created mothurOut class to handle logfiles

[mothur.git] / alignment.cpp

diff --git a/alignment.cpp b/alignment.cpp
index 2734c389cd0122add50ee1b3cc23cd879788ca0b..d543dbd38c2ef048aa1d536049e91d046a347685 100644 (file)
--- a/alignment.cpp
+++ b/alignment.cpp
@@ -21,13 +21,14 @@ Alignment::Alignment() {    /*      do nothing      */      }
 
 Alignment::Alignment(int A) : nCols(A), nRows(A) {
        try {
+               m = MothurOut::getInstance();
                alignment.resize(nRows);                        //      For the Gotoh and Needleman-Wunsch we initialize the dynamic programming
                for(int i=0;i<nRows;i++){                       //      matrix by initializing a matrix that is A x A.  By default we will set A
                        alignment[i].resize(nCols);             //      at 2000 for 16S rRNA gene sequences
                }       
        }
        catch(exception& e) {
-               errorOut(e, "Alignment", "Alignment");
+               m->errorOut(e, "Alignment", "Alignment");
                exit(1);
        }
 }
@@ -43,7 +44,7 @@ void Alignment::resize(int A) {
                }       
        }
        catch(exception& e) {
-               errorOut(e, "Alignment", "resize");
+               m->errorOut(e, "Alignment", "resize");
                exit(1);
        }
 }
@@ -107,7 +108,7 @@ void Alignment::traceBack(){                        //      This traceback routine is used by the dynamic
                seqBend = seqB.length() - seqBend - 1;
        }
        catch(exception& e) {
-               errorOut(e, "Alignment", "traceBack");
+               m->errorOut(e, "Alignment", "traceBack");
                exit(1);
        }
 }
@@ -120,7 +121,7 @@ Alignment::~Alignment(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "Alignment", "~Alignment");
+               m->errorOut(e, "Alignment", "~Alignment");
                exit(1);
        }
 }