fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / needlemanoverlap.cpp

diff --git a/needlemanoverlap.cpp b/needlemanoverlap.cpp
index d13925e3cff9f54c61df9435b7f9cb36f9468e34..1239beb1a2a9f61d3f8c2cec178161fb36a7b865 100644 (file)
--- a/needlemanoverlap.cpp
+++ b/needlemanoverlap.cpp
@@ -51,18 +51,21 @@ NeedlemanOverlap::~NeedlemanOverlap(){      /*      do nothing      */      }
 
 void NeedlemanOverlap::align(string A, string B){
        try {
+       
                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) { m->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) + "."); m->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
+       
                                //      number of errors
                                float diagonal;
                                if(seqB[i] == seqA[j])  {       diagonal = alignment[i-1][j-1].cValue + match;          }
                                else                                    {       diagonal = alignment[i-1][j-1].cValue + mismatch;       }
-                               
+                       
                                float up        = alignment[i-1][j].cValue + gap;
                                float left      = alignment[i][j-1].cValue + gap;