added logfile feature

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 2d3db22b08c66de9798128292dfe7be149bdc50f..0741ccd7ad444a250fa1dec5b23790771142a99c 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -82,7 +82,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                //      Part C of Fig. 2 from DeSantis et al.
                if((isalpha(newTemplateAlign[i]) != isalpha(tempAln[i]))){      //if there is a discrepancy between the regapped
                        
-//                     cout << i << '\t';cout.flush();
+
                        
                        //      Part D of Fig. 2 from DeSantis et al.           //      template sequence and the official template sequence
                        for(leftIndex=i-1;leftIndex>=0;leftIndex--){    //      then we've got problems...
@@ -92,7 +92,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                        break;
                                }
                        }
-//                     cout << leftIndex << '\t' << leftRoom << endl;
+
                        
                        for(rightIndex=i+1;rightIndex<longAlignmentLength;rightIndex++){
                                if(!isalpha(candAln[rightIndex])){
@@ -173,7 +173,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                        i -= insertLength;
                } 
        }
-//     cout << candAln << endl << tempAln << endl << newTemplateAlign << endl;
+
 }
 
 /**************************************************************************************************/
@@ -273,14 +273,14 @@ void Nast::regapSequences(){      //This is essentially part B in Fig 2. of DeSantis
                        //      would skip the gaps and not progress through full alignment sequence
                        //      not tested yet
                        
-                       cout << "We're into D" << ' ' << fullAlignIndex << ' ' << pairwiseAlignIndex <<  endl;
+                       mothurOut("We're into D " + toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); mothurOutEndLine();
                        pairwiseAlignIndex++;
                }
                else{
                        //      everything has a gap - not possible
                        //      not tested yet
                        
-                       cout << "We're into F" << ' ' << fullAlignIndex << ' ' << pairwiseAlignIndex <<  endl;
+                       mothurOut("We're into F " +  toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); mothurOutEndLine();
                        pairwiseAlignIndex++;
                        fullAlignIndex++;                       
                }               
@@ -306,17 +306,11 @@ void Nast::regapSequences(){      //This is essentially part B in Fig 2. of DeSantis
                candAln[i] = toupper(candAln[i]);                       //      everything is upper case
        }
 
-//     cout << candAln << endl;
-//     cout << tempAln << endl;
-//     cout << newTemplateAlign << endl;
 
        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.
        
-//     cout << candAln << endl;
-//     cout << tempAln << endl;
-//     cout << newTemplateAlign << endl;
 
        candidateSeq->setAligned(candAln);
 }