fixed sub.sample so that it will eliminate samples with abundances that are less...

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 1efaf5b5e3526b8ec53ff3651f9de4b540720b7e..66f1db23d633eb83b3706bd15f6deb48e8c7cb5b 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -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;
                                
@@ -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;