continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / needlemanoverlap.cpp

diff --git a/needlemanoverlap.cpp b/needlemanoverlap.cpp
index b14d8e3d10e42ee9c7a21f5595315b29ad172ff5..80ba4ca0aec06ea796a5a9bd7fbe7522f362157a 100644 (file)
--- a/needlemanoverlap.cpp
+++ b/needlemanoverlap.cpp
@@ -42,8 +42,6 @@ gap(gO), match(m), mismatch(mm), Alignment(r) {                                                       //      the gap openning penalt
                errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
                exit(1);
        }
-                                                                                                                               
-                                                                                                                                               
 }
 /**************************************************************************************************/
 
@@ -56,7 +54,7 @@ void NeedlemanOverlap::align(string A, string B){
                seqA = ' ' + A; lA = seqA.length();             //      algorithm requires a dummy space at the beginning of each string
                seqB = ' ' + B; lB = seqB.length();             //      algorithm requires a dummy space at the beginning of each string
 
-               if (lA > nRows) { mothurOut("Your one of your candidate sequences is longer than you longest template sequence."); mothurOutEndLine();  }
+               if (lA > nRows) { mothurOut("One of your candidate sequences is longer than you longest template sequence. Your longest template sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + "."); mothurOutEndLine();  }
                
                for(int i=1;i<lB;i++){                                  //      This code was largely translated from Perl code provided in Ex 3.1 
                        for(int j=1;j<lA;j++){                          //      of the O'Reilly BLAST book.  I found that the example output had a
@@ -90,10 +88,11 @@ void NeedlemanOverlap::align(string A, string B){
                                }
                        }
                }
+
                Overlap over;                                           
                over.setOverlap(alignment, lA, lB, 0);          //      Fix gaps at the beginning and end of the sequences
                traceBack();                                                            //      Traceback the alignment to populate seqAaln and seqBaln
-               
+       
        }
        catch(exception& e) {
                errorOut(e, "NeedlemanOverlap", "align");