finished chimeraslayer method and added get.listcount command

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 294940cd6aabd49f67aca028311d21529f0912ee..f247037cc915fd1d54d9d1e050abde8f73711fba 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -226,7 +226,7 @@ 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 +323,9 @@ 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 +340,11 @@ 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) {