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

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index 88cba6ecce59b98c874a119c84c494aa1e152156..8a596f3163c06dd55129cdc8de0f5779a5d6cb4d 100644 (file)
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -396,8 +396,8 @@ vector<seqDist> HCluster::getSeqsFNNN(){
                        
                        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);  }
                
                        //using cutoff
                        if (distance > cutoff) { break; }
@@ -760,8 +760,8 @@ int HCluster::processFile() {
                        
                        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);  }
                
                        //using cutoff
                        if (distance > cutoff) { break; }