1.12.0

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index b92927b1d3d51c0505fbcadd14231eade34b78e5..9a1ac215388e09e6477fffa034e0542c38c208b1 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -500,13 +500,16 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
                                        float overlapDistance;
                                        inOverlap >> firstName >> secondName >> overlapDistance; gobble(inOverlap);
                                        
-                                       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);  }
+                                       //commented out because we check this in readblast already
+                                       //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);  }
                                        
-                                       overlapNode.seq1 = itA->second;
-                                       overlapNode.seq2 = itB->second;
+                                       //overlapNode.seq1 = itA->second;
+                                       //overlapNode.seq2 = itB->second;
+                                       overlapNode.seq1 = nameMap->get(firstName);
+                                       overlapNode.seq2 = nameMap->get(secondName);
                                        overlapNode.dist = overlapDistance;
                                }else { inOverlap.close(); break; }
                        } 
@@ -517,14 +520,17 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
                                string name2 = nameMap->get(overlapNode.seq2);
                        
                                //use binInfo to find out if they are already in the same bin
-                               map<string, int>::iterator itBin1 = binInfo.find(name1);
-                               map<string, int>::iterator itBin2 = binInfo.find(name2);
+                               //map<string, int>::iterator itBin1 = binInfo.find(name1);
+                               //map<string, int>::iterator itBin2 = binInfo.find(name2);
                                
-                               if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
-                               if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
+                               //if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
+                               //if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
 
-                               int binKeep = itBin1->second;
-                               int binRemove = itBin2->second;
+                               //int binKeep = itBin1->second;
+                               //int binRemove = itBin2->second;
+                               
+                               int binKeep = binInfo[name1];
+                               int binRemove = binInfo[name2];
                        
                                //if not merge bins and update binInfo
                                if(binKeep != binRemove) {