added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 4ebde29f912f6e9a02d88dbee301488b52d4a082..4967f245fb11c2ff37195a83baf39d29667fc582 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -359,16 +359,19 @@ int GetOTURepCommand::execute(){
 
                        list = readMatrix->getListVector();
 
-                       SparseMatrix* matrix = readMatrix->getMatrix();
+                       SparseDistanceMatrix* matrix = readMatrix->getDMatrix();
                        
                        // Create a data structure to quickly access the distance information.
                        // It consists of a vector of distance maps, where each map contains
                        // all distances of a certain sequence. Vector and maps are accessed
                        // via the index of a sequence in the distance matrix
                        seqVec = vector<SeqMap>(list->size()); 
-                       for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
-                               if (m->control_pressed) { delete readMatrix; return 0; }
-                               seqVec[currentCell->row][currentCell->column] = currentCell->dist;
+            for (int i = 0; i < matrix->seqVec.size(); i++) {
+                for (int j = 0; j < matrix->seqVec[i].size(); j++) {
+                    if (m->control_pressed) { delete readMatrix; return 0; }
+                    //already added everyone else in row
+                    if (i < matrix->seqVec[i][j].index) {  seqVec[i][matrix->seqVec[i][j].index] = matrix->seqVec[i][j].dist;  }
+                }
                        }
                        //add dummy map for unweighted calc
                        SeqMap dummy;