X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequencedb.cpp;h=585b3b3d8347272cb7b47afc9a923fb0af28eaa9;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=b3da429fc57c9da7081640876ee9fbedda808e25;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/sequencedb.cpp b/sequencedb.cpp
index b3da429..585b3b3 100644
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -15,7 +15,7 @@
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB() {}
+SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  }
 /***********************************************************************/
 //the clear function free's the memory
 SequenceDB::~SequenceDB() { clear(); }
@@ -39,14 +39,14 @@ SequenceDB::SequenceDB(ifstream& filehandle) {
 			if (newSequence.getName() != "") {   data.push_back(newSequence);  }
 			
 			//takes care of white space
-			gobble(filehandle);
+			m->gobble(filehandle);
 		}
 
 		filehandle.close();
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "SequenceDB");
+		m->errorOut(e, "SequenceDB", "SequenceDB");
 		exit(1);
 	}
 }
@@ -67,7 +67,7 @@ string SequenceDB::readName(ifstream& in) {
 		return name;
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "readName");
+		m->errorOut(e, "SequenceDB", "readName");
 		exit(1);
 	}
 }
@@ -96,7 +96,7 @@ string SequenceDB::readSequence(ifstream& in) {
 		return sequence;
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "readSequence");
+		m->errorOut(e, "SequenceDB", "readSequence");
 		exit(1);
 	}
 }
@@ -114,7 +114,7 @@ void SequenceDB::set(int index, string newUnaligned) {
 		data[index] = Sequence(data[index].getName(), newUnaligned);
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "set");
+		m->errorOut(e, "SequenceDB", "set");
 		exit(1);
 	}
 }
@@ -126,7 +126,7 @@ void SequenceDB::set(int index, Sequence newSeq) {
 		data[index] = newSeq;
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "set");
+		m->errorOut(e, "SequenceDB", "set");
 		exit(1);
 	}
 }
@@ -144,7 +144,7 @@ void SequenceDB::resize(int newSize) {
 		data.resize(newSize);
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "resize");
+		m->errorOut(e, "SequenceDB", "resize");
 		exit(1);
 	}
 }
@@ -156,7 +156,7 @@ void SequenceDB::clear() {
 		data.clear();
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "clear");
+		m->errorOut(e, "SequenceDB", "clear");
 		exit(1);
 	}
 }
@@ -176,7 +176,7 @@ void SequenceDB::print(ostream& out) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "print");
+		m->errorOut(e, "SequenceDB", "print");
 		exit(1);
 	}
 }
@@ -188,7 +188,7 @@ void SequenceDB::push_back(Sequence newSequence) {
 		data.push_back(newSequence);
 	}
 	catch(exception& e) {
-		errorOut(e, "SequenceDB", "push_back");
+		m->errorOut(e, "SequenceDB", "push_back");
 		exit(1);
 	}
 }