X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.cpp;h=235216e8e59c82be596004559445c021312acb40;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=25b27604533cbefa4ba1748001a45622e9712547;hpb=3abb236c602eb168ee112f080b563ebe2c705029;p=mothur.git

diff --git a/alignment.cpp b/alignment.cpp
index 25b2760..235216e 100644
--- a/alignment.cpp
+++ b/alignment.cpp
@@ -21,17 +21,34 @@ 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);
 	}
 }
+/**************************************************************************************************/
+void Alignment::resize(int A) {
+	try {
+		nCols = A;
+		nRows = A;
 
+		alignment.resize(nRows);			
+		for(int i=0;i<nRows;i++){			
+			alignment[i].resize(nCols);		
+		}	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Alignment", "resize");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 void Alignment::traceBack(){			//	This traceback routine is used by the dynamic programming algorithms
@@ -92,7 +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);
 	}
 }
@@ -105,7 +122,7 @@ Alignment::~Alignment(){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Alignment", "~Alignment");
+		m->errorOut(e, "Alignment", "~Alignment");
 		exit(1);
 	}
 }