X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.cpp;h=03bf9bab62d34b657f1b4cb0dc076171e6d8d9d6;hb=8d809b3a13ee742f78613af4b8535ad8efae90a8;hp=2734c389cd0122add50ee1b3cc23cd879788ca0b;hpb=1244c4907c07baea86b0f0676d098a29d2e95a39;p=mothur.git

diff --git a/alignment.cpp b/alignment.cpp
index 2734c38..03bf9ba 100644
--- a/alignment.cpp
+++ b/alignment.cpp
@@ -15,19 +15,21 @@
 
 /**************************************************************************************************/
 
-Alignment::Alignment() {	/*	do nothing	*/	}
+Alignment::Alignment() {	m = MothurOut::getInstance(); /*	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 +45,7 @@ void Alignment::resize(int A) {
 		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "Alignment", "resize");
+		m->errorOut(e, "Alignment", "resize");
 		exit(1);
 	}
 }
@@ -107,7 +109,7 @@ 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 +122,7 @@ Alignment::~Alignment(){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Alignment", "~Alignment");
+		m->errorOut(e, "Alignment", "~Alignment");
 		exit(1);
 	}
 }