X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sparsematrix.cpp;fp=sparsematrix.cpp;h=6eaf3ec7d384786fb38ec98669c9db4612593000;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
new file mode 100644
index 0000000..6eaf3ec
--- /dev/null
+++ b/sparsematrix.cpp
@@ -0,0 +1,208 @@
+#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);
+	}	
+}
+
+/***********************************************************************/
+