created mothurOut class to handle logfiles

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index c91c9fab537172b3e02808b700af881affffc368..4a0b74aa412873b6bf98ee1b9e30e28a9cc8c21f 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -23,12 +23,13 @@
 
 Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method), candidateSeq(cand), templateSeq(temp) {
        try {
+               m = MothurOut::getInstance();
                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");
+               m->errorOut(e, "Nast", "Nast");
                exit(1);
        }
 }
@@ -78,7 +79,7 @@ void Nast::pairwiseAlignSeqs(){       //      Here we call one of the pairwise alignment me
                templateSeq->setPairwise(tempAln);                                      //      the candidate and template sequences
        }
        catch(exception& e) {
-               errorOut(e, "Nast", "pairwiseAlignSeqs");
+               m->errorOut(e, "Nast", "pairwiseAlignSeqs");
                exit(1);
        }       
 }
@@ -199,7 +200,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                }
        }
        catch(exception& e) {
-               errorOut(e, "Nast", "removeExtraGaps");
+               m->errorOut(e, "Nast", "removeExtraGaps");
                exit(1);
        }       
 }
@@ -302,14 +303,14 @@ 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
                                
-                               mothurOut("We're into D " + toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); mothurOutEndLine();
+                               m->mothurOut("We're into D " + toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); m->mothurOutEndLine();
                                pairwiseAlignIndex++;
                        }
                        else{
                                //      everything has a gap - not possible
                                //      not tested yet
                                
-                               mothurOut("We're into F " +  toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); mothurOutEndLine();
+                               m->mothurOut("We're into F " +  toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); m->mothurOutEndLine();
                                pairwiseAlignIndex++;
                                fullAlignIndex++;                       
                        }               
@@ -345,7 +346,7 @@ void Nast::regapSequences(){        //This is essentially part B in Fig 2. of DeSantis
                candidateSeq->setAligned(candAln);
        }
        catch(exception& e) {
-               errorOut(e, "Nast", "regapSequences");
+               m->errorOut(e, "Nast", "regapSequences");
                exit(1);
        }       
 }
@@ -380,7 +381,7 @@ float Nast::getSimilarityScore(){
                
        }
        catch(exception& e) {
-               errorOut(e, "Nast", "getSimilarityScore");
+               m->errorOut(e, "Nast", "getSimilarityScore");
                exit(1);
        }       
 }