chimeracode

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 294940cd6aabd49f67aca028311d21529f0912ee..c91c9fab537172b3e02808b700af881affffc368 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -26,13 +26,11 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
                maxInsertLength = 0;
                pairwiseAlignSeqs();    //      This is part A in Fig. 2 of DeSantis et al.
                regapSequences();               //      This is parts B-F in Fig. 2 of DeSantis et al.
-
        }
        catch(exception& e) {
                errorOut(e, "Nast", "Nast");
                exit(1);
        }
-
 }
 
 /**************************************************************************************************/
@@ -40,12 +38,12 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
 void Nast::pairwiseAlignSeqs(){        //      Here we call one of the pairwise alignment methods to align our unaligned candidate
                                                                //      and template sequences
        try {
-               
+
                alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
-       
+
                string candAln = alignment->getSeqAAln();
                string tempAln = alignment->getSeqBAln();
-
+       
                if(candAln == ""){
 
                        candidateSeq->setPairwise("");
@@ -78,7 +76,6 @@ void Nast::pairwiseAlignSeqs(){       //      Here we call one of the pairwise alignment me
 
                candidateSeq->setPairwise(candAln);                                     //      set the pairwise sequences in the Sequence objects for
                templateSeq->setPairwise(tempAln);                                      //      the candidate and template sequences
-
        }
        catch(exception& e) {
                errorOut(e, "Nast", "pairwiseAlignSeqs");
@@ -226,7 +223,7 @@ void Nast::regapSequences(){        //This is essentially part B in Fig 2. of DeSantis
                        candidateSeq->setAligned(candAln);
                        return;
                }
-               
+       
                int fullAlignIndex = 0;
                int pairwiseAlignIndex = 0;
                string newTemplateAlign = "";                                   //      this is going to be messy so we want a temporary template
@@ -323,7 +320,9 @@ void Nast::regapSequences(){        //This is essentially part B in Fig 2. of DeSantis
                        newTemplateAlign += tempAln[i];//
                }
                
-               int start, end;
+               int start = 0;
+               int end = candAln.length()-1;
+
                for(int i=0;i<candAln.length();i++){
                        if(candAln[i] == 'Z' || !isalnum(candAln[i]))   {       candAln[i] = '.';       }       //      if we padded the alignemnt from
                        else{                   start = i;                      break;          }                                                       //      blast with Z's, change them to
@@ -338,11 +337,11 @@ void Nast::regapSequences(){      //This is essentially part B in Fig 2. of DeSantis
                        candAln[i] = toupper(candAln[i]);                       //      everything is upper case
                }
                
-       
+
                if(candAln.length() != tempAln.length()){               //      if the regapped candidate sequence is longer than the official
                        removeExtraGaps(candAln, tempAln, newTemplateAlign);//  template alignment then we need to do steps C-F in Fig.
                }                                                                                               //      2 of Desantis et al.
-                       
+
                candidateSeq->setAligned(candAln);
        }
        catch(exception& e) {