X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fileoutput.cpp;h=117f8ab1c3a9a93c5f80f38613c4aefa1c898e32;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=cd3a1c74084de46dd7f5c7805d3425f0d0dd3ecb;hpb=5b9b3e01150055e3b4bb1a911ea4c61d0b755e89;p=mothur.git

diff --git a/fileoutput.cpp b/fileoutput.cpp
index cd3a1c7..117f8ab 100644
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -40,7 +40,7 @@ void ThreeColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "ThreeColumnFile", "initFile");
+		m->errorOut(e, "ThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -60,7 +60,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ThreeColumnFile", "output");
+		m->errorOut(e, "ThreeColumnFile", "output");
 		exit(1);
 	}
 }
@@ -81,14 +81,16 @@ void ThreeColumnFile::resetFile(){
 		remove(inName.c_str());
 		renameOk = rename(outName.c_str(), inName.c_str());
 		
+		//renameFile(outName, inName);
+		
 		//checks to make sure user was able to rename and remove successfully
 		if ((renameOk != 0)) { 
-			mothurOut("Unable to rename " + outName); mothurOutEndLine();
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
 			perror(" : ");
 		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "ThreeColumnFile", "resetFile");
+		m->errorOut(e, "ThreeColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -132,7 +134,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "ColumnFile", "initFile");
+		m->errorOut(e, "ColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -162,7 +164,7 @@ void ColumnFile::output(vector<double> data){
 
 	}
 	catch(exception& e) {
-		errorOut(e, "ColumnFile", "output");
+		m->errorOut(e, "ColumnFile", "output");
 		exit(1);
 	}
 }
@@ -183,14 +185,16 @@ void ColumnFile::resetFile(){
 		remove(inName.c_str());
 		renameOk = rename(outName.c_str(), inName.c_str());
 		
+		//renameFile(outName, inName);
+		
 		//checks to make sure user was able to rename and remove successfully
 		if ((renameOk != 0)) { 
-			mothurOut("Unable to rename " + outName); mothurOutEndLine();
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
 			perror(" : ");
 		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "ColumnFile", "resetFile");
+		m->errorOut(e, "ColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -227,7 +231,7 @@ void SharedThreeColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedThreeColumnFile", "initFile");
+		m->errorOut(e, "SharedThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -248,7 +252,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedThreeColumnFile", "output");
+		m->errorOut(e, "SharedThreeColumnFile", "output");
 		exit(1);
 	}
 }
@@ -265,17 +269,20 @@ void SharedThreeColumnFile::resetFile(){
 			outFile.close();
 		}
 		counter = 1;
+		
 		remove(inName.c_str());
 		renameOk = rename(outName.c_str(), inName.c_str());
 		
+		//renameFile(outName, inName);
+		
 		//checks to make sure user was able to rename and remove successfully
 		if ((renameOk != 0)) { 
-			mothurOut("Unable to rename " + outName); mothurOutEndLine();
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
 			perror(" : ");
 		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedThreeColumnFile", "resetFile");
+		m->errorOut(e, "SharedThreeColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -313,7 +320,7 @@ void OneColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "OneColumnFile", "initFile");
+		m->errorOut(e, "OneColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -333,7 +340,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "OneColumnFile", "output");
+		m->errorOut(e, "OneColumnFile", "output");
 		exit(1);
 	}
 }
@@ -345,22 +352,25 @@ void OneColumnFile::resetFile(){
 		if(counter != 0){
 			outFile.close();
 			inFile.close();
-		}
-		else{
+		}else{
 			outFile.close();
 		}	
 		counter = 1;
+		
 		remove(inName.c_str());
 		renameOk = rename(outName.c_str(), inName.c_str());
 		
+		//renameFile(outName, inName);
+		
 		//checks to make sure user was able to rename and remove successfully
 		if ((renameOk != 0)) { 
-			mothurOut("Unable to rename " + outName); mothurOutEndLine();
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
 			perror(" : ");
 		}	
+
 	}
 	catch(exception& e) {
-		errorOut(e, "OneColumnFile", "resetFile");
+		m->errorOut(e, "OneColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -399,7 +409,7 @@ void SharedOneColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOneColumnFile", "initFile");
+		m->errorOut(e, "SharedOneColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -426,7 +436,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 			}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOneColumnFile", "output");
+		m->errorOut(e, "SharedOneColumnFile", "output");
 		exit(1);
 	}
 }
@@ -445,17 +455,18 @@ void SharedOneColumnFile::resetFile(){
 		counter = 1;
 
 		remove(inName.c_str());
-
 		renameOk = rename(outName.c_str(), inName.c_str());
 		
+		//renameFile(outName, inName);
+		
 		//checks to make sure user was able to rename and remove successfully
 		if ((renameOk != 0)) { 
-			mothurOut("Unable to rename " + outName); mothurOutEndLine();
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
 			perror(" : ");
 		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOneColumnFile", "resetFile");
+		m->errorOut(e, "SharedOneColumnFile", "resetFile");
 		exit(1);
 	}
 }