X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sparsematrix.cpp;fp=sparsematrix.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=3a0ec6521720c1f89eb7c54ce47f60a2f81d364a;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
deleted file mode 100644
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);
-	}
-}
-
-/***********************************************************************/
-