X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=238ffa5ff227eb85bae8dff594a7d1f97d357280;hb=4dbf93479b205ec5d72663e5b01611000266bc13;hp=5a2c0022bf68ef4756d71ad6278b171bbce0f602;hpb=f89b6501b7d80e705b6c50ff2c8bdd8bb5d2edf7;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 5a2c002..238ffa5 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-SetDirectoryCommand::SetDirectoryCommand(string option){
+SetDirectoryCommand::SetDirectoryCommand(string option)  {
 	try {
 		abort = false;
 		
@@ -39,12 +39,12 @@ SetDirectoryCommand::SetDirectoryCommand(string option){
 			if (input == "not found") {  input = "";  }
 				
 			if ((input == "") && (output == "")) {	
-				mothurOut("You must provide either an input or output for the set.outdir command."); mothurOutEndLine(); abort = true;
+				m->mothurOut("You must provide either an input or output for the set.outdir command."); m->mothurOutEndLine(); abort = true;
 			}
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
+		m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
 		exit(1);
 	}
 }
@@ -52,17 +52,17 @@ SetDirectoryCommand::SetDirectoryCommand(string option){
 
 void SetDirectoryCommand::help(){
 	try {
-		mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
-		mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
-		mothurOut("The set.dir command parameter is output and is required.\n");
-		mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
-		mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
-		mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
-		mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
-		mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
+		m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
+		m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
+		m->mothurOut("The set.dir command parameter is output and is required.\n");
+		m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
+		m->mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
+		m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
+		m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
 	}
 	catch(exception& e) {
-		errorOut(e, "SetDirectoryCommand", "help");
+		m->errorOut(e, "SetDirectoryCommand", "help");
 		exit(1);
 	}
 }
@@ -79,7 +79,6 @@ int SetDirectoryCommand::execute(){
 		
 		commandFactory = CommandFactory::getInstance();
 		
-		
 		//redirect output
 		if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 		else {
@@ -97,11 +96,11 @@ int SetDirectoryCommand::execute(){
 			ofstream out;
 			out.open(outTemp.c_str(), ios::trunc);
 			if(!out) {
-				mothurOut(output + " directory does not exist or is not writable."); mothurOutEndLine(); 
+				m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
 				out.close();
 				remove(outTemp.c_str());
-				mothurOut("Changing output directory to " + output); mothurOutEndLine();  
+				m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
 				commandFactory->setOutputDirectory(output);
 			}
 		}
@@ -123,11 +122,11 @@ int SetDirectoryCommand::execute(){
 			ofstream in;
 			in.open(inTemp.c_str(), ios::trunc);
 			if(!in) {
-				mothurOut(input + " directory does not exist or is not writable."); mothurOutEndLine(); 
+				m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
 				in.close();
 				remove(inTemp.c_str());
-				mothurOut("Changing input directory to " + input); mothurOutEndLine();  
+				m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
 				commandFactory->setInputDirectory(input); 
 			}
 		}
@@ -135,7 +134,7 @@ int SetDirectoryCommand::execute(){
 		return 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
+		m->errorOut(e, "SetDirectoryCommand", "execute");
 		exit(1);
 	}
 }