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

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 2d4947745be0a52fafba4c33f38fb6504ede2288..5f2441515378031891c78d2fbb809c816e885cec 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -54,7 +54,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
                
                //create objects needed for read
                if (!hclusterWanted) {
-                       matrix = new SparseMatrix();
+                       matrix = new SparseDistanceMatrix();
+            matrix->resize(nseqs);
                }else{
                        overlapFile = m->getRootName(blastfile) + "overlap.dist";
                        distFile = m->getRootName(blastfile) + "hclusterDists.dist";
@@ -185,8 +186,13 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                                        //is this distance below cutoff
                                                        if (distance < cutoff) {
                                                                if (!hclusterWanted) {
-                                                                       PCell value(itA->second, it->first, distance);
-                                                                       matrix->addCell(value);
+                                    if (itA->second < it->first) {
+                                        PDistCell value(it->first, distance);
+                                        matrix->addCell(itA->second, value);
+                                    }else {
+                                        PDistCell value(itA->second, distance);
+                                        matrix->addCell(it->first, value);
+                                    }
                                                                }else{
                                                                        outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                                                }
@@ -252,8 +258,13 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                //is this distance below cutoff
                                if (distance < cutoff) {
                                        if (!hclusterWanted) {
-                                               PCell value(itA->second, it->first, distance);
-                                               matrix->addCell(value);
+                                               if (itA->second < it->first) {
+                            PDistCell value(it->first, distance);
+                            matrix->addCell(itA->second, value);
+                        }else {
+                            PDistCell value(itA->second, distance);
+                            matrix->addCell(it->first, value);
+                        }
                                        }else{
                                                outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                        }