X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=singlelinkage.cpp;h=3af1ea0c346030eb6f8eda3527ffc7a882c1b950;hp=9f015db7359879be53da5e6001889117c7e5f7c6;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3

diff --git a/singlelinkage.cpp b/singlelinkage.cpp
index 9f015db..3af1ea0 100644
--- a/singlelinkage.cpp
+++ b/singlelinkage.cpp
@@ -5,8 +5,8 @@
 
 /***********************************************************************/
 
-SingleLinkage::SingleLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c) :
-Cluster(rav, lv, dm, c)
+SingleLinkage::SingleLinkage(RAbundVector* rav, ListVector* lv, SparseDistanceMatrix* dm, float c, string s) :
+Cluster(rav, lv, dm, c, s)
 {}
 
 
@@ -18,9 +18,11 @@ string SingleLinkage::getTag() {
 
 /***********************************************************************/
 //This function clusters based on the single linkage method.
-void  SingleLinkage::update(){
+void SingleLinkage::update(double& cutOFF){
 	try {
-		getRowColCells();	
+		smallCol = dMatrix->getSmallestCell(smallRow);
+        nColCells = dMatrix->seqVec[smallCol].size();
+        nRowCells = dMatrix->seqVec[smallRow].size();	
 	
 		vector<bool> deleted(nRowCells, false);
 		int rowInd;
@@ -30,57 +32,48 @@ void  SingleLinkage::update(){
 		// The vector has to be traversed in reverse order to preserve the index
 		// for faster removal in removeCell()
 		for (int i=nRowCells-1;i>=0;i--) {
-			if ((rowCells[i]->row == smallRow) && (rowCells[i]->column == smallCol)) {
-				rowInd = i;   // The index of the smallest distance cell in rowCells
-			} else {
-				if (rowCells[i]->row == smallRow) {
-					search = rowCells[i]->column;
-				} else {
-					search = rowCells[i]->row;
-				}
-		
-				for (int j=0;j<nColCells;j++) {
-					if (!((colCells[j]->row == smallRow) && (colCells[j]->column == smallCol))) {
-						if (colCells[j]->row == search || colCells[j]->column == search) {
-							changed = updateDistance(colCells[j], rowCells[i]);
-							// If the cell's distance changed and it had the same distance as 
-							// the smallest distance, invalidate the mins vector in SparseMatrix
-							if (changed) {
-								if (colCells[j]->vectorMap != NULL) {
-									*(colCells[j]->vectorMap) = NULL;
-									colCells[j]->vectorMap = NULL;
-								}
-							}
-							removeCell(rowCells[i], i , -1);
-							deleted[i] = true;
-							break;
-						}
-					}
-				}
-				if (!deleted[i]) {
-					// Assign the cell to the new cluster 
-					// remove the old cell from seqVec and add the cell
-					// with the new row and column assignment again
-					removeCell(rowCells[i], i , -1, false);
-					if (search < smallCol){
-						rowCells[i]->row = smallCol;
-						rowCells[i]->column = search;
-					} else {
-						rowCells[i]->row = search;
-						rowCells[i]->column = smallCol;
-					}
-					seqVec[rowCells[i]->row].push_back(rowCells[i]);
-					seqVec[rowCells[i]->column].push_back(rowCells[i]);
-				}
-			}	
+                if (dMatrix->seqVec[smallRow][i].index == smallCol) {
+                    rowInd = i;   // The index of the smallest distance cell in rowCells
+                } else {
+                    search = dMatrix->seqVec[smallRow][i].index;
+                    
+                    for (int j=0;j<nColCells;j++) {
+                        if (dMatrix->seqVec[smallCol][j].index != smallRow) { //if you are not the small cell
+                            if (dMatrix->seqVec[smallCol][j].index == search) {
+                                changed = updateDistance(dMatrix->seqVec[smallCol][j], dMatrix->seqVec[smallRow][i]);
+                                dMatrix->updateCellCompliment(smallCol, j);
+                                dMatrix->rmCell(smallRow, i);
+                                deleted[i] = true;
+                                break;
+                            }
+                        }
+                    }
+                    if (!deleted[i]) {
+                        // Assign the cell to the new cluster 
+                        // remove the old cell from seqVec and add the cell
+                        // with the new row and column assignment again
+                        float distance =  dMatrix->seqVec[smallRow][i].dist;
+                        dMatrix->rmCell(smallRow, i);
+                        if (search < smallCol){
+                            PDistCell value(smallCol, distance);
+                            dMatrix->addCell(search, value);
+                        } else {
+                            PDistCell value(search, distance);
+                            dMatrix->addCell(smallCol, value);
+                        }
+                        sort(dMatrix->seqVec[smallCol].begin(), dMatrix->seqVec[smallCol].end(), compareIndexes);
+                        sort(dMatrix->seqVec[search].begin(), dMatrix->seqVec[search].end(), compareIndexes); 
+                    }
+                }
 		}
 		clusterBins();
 		clusterNames();
 		// remove also the cell with the smallest distance
-		removeCell(rowCells[rowInd], -1 , -1);
+
+		dMatrix->rmCell(smallRow, rowInd);
 	}
 	catch(exception& e) {
-		errorOut(e, "SingleLinkage", "update");
+		m->errorOut(e, "SingleLinkage", "update");
 		exit(1);
 	}
 }
@@ -88,16 +81,16 @@ void  SingleLinkage::update(){
 
 /***********************************************************************/
 //This function updates the distance based on the nearest neighbor method.
-bool SingleLinkage::updateDistance(MatData& colCell, MatData& rowCell) {
+bool SingleLinkage::updateDistance(PDistCell& colCell, PDistCell& rowCell) {
 	try {
 		bool changed = false;
-		if (colCell->dist > rowCell->dist) {
-			colCell->dist = rowCell->dist;
+		if (colCell.dist > rowCell.dist) {
+			colCell.dist = rowCell.dist;
 		}
 		return(changed);
 	}
 	catch(exception& e) {
-		errorOut(e, "SingleLinkage", "updateDistance");
+		m->errorOut(e, "SingleLinkage", "updateDistance");
 		exit(1);
 	}
 }