X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readblast.cpp;h=2d4947745be0a52fafba4c33f38fb6504ede2288;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=1efaf5b5e3526b8ec53ff3651f9de4b540720b7e;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/readblast.cpp b/readblast.cpp
index 1efaf5b..2d49477 100644
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -66,7 +66,7 @@ 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 +90,8 @@ 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 +117,7 @@ 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 +143,8 @@ 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;
@@ -210,8 +210,8 @@ 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;
 						
@@ -271,7 +271,7 @@ 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 +286,7 @@ 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;
 		}