moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sparsematrix.cpp

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
deleted file mode 100644 (file)
index 3a0ec65..0000000
--- a/sparsematrix.cpp
+++ /dev/null
@@ -1,177 +0,0 @@
-
-#include "sparsematrix.hpp"
-#include "listvector.hpp"
-
-
-/***********************************************************************/
-
-SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){  m = MothurOut::getInstance();  }
-
-/***********************************************************************/
-
-int SparseMatrix::getNNodes(){
-       return numNodes; 
-}
-
-/***********************************************************************/
-
-float SparseMatrix::getSmallDist(){
-       return smallDist;
-}
-
-/***********************************************************************/
-
-MatData SparseMatrix::rmCell(MatData data){
-       try {
-               if(data->vectorMap != NULL ){
-                       *(data->vectorMap) = NULL;
-                       data->vectorMap = NULL;
-               }
-               data = matrix.erase(data);              
-               numNodes--;
-               return(data);
-       //  seems like i should be updating smallDist here, but the only time we remove cells is when
-       //  clustering and the clustering algorithm updates smallDist
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "rmCell");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void SparseMatrix::addCell(PCell value){
-       try {
-               matrix.push_back(value);
-               numNodes++;
-               if(value.dist < smallDist){
-                       smallDist = value.dist;
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "addCell");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void SparseMatrix::clear(){
-       try {
-               matrix.clear();
-               mins.clear();
-               numNodes = 0;
-               minsIndex = 0;
-               smallDist = 1e6;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "clear");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-MatData SparseMatrix::begin(){
-       return matrix.begin();  
-}
-
-/***********************************************************************/
-
-MatData SparseMatrix::end(){
-       return matrix.end();    
-}
-
-/***********************************************************************/
-
-void SparseMatrix::print(){
-       try {
-               int index = 0;
-       
-               cout << endl << "Index\tRow\tColumn\tDistance" << endl;
-       
-               for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-                       cout << index << '\t' << currentCell->row  << '\t' << currentCell->column << '\t' << currentCell->dist << endl;
-                       index++;
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "print");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void SparseMatrix::print(ListVector* list){
-       try {
-               int index = 0;
-       
-               m->mothurOutEndLine(); m->mothurOut("Index\tRow\tColumn\tDistance"); m->mothurOutEndLine();
-       
-               for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-                       m->mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); m->mothurOutEndLine();
-                       index++;
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "print");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-PCell* SparseMatrix::getSmallestCell(){
-       try {
-       //      this is where I check to see if the next small distance has the correct distance
-       //      if it doesn't then I remove the offending Cell -> should also be able to check for
-       //      invalid iterator / pointer -- right???
-       
-               while(!mins.empty() && mins.back() == NULL){
-                       mins.pop_back();                
-               }
-       
-       //      if the mins vector is empty go here...
-               if(mins.empty()){               
-                       mins.clear();
-       
-                       smallDist = begin()->dist;  //set the first candidate small distance
-               
-                       for(MatData currentCell=begin();currentCell!=end();currentCell++){
-                       
-                               float dist = currentCell->dist;
-                       
-                               if(dist < smallDist){  //found a new smallest distance
-                                       mins.clear();
-                                       smallDist = dist;
-                                       mins.push_back(&*currentCell);  //this is the address of the data in the list being pointed to by the MatData iterator
-                               }
-                               else if(dist == smallDist){  //if a subsequent distance is the same as mins distance add the new iterator to the mins vector
-                                       mins.push_back(&*currentCell); //this is the address of the data in the list being pointed to by the MatData iterator
-                               }
-
-                       }
-                       random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
-
-                       for(int i=0;i<mins.size();i++){
-                               mins[i]->vectorMap = &mins[i];  //assign vectorMap to the address for the container
-                       }
-                       
-               }
-       
-               smallCell = mins.back();        //make the smallestCell the last element of the vector
-
-               mins.pop_back();                        //remove the last element from the vector
-
-               return smallCell;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "getSmallestCell");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-