X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readblast.cpp;h=5f2441515378031891c78d2fbb809c816e885cec;hb=b866e1519a60681527244036428104ad1cb90c93;hp=1efaf5b5e3526b8ec53ff3651f9de4b540720b7e;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/readblast.cpp b/readblast.cpp
index 1efaf5b..5f24415 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;
 		}
 		
@@ -90,8 +91,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
 				//convert name to number
 				map<string,int>::iterator itA = nameMap->find(firstName);
 				map<string,int>::iterator itB = nameMap->find(secondName);
-				if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
-				if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+				if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+				if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 				
 				thisRowsBlastScores[itB->second] = score;
 				
@@ -117,7 +118,7 @@ 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;
 			}
@@ -143,8 +144,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
 						//convert name to number
 						map<string,int>::iterator itA = nameMap->find(firstName);
 						map<string,int>::iterator itB = nameMap->find(secondName);
-						if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
-						if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+						if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+						if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 						
 						//save score
 						thisRowsBlastScores[itB->second] = score;
@@ -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;
 								}
@@ -210,8 +216,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
 						//convert name to number
 						map<string,int>::iterator itA = nameMap->find(firstName);
 						map<string,int>::iterator itB = nameMap->find(secondName);
-						if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
-						if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+						if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+						if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 						
 						thisRowsBlastScores[itB->second] = score;
 						
@@ -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;
 		}