells.clear();
  33                 colCells.clear();
  34
  35                 for(MatData currentCell=dMatrix->begin();currentCell!=dMatrix->end();currentCell++){
  36
  37                         if(&*currentCell == smallCell){                         //put the smallest cell first
  38                                 rowCells.insert(rowCells.begin(), currentCell);
  39                                 colCells.insert(colCells.begin(), currentCell);
  40                         }
  41                         else if(currentCell->row == smallRow){
  42                                 rowCells.push_back(currentCell);
  43                         }
  44                         else if(currentCell->column == smallRow){
  45                                 rowCells.push_back(currentCell);
  46                         }
  47                         else if(currentCell->row == smallCol){
  48                                 colCells.push_back(currentCell);
  49                         }
  50                         else if(currentCell->column == smallCol){
  51                                 colCells.push_back(currentCell);
  52                         }
  53                 }
  54
  55                 nRowCells = rowCells.size();
  56                 nColCells = colCells.size();
  57         }
  58         catch(exception& e) {
  59                 cout << "Standard Error: " << e.what() << " has occurred in the Cluster class Function getRowColCells. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  60                 exit(1);
  61         }
  62         catch(...) {
  63                 cout << "An unknown error has occurred in the Cluster class function getRowColCells. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  64                 exit(1);
  65         }
  66 }
  67
  68 /***********************************************************************/
  69
  70 void Cluster::clusterBins(){
  71         try {
  72         //      cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol);
  73
  74                 rabund->set(smallCol, rabund->get(smallRow)+rabund->get(smallCol));
  75                 rabund->set(smallRow, 0);
  76                 rabund->setLabel(toString(smallDist));
  77
  78         //      cout << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol) << endl;
  79         }
  80         catch(exception& e) {
  81                 cout << "Standard Error: " << e.what() << " has occurred in the Cluster class Function clusterBins. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  82                 exit(1);
  83         }
  84         catch(...) {
  85                 cout << "An unknown error has occurred in the Cluster class function clusterBins. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  86                 exit(1);
  87         }
  88
  89
  90 }
  91
  92 /***********************************************************************/
  93
  94 void Cluster::clusterNames(){
  95         try {
  96         //      cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << list->get(smallRow) << '\t' << list->get(smallCol);
  97
  98                 list->set(smallCol, list->get(smallRow)+','+list->get(smallCol));
  99                 list->set(smallRow, "");
 100                 list->setLabel(toString(smallDist));
 101
 102         //      cout << '\t' << list->get(smallRow) << '\t' << list->get(smallCol) << endl;
 103     }
 104         catch(exception& e) {
 105                 cout << "Standard Error: " << e.what() << " has occurred in the Cluster class Function clusterNames. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108         catch(...) {
 109                 cout << "An unknown error has occurred in the Cluster class function clusterNames. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112 }
 113
 114 /***********************************************************************/
 115