--- /dev/null
+#include <vector>
+#include <iostream>
+#include <list>
+#include "utilities.hpp"
+#include "sparsematrix.hpp"
+#include "listvector.hpp"
+#include <exception>
+
+using namespace std;
+
+typedef list<PCell>::iterator MatData;
+
+/***********************************************************************/
+
+SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){};
+
+/***********************************************************************/
+
+int SparseMatrix::getNNodes(){
+ return numNodes;
+}
+
+/***********************************************************************/
+
+float SparseMatrix::getSmallDist(){
+ return smallDist;
+}
+
+/***********************************************************************/
+
+void SparseMatrix::rmCell(MatData data){
+ try {
+ if(data->vectorMap != NULL ){
+ *(data->vectorMap) = NULL;
+ data->vectorMap = NULL;
+ }
+ matrix.erase(data);
+ numNodes--;
+
+ // 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function rmCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SparseMatrix class function rmCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SparseMatrix::addCell(PCell value){
+ try {
+ matrix.push_back(value);
+ numNodes++;
+ if(value.dist < smallDist){
+ smallDist = value.dist;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function addCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SparseMatrix class function addCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SparseMatrix::clear(){
+ try {
+ matrix.clear();
+ mins.clear();
+ numNodes = 0;
+ minsIndex = 0;
+ smallDist = 1e6;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SparseMatrix class function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SparseMatrix class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SparseMatrix::print(ListVector* list){
+ try {
+ int index = 0;
+
+ cout << endl << "Index\tRow\tColumn\tDistance" << endl;
+
+ for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
+ cout << index << '\t' << list->get(currentCell->row) << '\t' << list->get(currentCell->column) << '\t' << currentCell->dist << endl;
+ index++;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SparseMatrix class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function getSmallestCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SparseMatrix class function getSmallestCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
projects / mothur.git / blobdiff