X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readblast.cpp;h=84fddcf263cfdeb572f72ff3bd658325f31271e0;hp=66f1db23d633eb83b3706bd15f6deb48e8c7cb5b;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=5cc45e630ccee2c3503e1bfe7e9b3524898cef8a

diff --git a/readblast.cpp b/readblast.cpp
index 66f1db2..84fddcf 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";
@@ -66,7 +67,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
 		if (m->control_pressed) { 
 			fileHandle.close();
 			if (!hclusterWanted) {  delete matrix; }
-			else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
+			else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
 			return 0;
 		}
 		
@@ -110,14 +111,14 @@ int ReadBlast::read(NameAssignment* nameMap) {
 			}
 		}else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 
-				
+       
 		//read file
 		while(!fileHandle.eof()){  
 		
 			if (m->control_pressed) { 
 				fileHandle.close();
 				if (!hclusterWanted) {  delete matrix; }
-				else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
+				else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
 				delete reading;
 				return 0;
 			}
@@ -185,9 +186,14 @@ 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);
-								}else{
+                                    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;
 					}
@@ -271,7 +282,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
 		if (m->control_pressed) { 
 				fileHandle.close();
 				if (!hclusterWanted) {  delete matrix; }
-				else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
+				else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
 				delete reading;
 				return 0;
 		}
@@ -286,7 +297,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
 		if (m->control_pressed) { 
 				fileHandle.close();
 				if (!hclusterWanted) {  delete matrix; }
-				else {  remove(overlapFile.c_str());  remove(distFile.c_str());  }
+				else {  m->mothurRemove(overlapFile);  m->mothurRemove(distFile);  }
 				delete reading;
 				return 0;
 		}
@@ -337,7 +348,12 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
 			//is this a new name?
 			if (name != prevName) {
 				prevName = name;
-				nameMap->push_back(name);
+                
+                if (nameMap->get(name) != -1) { m->mothurOut("[ERROR]: trying to exact names from blast file, and I found dups.  Are you sequence names unique? quitting.\n"); m->control_pressed = true; }
+                else {
+                    nameMap->push_back(name);
+                }
+                //outName << name << '\t' << name << endl;
 				num++;
 			}
 		}