bug fixes

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 04f97a8c2e22e0ccef1f8322ec23be45615b6380..78fa266105c6be21ce5442250ef8c00f389ab078 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -74,14 +74,14 @@ Sequence::Sequence(istringstream& fastaString){
                                }
                        }
                        
-                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaString);              
                        setAligned(sequence);   
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence);         
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -116,13 +116,14 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
                                }
                        }
                        
-                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaString);              
                        
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence);         
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -160,15 +161,15 @@ Sequence::Sequence(ifstream& fastaFile){
                        }
                        
                        //read real sequence
-                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
+                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){  break;      }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaFile);                
-               
+       
                        setAligned(sequence);   
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence); 
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-               
+
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -202,14 +203,14 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
                        }
                        
                        //read real sequence
-                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
+                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){       break; }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaFile);                
                        
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence); 
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");