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