X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readblast.cpp;h=e98b69c68bfdb8f90fa841429cf4d607ba6fe1c3;hb=38029939675c5bf5e449eac90f801b35064b3a36;hp=2d4947745be0a52fafba4c33f38fb6504ede2288;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/readblast.cpp b/readblast.cpp
index 2d49477..e98b69c 100644
--- 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";
@@ -109,8 +110,9 @@ int ReadBlast::read(NameAssignment* nameMap) {
 				}
 			}
 		}else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
-
-				
+string outDistFilem = "../kathryn/blastDist.dist";
+        ofstream outMDist;
+        m->openOutputFile(outDistFilem, outMDist);
 		//read file
 		while(!fileHandle.eof()){  
 		
@@ -185,8 +187,14 @@ 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);
+                                    }
+                                    outMDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 								}else{
 									outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 								}
@@ -252,8 +260,13 @@ 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;
 					}
@@ -313,8 +326,8 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
 		ifstream in;
 		m->openInputFile(blastfile, in);
 		
-		//ofstream outName;
-		//m->openOutputFile((blastfile + ".tempOutNames"), outName);
+		ofstream outName;
+		m->openOutputFile((blastfile + ".tempOutNames"), outName);
 		
 		//read first line
 		in >> prevName;
@@ -338,6 +351,7 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
 			if (name != prevName) {
 				prevName = name;
 				nameMap->push_back(name);
+                outName << name << '\t' << name << endl;
 				num++;
 			}
 		}