sparsematrix.cpp

   1
   2 #include "sparsematrix.hpp"
   3 #include "listvector.hpp"
   4
   5 typedef list<PCell>::iterator MatData;
   6
   7 /***********************************************************************/
   8
   9 SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){}
  10
  11 /***********************************************************************/
  12
  13 int SparseMatrix::getNNodes(){
  14         return numNodes;
  15 }
  16
  17 /***********************************************************************/
  18
  19 float SparseMatrix::getSmallDist(){
  20         return smallDist;
  21 }
  22
  23 /***********************************************************************/
  24
  25 void SparseMatrix::rmCell(MatData data){
  26         try {
  27                 if(data->vectorMap != NULL ){
  28                         *(data->vectorMap) = NULL;
  29                         data->vectorMap = NULL;
  30                 }
  31                 matrix.erase(data);
  32                 numNodes--;
  33
  34         //  seems like i should be updating smallDist here, but the only time we remove cells is when
  35         //  clustering and the clustering algorithm updates smallDist
  36         }
  37         catch(exception& e) {
  38                 errorOut(e, "SparseMatrix", "rmCell");
  39                 exit(1);
  40         }
  41 }
  42
  43 /***********************************************************************/
  44
  45 void SparseMatrix::addCell(PCell value){
  46         try {
  47                 matrix.push_back(value);
  48                 numNodes++;
  49                 if(value.dist < smallDist){
  50                         smallDist = value.dist;
  51                 }
  52         }
  53         catch(exception& e) {
  54                 errorOut(e, "SparseMatrix", "addCell");
  55                 exit(1);
  56         }
  57 }
  58
  59 /***********************************************************************/
  60
  61 void SparseMatrix::clear(){
  62         try {
  63                 matrix.clear();
  64                 mins.clear();
  65                 numNodes = 0;
  66                 minsIndex = 0;
  67                 smallDist = 1e6;
  68         }
  69         catch(exception& e) {
  70                 errorOut(e, "SparseMatrix", "clear");
  71                 exit(1);
  72         }
  73 }
  74
  75 /***********************************************************************/
  76
  77 MatData SparseMatrix::begin(){
  78         return matrix.begin();
  79 }
  80
  81 /***********************************************************************/
  82
  83 MatData SparseMatrix::end(){
  84         return matrix.end();
  85 }
  86
  87 /***********************************************************************/
  88
  89 void SparseMatrix::print(){
  90         try {
  91                 int index = 0;
  92
  93                 mothurOutEndLine();
  94                 mothurOut("Index\tRow\tColumn\tDistance");
  95                 mothurOutEndLine();
  96
  97                 for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
  98                         mothurOut(toString(index) + "\t" + toString(currentCell->row)  + "\t" + toString(currentCell->column) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
  99                         index++;
 100                 }
 101         }
 102         catch(exception& e) {
 103                 errorOut(e, "SparseMatrix", "print");
 104                 exit(1);
 105         }
 106 }
 107
 108 /***********************************************************************/
 109
 110 void SparseMatrix::print(ListVector* list){
 111         try {
 112                 int index = 0;
 113
 114                 mothurOutEndLine();
 115                 mothurOut("Index\tRow\tColumn\tDistance");
 116                 mothurOutEndLine();
 117
 118
 119                 for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
 120                         mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
 121                         index++;
 122                 }
 123         }
 124         catch(exception& e) {
 125                 errorOut(e, "SparseMatrix", "print");
 126                 exit(1);
 127         }
 128 }
 129
 130 /***********************************************************************/
 131
 132 PCell* SparseMatrix::getSmallestCell(){
 133         try {
 134         //      this is where I check to see if the next small distance has the correct distance
 135         //      if it doesn't then I remove the offending Cell -> should also be able to check for
 136         //      invalid iterator / pointer -- right???
 137
 138                 while(!mins.empty() && mins.back() == NULL){
 139                         mins.pop_back();
 140                 }
 141
 142         //      if the mins vector is empty go here...
 143                 if(mins.empty()){
 144                         mins.clear();
 145
 146                         smallDist = begin()->dist;  //set the first candidate small distance
 147
 148                         for(MatData currentCell=begin();currentCell!=end();currentCell++){
 149
 150                                 float dist = currentCell->dist;
 151
 152                                 if(dist < smallDist){  //found a new smallest distance
 153                                         mins.clear();
 154                                         smallDist = dist;
 155                                         mins.push_back(&*currentCell);  //this is the address of the data in the list being pointed to by the MatData iterator
 156                                 }
 157                                 else if(dist == smallDist){  //if a subsequent distance is the same as mins distance add the new iterator to the mins vector
 158                                         mins.push_back(&*currentCell); //this is the address of the data in the list being pointed to by the MatData iterator
 159                                 }
 160
 161                         }
 162                         random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
 163
 164                         for(int i=0;i<mins.size();i++){
 165                                 mins[i]->vectorMap = &mins[i];  //assign vectorMap to the address for the container
 166                         }
 167
 168                 }
 169
 170                 smallCell = mins.back();        //make the smallestCell the last element of the vector
 171
 172                 mins.pop_back();                        //remove the last element from the vector
 173
 174                 return smallCell;
 175         }
 176         catch(exception& e) {
 177                 errorOut(e, "SparseMatrix", "getSmallestCell");
 178                 exit(1);
 179         }
 180 }
 181
 182 /***********************************************************************/
 183